* CPV: sci-biology/wgs-assembler-6.1 * REPO: gentoo * USE: elibc_glibc kernel_linux test userland_GNU x86 >>> Unpacking source... >>> Unpacking wgs-6.1.tar.bz2 to /var/tmp/portage/sci-biology/wgs-assembler-6.1/work >>> Source unpacked in /var/tmp/portage/sci-biology/wgs-assembler-6.1/work >>> Preparing source in /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1 ... WARNING: 'python' program found, but can't find include file 'Python.h' -- is python installed correctly? WARNING: Set PYTHONHOME to the directory containing include/Pyhton.h WARNING: Will not build ATAC. i686-pc-linux-gnu-gcc -O2 -pipe -L/usr/local/lib -o ./makepath build/makepath.c -pthread -ldl -lm -lbz2 Configured. >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1 ... make -j14 -C kmer -j1 install make: Entering directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer' making ../kmer/libutil/kazlib/sfx.c.d making ../kmer/libutil/kazlib/list.c.d making ../kmer/libutil/kazlib/hash.c.d making ../kmer/libutil/kazlib/except.c.d making ../kmer/libutil/kazlib/dict.c.d i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/mt19937ar/mt19937ar.o -c ../kmer/libutil/mt19937ar/mt19937ar.c i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/mt19937ar/mt19937ar-test.o -c ../kmer/libutil/mt19937ar/mt19937ar-test.c i686-pc-linux-gnu-gcc -L/usr/local/lib -o ../kmer/libutil/mt19937ar/mt19937ar-test ../kmer/libutil/mt19937ar/mt19937ar.o ../kmer/libutil/mt19937ar/mt19937ar-test.o -pthread -ldl -lm -lbz2 ../kmer/libutil/mt19937ar/mt19937ar-test | diff - ../kmer/libutil/mt19937ar/mt19937ar.out > ../kmer/libutil/mt19937ar/diffs 2>&1 if test -s ../kmer/libutil/mt19937ar/diffs ; then echo 'MT19937: TEST FAILED'; else echo 'MT19937: Test Passed'; fi MT19937: Test Passed touch ../kmer/libutil/mt19937ar/test.c ../kmer/libutil/mt19937ar/mt19937ar-test | diff - ../kmer/libutil/mt19937ar/mt19937ar.out making ../kmer/libutil/mt19937ar/test.c.d making ../kmer/libutil/mt19937ar/mt19937ar.c.d making ../kmer/libutil/sweatShop.C.d making ../kmer/libutil/speedCounter.C.d making ../kmer/libutil/recordFile.C.d making ../kmer/libutil/readBuffer.C.d making ../kmer/libutil/intervalList.C.d making ../kmer/libutil/fibonacciNumbers.C.d making ../kmer/libutil/bitPackedFile.C.d making ../kmer/libutil/bitPackedArray.C.d making ../kmer/libutil/bigQueue.C.d making ../kmer/libutil/util.c.d making ../kmer/libutil/qsort_mt.c.d making ../kmer/libutil/palloc.c.d making ../kmer/libutil/md5.c.d making ../kmer/libutil/file.c.d making ../kmer/libseq/test-merStream.C.d making ../kmer/libseq/test-seqStream.C.d making ../kmer/libseq/test-seqCache.C.d making ../kmer/libseq/merStream.C.d making ../kmer/libseq/seqStream.C.d making ../kmer/libseq/seqCache.C.d making ../kmer/libseq/seqFactory.C.d making ../kmer/libseq/sffFile.C.d making ../kmer/libseq/seqStore.C.d making ../kmer/libseq/fastaStdin.C.d making ../kmer/libseq/fastaFile.C.d making ../kmer/libbio/reversecomplement.c.d making ../kmer/libbio/halign.c.d making ../kmer/libbio/alphabet-colorspace.c.d making ../kmer/libbio/alphabet-acgtspace.c.d making ../kmer/libbio/alphabet.c.d making ../kmer/libmeryl/libmeryl.C.d making ../kmer/libkmer/mask.C.d making ../kmer/libkmer/percentCovered.C.d making ../kmer/libkmer/driver-posDB.C.d making ../kmer/libkmer/driver-existDB.C.d making ../kmer/libkmer/positionDB.C.d making ../kmer/libkmer/positionDB-sort.C.d making ../kmer/libkmer/positionDB-mismatch.C.d making ../kmer/libkmer/positionDB-file.C.d making ../kmer/libkmer/positionDB-dump.C.d making ../kmer/libkmer/positionDB-access.C.d making ../kmer/libkmer/existDB.C.d making ../kmer/libkmer/existDB-state.C.d making ../kmer/libkmer/existDB-create-from-meryl.C.d making ../kmer/libkmer/existDB-create-from-fasta.C.d making meryl/maskMers.C.d making meryl/mapMers-depth.C.d making meryl/mapMers.C.d making meryl/asmMerQC.C.d making meryl/meryl.C.d making meryl/unaryOp.C.d making meryl/merge.C.d making meryl/estimate.C.d making meryl/dump.C.d making meryl/build-threads.C.d making meryl/build.C.d making meryl/binaryOp.C.d making meryl/args.C.d make: Leaving directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer' make: Entering directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer' i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/meryl.o -c meryl/meryl.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/args.o -c meryl/args.C meryl/args.C: In member function ‘bool merylArgs::writeConfig()’: meryl/args.C:568:49: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/args.C:570:40: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/args.C: In constructor ‘merylArgs::merylArgs(const char*)’: meryl/args.C:509:36: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/args.C:517:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/args.C: In function ‘char* readString(FILE*)’: meryl/args.C:40:36: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/args.C:50:37: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/args.C: In function ‘bool writeString(const char*, FILE*)’: meryl/args.C:19:39: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/args.C:20:39: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/args.C:22:39: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/binaryOp.o -c meryl/binaryOp.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build.o -c meryl/build.C meryl/build.C:243:2: warning: #warning not submitting prepareBatch to grid meryl/build.C: In function ‘void build(merylArgs*)’: meryl/build.C:765:41: warning: deprecated conversion from string constant to ‘char*’ meryl/build.C:766:41: warning: deprecated conversion from string constant to ‘char*’ meryl/build.C:767:41: warning: deprecated conversion from string constant to ‘char*’ meryl/build.C:771:22: warning: deprecated conversion from string constant to ‘char*’ meryl/build.C:776:22: warning: deprecated conversion from string constant to ‘char*’ meryl/build.C:783:41: warning: deprecated conversion from string constant to ‘char*’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/build-threads.o -c meryl/build-threads.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/dump.o -c meryl/dump.C meryl/dump.C:50:2: warning: #warning make this a test i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/estimate.o -c meryl/estimate.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/merge.o -c meryl/merge.C meryl/merge.C: In function ‘void multipleOperations(merylArgs*)’: meryl/merge.C:32:96: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘u32bit’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/unaryOp.o -c meryl/unaryOp.C rm -f meryl/libmerylguts.a && ar ruvs meryl/libmerylguts.a meryl/args.o meryl/binaryOp.o meryl/build.o meryl/build-threads.o meryl/dump.o meryl/estimate.o meryl/merge.o meryl/unaryOp.o ar: creating meryl/libmerylguts.a a - meryl/args.o a - meryl/binaryOp.o a - meryl/build.o a - meryl/build-threads.o a - meryl/dump.o a - meryl/estimate.o a - meryl/merge.o a - meryl/unaryOp.o i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libmeryl/libmeryl.o -c ../kmer/libmeryl/libmeryl.C ../kmer/libmeryl/libmeryl.C:72:2: warning: #warning not checking pmagic ../kmer/libmeryl/libmeryl.C:6:24: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libmeryl/libmeryl.C:7:24: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libmeryl/libmeryl.C:8:24: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libmeryl/libmeryl.C:9:24: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libmeryl/libmeryl.C:10:24: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libmeryl/libmeryl.C:11:24: warning: deprecated conversion from string constant to ‘char*’ rm -f ../kmer/libmeryl/libmeryl.a && ar ruvs ../kmer/libmeryl/libmeryl.a ../kmer/libmeryl/libmeryl.o ar: creating ../kmer/libmeryl/libmeryl.a a - ../kmer/libmeryl/libmeryl.o i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/fastaFile.o -c ../kmer/libseq/fastaFile.C ../kmer/libseq/fastaFile.C: In member function ‘void fastaFile::constructIndex()’: ../kmer/libseq/fastaFile.C:515:55: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘u32bit’ ../kmer/libseq/fastaFile.C:566:76: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/fastaFile.C:567:76: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/fastaFile.C:568:76: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/fastaFile.C: In member function ‘void fastaFile::loadIndex(char*)’: ../kmer/libseq/fastaFile.C:350:49: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/fastaFile.C:370:71: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/fastaFile.C:371:71: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/fastaStdin.o -c ../kmer/libseq/fastaStdin.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/seqStore.o -c ../kmer/libseq/seqStore.C ../kmer/libseq/seqStore.C: In member function ‘void seqStore::loadIndex()’: ../kmer/libseq/seqStore.C:320:199: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 4 has type ‘long unsigned int’ ../kmer/libseq/seqStore.C:321:199: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 4 has type ‘long unsigned int’ ../kmer/libseq/seqStore.C:322:199: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 4 has type ‘long unsigned int’ ../kmer/libseq/seqStore.C: In function ‘void constructSeqStore(char*, seqCache*)’: ../kmer/libseq/seqStore.C:562:66: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C:566:63: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C:570:51: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C:573:46: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C: In member function ‘void seqStore::loadIndex()’: ../kmer/libseq/seqStore.C:318:50: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C:329:73: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C:332:70: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C:336:67: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C: In member function ‘virtual seqFile* seqStore::openFile(const char*)’: ../kmer/libseq/seqStore.C:73:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C:74:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libseq/seqStore.C: In constructor ‘seqStore::seqStore(const char*)’: ../kmer/libseq/seqStore.C:21:50: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result In file included from /usr/include/string.h:642:0, from ../kmer/libutil/u32bitList.H:4, from ../kmer/libutil/util++.H:29, from ../kmer/libseq/seqStore.H:4, from ../kmer/libseq/seqStore.C:2: In function ‘void* memset(void*, int, size_t)’, inlined from ‘void constructSeqStore(char*, seqCache*)’ at ../kmer/libseq/seqStore.C:396:43: /usr/include/bits/string3.h:83:32: warning: call to ‘__warn_memset_zero_len’ declared with attribute warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/sffFile.o -c ../kmer/libseq/sffFile.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/seqFactory.o -c ../kmer/libseq/seqFactory.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/seqCache.o -c ../kmer/libseq/seqCache.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/seqStream.o -c ../kmer/libseq/seqStream.C ../kmer/libseq/seqStream.C: In constructor ‘seqStream::seqStream(const char*)’: ../kmer/libseq/seqStream.C:23:66: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ ../kmer/libseq/seqStream.C:23:66: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 4 has type ‘u32bit’ ../kmer/libseq/seqStream.C: In member function ‘void seqStream::tradeSpaceForTime()’: ../kmer/libseq/seqStream.C:147:90: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘u64bit’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/merStream.o -c ../kmer/libseq/merStream.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/test-seqCache.o -c ../kmer/libseq/test-seqCache.C In file included from ../kmer/libseq/test-seqCache.C:7:0: ../kmer/libseq/test-correctSequence.H: In function ‘void generateCorrectSequence(u32bit, u32bit, u32bit)’: ../kmer/libseq/test-correctSequence.H:45:55: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘u32bit’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/test-seqStream.o -c ../kmer/libseq/test-seqStream.C In file included from ../kmer/libseq/test-seqStream.C:7:0: ../kmer/libseq/test-correctSequence.H: In function ‘void generateCorrectSequence(u32bit, u32bit, u32bit)’: ../kmer/libseq/test-correctSequence.H:45:55: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘u32bit’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libutil/ -I../kmer/libbio/ -I../kmer/libseq/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libseq/test-merStream.o -c ../kmer/libseq/test-merStream.C ../kmer/libseq/test-merStream.C:11:2: warning: #warning HOW DO WE TEST IF WE GET ALL THE MERS? In file included from ../kmer/libseq/test-merStream.C:7:0: ../kmer/libseq/test-correctSequence.H: In function ‘void generateCorrectSequence(u32bit, u32bit, u32bit)’: ../kmer/libseq/test-correctSequence.H:45:55: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘u32bit’ ../kmer/libseq/test-merStream.C: In function ‘int main(int, char**)’: ../kmer/libseq/test-merStream.C:219:80: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libseq/test-merStream.C:223:64: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libseq/test-merStream.C:225:64: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libseq/test-merStream.C:228:64: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libseq/test-merStream.C:239:90: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libseq/test-merStream.C:243:60: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libseq/test-merStream.C:245:60: warning: deprecated conversion from string constant to ‘char*’ ../kmer/libseq/test-merStream.C:248:60: warning: deprecated conversion from string constant to ‘char*’ rm -f ../kmer/libseq/libseq.a && ar ruvs ../kmer/libseq/libseq.a ../kmer/libseq/fastaFile.o ../kmer/libseq/fastaStdin.o ../kmer/libseq/seqStore.o ../kmer/libseq/sffFile.o ../kmer/libseq/seqFactory.o ../kmer/libseq/seqCache.o ../kmer/libseq/seqStream.o ../kmer/libseq/merStream.o ../kmer/libseq/test-seqCache.o ../kmer/libseq/test-seqStream.o ../kmer/libseq/test-merStream.o ar: creating ../kmer/libseq/libseq.a a - ../kmer/libseq/fastaFile.o a - ../kmer/libseq/fastaStdin.o a - ../kmer/libseq/seqStore.o a - ../kmer/libseq/sffFile.o a - ../kmer/libseq/seqFactory.o a - ../kmer/libseq/seqCache.o a - ../kmer/libseq/seqStream.o a - ../kmer/libseq/merStream.o a - ../kmer/libseq/test-seqCache.o a - ../kmer/libseq/test-seqStream.o a - ../kmer/libseq/test-merStream.o i686-pc-linux-gnu-gcc -O2 -pipe -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libbio/alphabet.o -c ../kmer/libbio/alphabet.c i686-pc-linux-gnu-gcc -O2 -pipe -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libbio/alphabet-acgtspace.o -c ../kmer/libbio/alphabet-acgtspace.c i686-pc-linux-gnu-gcc -O2 -pipe -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libbio/alphabet-colorspace.o -c ../kmer/libbio/alphabet-colorspace.c i686-pc-linux-gnu-gcc -O2 -pipe -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libbio/halign.o -c ../kmer/libbio/halign.c i686-pc-linux-gnu-gcc -O2 -pipe -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libbio/reversecomplement.o -c ../kmer/libbio/reversecomplement.c rm -f ../kmer/libbio/libbio.a && ar ruvs ../kmer/libbio/libbio.a ../kmer/libbio/alphabet.o ../kmer/libbio/alphabet-acgtspace.o ../kmer/libbio/alphabet-colorspace.o ../kmer/libbio/halign.o ../kmer/libbio/reversecomplement.o ar: creating ../kmer/libbio/libbio.a a - ../kmer/libbio/alphabet.o a - ../kmer/libbio/alphabet-acgtspace.o a - ../kmer/libbio/alphabet-colorspace.o a - ../kmer/libbio/halign.o a - ../kmer/libbio/reversecomplement.o i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/file.o -c ../kmer/libutil/file.c ../kmer/libutil/file.c: In function ‘copyFile’: ../kmer/libutil/file.c:223:13: warning: ignoring return value of ‘fwrite’, declared with attribute warn_unused_result i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/md5.o -c ../kmer/libutil/md5.c i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/palloc.o -c ../kmer/libutil/palloc.c i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/qsort_mt.o -c ../kmer/libutil/qsort_mt.c i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/util.o -c ../kmer/libutil/util.c i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/bigQueue.o -c ../kmer/libutil/bigQueue.C ../kmer/libutil/bigQueue.C: In member function ‘bool bigQueue::next()’: ../kmer/libutil/bigQueue.C:302:60: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libutil/bigQueue.C: In member function ‘void bigQueue::mergeTemporaryFiles()’: ../kmer/libutil/bigQueue.C:204:59: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libutil/bigQueue.C:236:49: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libutil/bigQueue.C:255:62: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libutil/bigQueue.C: In member function ‘void bigQueue::sortAndWriteBuffer()’: ../kmer/libutil/bigQueue.C:147:82: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libutil/bigQueue.C: In member function ‘void bigQueue::add(void*)’: ../kmer/libutil/bigQueue.C:110:75: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/bitPackedArray.o -c ../kmer/libutil/bitPackedArray.C i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/bitPackedFile.o -c ../kmer/libutil/bitPackedFile.C ../kmer/libutil/bitPackedFile.C: In member function ‘void bitPackedFile::flushDirty()’: ../kmer/libutil/bitPackedFile.C:230:47: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/bitPackedFile.C: In constructor ‘bitPackedFile::bitPackedFile(const char*, u64bit, bool)’: ../kmer/libutil/bitPackedFile.C:107:41: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/bitPackedFile.C:108:38: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/bitPackedFile.C:109:38: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/fibonacciNumbers.o -c ../kmer/libutil/fibonacciNumbers.C i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/intervalList.o -c ../kmer/libutil/intervalList.C i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/readBuffer.o -c ../kmer/libutil/readBuffer.C ../kmer/libutil/readBuffer.C: In constructor ‘readBuffer::readBuffer(const char*, u32bit)’: ../kmer/libutil/readBuffer.C:39:39: warning: too many arguments for format i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/recordFile.o -c ../kmer/libutil/recordFile.C ../kmer/libutil/recordFile.C: In member function ‘void recordFile::seek(u64bit, bool)’: ../kmer/libutil/recordFile.C:231:43: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C: In member function ‘void recordFile::flushDirty()’: ../kmer/libutil/recordFile.C:197:41: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C: In destructor ‘recordFile::~recordFile()’: ../kmer/libutil/recordFile.C:151:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:152:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:153:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:154:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:155:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:156:65: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C: In constructor ‘recordFile::recordFile(const char*, u32bit, u32bit, char)’: ../kmer/libutil/recordFile.C:68:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:69:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:70:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:71:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:72:53: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:73:65: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:112:52: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:113:52: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:114:52: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:115:52: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:116:52: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result ../kmer/libutil/recordFile.C:117:64: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/speedCounter.o -c ../kmer/libutil/speedCounter.C i686-pc-linux-gnu-g++ -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/sweatShop.o -c ../kmer/libutil/sweatShop.C i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/kazlib/dict.o -c ../kmer/libutil/kazlib/dict.c i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/kazlib/except.o -c ../kmer/libutil/kazlib/except.c i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/kazlib/hash.o -c ../kmer/libutil/kazlib/hash.c ../kmer/libutil/kazlib/hash.c: In function ‘hash_free_nodes’: ../kmer/libutil/kazlib/hash.c:342:13: warning: ‘hs.hash_chain’ may be used uninitialized in this function i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/kazlib/list.o -c ../kmer/libutil/kazlib/list.c i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/kazlib/sfx.o -c ../kmer/libutil/kazlib/sfx.c rm -f ../kmer/libutil/libutil.a && ar ruvs ../kmer/libutil/libutil.a ../kmer/libutil/file.o ../kmer/libutil/md5.o ../kmer/libutil/palloc.o ../kmer/libutil/qsort_mt.o ../kmer/libutil/util.o ../kmer/libutil/bigQueue.o ../kmer/libutil/bitPackedArray.o ../kmer/libutil/bitPackedFile.o ../kmer/libutil/fibonacciNumbers.o ../kmer/libutil/intervalList.o ../kmer/libutil/readBuffer.o ../kmer/libutil/recordFile.o ../kmer/libutil/speedCounter.o ../kmer/libutil/sweatShop.o ../kmer/libutil/mt19937ar/mt19937ar.o ../kmer/libutil/kazlib/dict.o ../kmer/libutil/kazlib/except.o ../kmer/libutil/kazlib/hash.o ../kmer/libutil/kazlib/list.o ../kmer/libutil/kazlib/sfx.o ar: creating ../kmer/libutil/libutil.a a - ../kmer/libutil/file.o a - ../kmer/libutil/md5.o a - ../kmer/libutil/palloc.o a - ../kmer/libutil/qsort_mt.o a - ../kmer/libutil/util.o a - ../kmer/libutil/bigQueue.o a - ../kmer/libutil/bitPackedArray.o a - ../kmer/libutil/bitPackedFile.o a - ../kmer/libutil/fibonacciNumbers.o a - ../kmer/libutil/intervalList.o a - ../kmer/libutil/readBuffer.o a - ../kmer/libutil/recordFile.o a - ../kmer/libutil/speedCounter.o a - ../kmer/libutil/sweatShop.o a - ../kmer/libutil/mt19937ar/mt19937ar.o a - ../kmer/libutil/kazlib/dict.o a - ../kmer/libutil/kazlib/except.o a - ../kmer/libutil/kazlib/hash.o a - ../kmer/libutil/kazlib/list.o a - ../kmer/libutil/kazlib/sfx.o i686-pc-linux-gnu-g++ -L/usr/local/lib -o meryl/meryl meryl/meryl.o meryl/libmerylguts.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/asmMerQC.o -c meryl/asmMerQC.C meryl/asmMerQC.C: In function ‘void compare(merylStreamReader*, merylStreamReader*, kMer&, u32bit, u32bit (*)[6])’: meryl/asmMerQC.C:111:12: warning: suggest explicit braces to avoid ambiguous ‘else’ meryl/asmMerQC.C:130:10: warning: suggest explicit braces to avoid ambiguous ‘else’ meryl/asmMerQC.C:149:8: warning: suggest explicit braces to avoid ambiguous ‘else’ meryl/asmMerQC.C: In function ‘int main(int, char**)’: meryl/asmMerQC.C:384:81: warning: deprecated conversion from string constant to ‘char*’ meryl/asmMerQC.C:385:81: warning: deprecated conversion from string constant to ‘char*’ meryl/asmMerQC.C:386:81: warning: deprecated conversion from string constant to ‘char*’ meryl/asmMerQC.C:387:81: warning: deprecated conversion from string constant to ‘char*’ meryl/asmMerQC.C:388:81: warning: deprecated conversion from string constant to ‘char*’ meryl/asmMerQC.C:389:81: warning: deprecated conversion from string constant to ‘char*’ i686-pc-linux-gnu-g++ -L/usr/local/lib -o meryl/asmMerQC meryl/asmMerQC.o ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers.o -c meryl/mapMers.C In file included from meryl/mapMers.C:9:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/existDB-create-from-fasta.o -c ../kmer/libkmer/existDB-create-from-fasta.C In file included from ../kmer/libkmer/existDB-create-from-fasta.C:5:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/existDB-create-from-meryl.o -c ../kmer/libkmer/existDB-create-from-meryl.C In file included from ../kmer/libkmer/existDB-create-from-meryl.C:5:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/existDB-state.o -c ../kmer/libkmer/existDB-state.C In file included from ../kmer/libkmer/existDB-state.C:5:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ ../kmer/libkmer/existDB-state.C: In member function ‘bool existDB::loadState(const char*, bool, bool)’: ../kmer/libkmer/existDB-state.C:77:36: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:116:48: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:117:40: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:118:40: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:119:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:120:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:121:42: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:122:42: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:123:42: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:125:48: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:126:48: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:127:48: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:137:58: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:138:58: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:139:58: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C: In member function ‘void existDB::saveState(const char*)’: ../kmer/libkmer/existDB-state.C:35:37: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:37:49: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:38:41: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:39:41: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:40:40: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:41:40: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:42:43: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:43:43: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:44:43: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:46:49: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:47:49: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:48:49: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:50:57: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:51:57: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result ../kmer/libkmer/existDB-state.C:52:57: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/existDB.o -c ../kmer/libkmer/existDB.C In file included from ../kmer/libkmer/existDB.C:5:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/positionDB-access.o -c ../kmer/libkmer/positionDB-access.C ../kmer/libkmer/positionDB-access.C: In member function ‘void positionDB::filter(u64bit, u64bit)’: ../kmer/libkmer/positionDB-access.C:204:11: warning: unused variable ‘vv’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/positionDB-dump.o -c ../kmer/libkmer/positionDB-dump.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/positionDB-file.o -c ../kmer/libkmer/positionDB-file.C ../kmer/libkmer/positionDB-file.C: In member function ‘void positionDB::saveState(const char*)’: ../kmer/libkmer/positionDB-file.C:37:39: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libkmer/positionDB-file.C:39:39: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result ../kmer/libkmer/positionDB-file.C:95:39: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/positionDB-mismatch.o -c ../kmer/libkmer/positionDB-mismatch.C i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/positionDB-sort.o -c ../kmer/libkmer/positionDB-sort.C ../kmer/libkmer/positionDB-sort.C: In member function ‘void positionDB::sortAndRepackBucket(u64bit)’: ../kmer/libkmer/positionDB-sort.C:37:86: warning: format ‘%10lu’ expects type ‘long unsigned int’, but argument 3 has type ‘u64bit’ ../kmer/libkmer/positionDB-sort.C:37:86: warning: format ‘%10lu’ expects type ‘long unsigned int’, but argument 4 has type ‘u64bit’ ../kmer/libkmer/positionDB-sort.C:37:86: warning: format ‘%10lu’ expects type ‘long unsigned int’, but argument 5 has type ‘u64bit’ i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/positionDB.o -c ../kmer/libkmer/positionDB.C In file included from ../kmer/libkmer/positionDB.C:7:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ rm -f ../kmer/libkmer/libkmer.a && ar ruvs ../kmer/libkmer/libkmer.a ../kmer/libkmer/existDB-create-from-fasta.o ../kmer/libkmer/existDB-create-from-meryl.o ../kmer/libkmer/existDB-state.o ../kmer/libkmer/existDB.o ../kmer/libkmer/positionDB-access.o ../kmer/libkmer/positionDB-dump.o ../kmer/libkmer/positionDB-file.o ../kmer/libkmer/positionDB-mismatch.o ../kmer/libkmer/positionDB-sort.o ../kmer/libkmer/positionDB.o ar: creating ../kmer/libkmer/libkmer.a a - ../kmer/libkmer/existDB-create-from-fasta.o a - ../kmer/libkmer/existDB-create-from-meryl.o a - ../kmer/libkmer/existDB-state.o a - ../kmer/libkmer/existDB.o a - ../kmer/libkmer/positionDB-access.o a - ../kmer/libkmer/positionDB-dump.o a - ../kmer/libkmer/positionDB-file.o a - ../kmer/libkmer/positionDB-mismatch.o a - ../kmer/libkmer/positionDB-sort.o a - ../kmer/libkmer/positionDB.o i686-pc-linux-gnu-g++ -L/usr/local/lib -o meryl/mapMers meryl/mapMers.o ../kmer/libkmer/libkmer.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/mapMers-depth.o -c meryl/mapMers-depth.C In file included from meryl/mapMers-depth.C:9:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ meryl/mapMers-depth.C: In function ‘int main(int, char**)’: meryl/mapMers-depth.C:86:67: warning: format ‘%6lu’ expects type ‘long unsigned int’, but argument 4 has type ‘int’ meryl/mapMers-depth.C:91:65: warning: format ‘%6lu’ expects type ‘long unsigned int’, but argument 4 has type ‘int’ i686-pc-linux-gnu-g++ -L/usr/local/lib -o meryl/mapMers-depth meryl/mapMers-depth.o ../kmer/libkmer/libkmer.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/testPositionBias.o -c meryl/testPositionBias.C meryl/testPositionBias.C: In function ‘void showBias(u32bit)’: meryl/testPositionBias.C:54:43: warning: deprecated conversion from string constant to ‘char*’ meryl/testPositionBias.C:55:50: warning: deprecated conversion from string constant to ‘char*’ meryl/testPositionBias.C:56:60: warning: deprecated conversion from string constant to ‘char*’ meryl/testPositionBias.C: In function ‘double computeRMSD(u32bit)’: meryl/testPositionBias.C:83:43: warning: deprecated conversion from string constant to ‘char*’ meryl/testPositionBias.C:84:50: warning: deprecated conversion from string constant to ‘char*’ meryl/testPositionBias.C:85:60: warning: deprecated conversion from string constant to ‘char*’ i686-pc-linux-gnu-g++ -L/usr/local/lib -o meryl/testPositionBias meryl/testPositionBias.o ../kmer/libkmer/libkmer.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libkmer/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o meryl/maskMers.o -c meryl/maskMers.C meryl/maskMers.C: In member function ‘void merMaskedSequence::saveMasking()’: meryl/maskMers.C:166:59: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C:167:59: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C:168:59: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C:171:67: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C:172:67: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C: In member function ‘void merMaskedSequence::loadMasking(u32bit)’: meryl/maskMers.C:125:52: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C:126:52: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C:134:59: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C:149:68: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result meryl/maskMers.C:150:68: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -L/usr/local/lib -o meryl/maskMers meryl/maskMers.o ../kmer/libkmer/libkmer.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/driver-existDB.o -c ../kmer/libkmer/driver-existDB.C In file included from ../kmer/libkmer/driver-existDB.C:7:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ ../kmer/libkmer/driver-existDB.C: In function ‘int testExhaustive(char*, char*, u32bit)’: ../kmer/libkmer/driver-existDB.C:102:55: warning: format ‘%016lx’ expects type ‘long unsigned int’, but argument 3 has type ‘u64bit’ ../kmer/libkmer/driver-existDB.C:104:63: warning: format ‘%016lx’ expects type ‘long unsigned int’, but argument 3 has type ‘u64bit’ ../kmer/libkmer/driver-existDB.C:118:36: warning: format ‘%016lx’ expects type ‘long unsigned int’, but argument 3 has type ‘u64bit’ i686-pc-linux-gnu-g++ -L/usr/local/lib -o ../kmer/libkmer/existDB ../kmer/libkmer/driver-existDB.o ../kmer/libkmer/libkmer.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/driver-posDB.o -c ../kmer/libkmer/driver-posDB.C In file included from ../kmer/libkmer/driver-posDB.C:7:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ i686-pc-linux-gnu-g++ -L/usr/local/lib -o ../kmer/libkmer/positionDB ../kmer/libkmer/driver-posDB.o ../kmer/libkmer/libkmer.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/percentCovered.o -c ../kmer/libkmer/percentCovered.C In file included from ../kmer/libkmer/percentCovered.C:3:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ i686-pc-linux-gnu-g++ -L/usr/local/lib -o ../kmer/libkmer/percentCovered ../kmer/libkmer/percentCovered.o ../kmer/libkmer/libkmer.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -O2 -pipe -I../kmer/libmeryl/ -I../kmer/libbio/ -I../kmer/libseq/ -I../kmer/libutil/ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libkmer/mask.o -c ../kmer/libkmer/mask.C In file included from ../kmer/libkmer/mask.C:7:0: ../kmer/libkmer/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: ../kmer/libkmer/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ i686-pc-linux-gnu-g++ -L/usr/local/lib -o ../kmer/libkmer/mask ../kmer/libkmer/mask.o ../kmer/libkmer/libkmer.a ../kmer/libmeryl/libmeryl.a ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -L/usr/local/lib -o ../kmer/libseq/test-seqCache ../kmer/libseq/test-seqCache.o ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -L/usr/local/lib -o ../kmer/libseq/test-seqStream ../kmer/libseq/test-seqStream.o ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-g++ -L/usr/local/lib -o ../kmer/libseq/test-merStream ../kmer/libseq/test-merStream.o ../kmer/libseq/libseq.a ../kmer/libbio/libbio.a ../kmer/libutil/libutil.a -pthread -ldl -lm -lbz2 ../kmer/libseq/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters i686-pc-linux-gnu-gcc -O2 -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_REENTRANT -O3 -D_THREAD_SAFE -pthread -fmessage-length=0 -Wall -Wno-char-subscripts -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -o ../kmer/libutil/mt19937ar/test.o -c ../kmer/libutil/mt19937ar/test.c rm -f ../kmer/libutil/mt19937ar/libmt19937ar.a && ar ruvs ../kmer/libutil/mt19937ar/libmt19937ar.a ../kmer/libutil/mt19937ar/mt19937ar.o ../kmer/libutil/mt19937ar/test.o ar: creating ../kmer/libutil/mt19937ar/libmt19937ar.a a - ../kmer/libutil/mt19937ar/mt19937ar.o a - ../kmer/libutil/mt19937ar/test.o rm -f ../kmer/libutil/kazlib/libkaz.a && ar ruvs ../kmer/libutil/kazlib/libkaz.a ../kmer/libutil/kazlib/dict.o ../kmer/libutil/kazlib/except.o ../kmer/libutil/kazlib/hash.o ../kmer/libutil/kazlib/list.o ../kmer/libutil/kazlib/sfx.o ar: creating ../kmer/libutil/kazlib/libkaz.a a - ../kmer/libutil/kazlib/dict.o a - ../kmer/libutil/kazlib/except.o a - ../kmer/libutil/kazlib/hash.o a - ../kmer/libutil/kazlib/list.o a - ../kmer/libutil/kazlib/sfx.o make: Leaving directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer' make -j14 -C src -j1 SITE_NAME=LOCAL make: Entering directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src' make: Leaving directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src' make: Entering directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src' g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_global.o AS_global.C * Make Target is objs ############################## AS_RUN ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragmentDepth.o fragmentDepth.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/markUniqueUnique.o markUniqueUnique.C ############################## AS_UTL ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Hash.o AS_UTL_Hash.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_heap.o AS_UTL_heap.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Var.o AS_UTL_Var.C AS_UTL_Hash.C: In function ‘int DeleteFromHashTable_AS(HashTable_AS*, uint64, uint32)’: AS_UTL_Hash.C:439:3: warning: comparison between signed and unsigned integer expressions AS_UTL_Hash.C: In function ‘uint64 ReplaceInHashTable_AS(HashTable_AS*, uint64, uint32, uint64, uint32)’: AS_UTL_Hash.C:505:3: warning: comparison between signed and unsigned integer expressions AS_UTL_Hash.C: In function ‘int LookupInHashTable_AS(HashTable_AS*, uint64, uint32, uint64*, uint32*)’: AS_UTL_Hash.C:559:3: warning: comparison between signed and unsigned integer expressions AS_UTL_heap.C: In function ‘void* NextHeapIterator_AS(HeapIterator_AS*)’: AS_UTL_heap.C:78:42: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_rand.o AS_UTL_rand.C AS_UTL_Var.C: In function ‘int MakeRoom_VA(VarArrayType*, size_t)’: AS_UTL_Var.C:145:19: warning: comparison between signed and unsigned integer expressions AS_UTL_Var.C: In function ‘void ReadVA(FILE*, VarArrayType*, FileVarArrayType*)’: AS_UTL_Var.C:343:58: warning: format ‘%lld’ expects type ‘long long int’, but argument 4 has type ‘size_t’ AS_UTL_Var.C:343:58: warning: format ‘%lld’ expects type ‘long long int’, but argument 5 has type ‘size_t’ g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_interval.o AS_UTL_interval.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UnionFind_AS.o UnionFind_AS.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_skiplist.o AS_UTL_skiplist.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_alloc.o AS_UTL_alloc.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fileIO.o AS_UTL_fileIO.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_qsort_mt.o AS_UTL_qsort_mt.C AS_UTL_fileIO.C: In function ‘off_t AS_UTL_sizeOfFile(const char*)’: AS_UTL_fileIO.C:263:35: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result AS_UTL_fileIO.C:264:43: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result AS_UTL_qsort_mt.C: In function ‘void qsort_mt(void*, size_t, size_t, int (*)(const void*, const void*), int, int)’: AS_UTL_qsort_mt.C:153:11: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fasta.o AS_UTL_fasta.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_UID.o AS_UTL_UID.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_reverseComplement.o AS_UTL_reverseComplement.C ############################## AS_UID ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/uidclient.o uidclient.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/uidserver.o uidserver.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SYS_UIDclient_LOCAL.o SYS_UIDclient_LOCAL.C uidserver.C:182:2: warning: #warning PRUNING DOES NOT SEEM TO WORK uidserver_common.h: In function ‘int32 writeDatabase()’: uidserver_common.h:115:40: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result uidserver_common.h: In function ‘int32 readDatabase()’: uidserver_common.h:143:39: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result SYS_UIDclient_LOCAL.C: In function ‘uint64 getGUIDBlock(int)’: SYS_UIDclient_LOCAL.C:61:37: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result ############################## AS_MSG ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg.o AS_MSG_pmesg.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg1.o AS_MSG_pmesg1.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg2.o AS_MSG_pmesg2.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/remove_fragment.o remove_fragment.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ExtractMessages.o ExtractMessages.C ############################## AS_PER ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_genericStore.o AS_PER_genericStore.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkLibrary.o AS_PER_gkLibrary.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore.o AS_PER_gkStore.C AS_PER_genericStore.C: In function ‘StoreStruct* openStore(const char*, const char*)’: AS_PER_genericStore.C:64:78: warning: too few arguments for format AS_PER_genericStore.C: In function ‘StoreStruct* convertStoreToPartialMemoryStore(StoreStruct*, int64, int64)’: AS_PER_genericStore.C:588:149: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘int64’ AS_PER_genericStore.C:588:149: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘int64’ g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_IID.o AS_PER_gkStore_IID.C AS_PER_gkLibrary.C: In member function ‘void gkLibrary::gkLibrary_decodeFeatures(LibraryMesg*)’: AS_PER_gkLibrary.C:63:22: warning: comparison between signed and unsigned integer expressions AS_PER_gkLibrary.C: In member function ‘void gkLibrary::gkLibrary_encodeFeatures(LibraryMesg*)’: AS_PER_gkLibrary.C:157:45: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ AS_PER_gkLibrary.C:165:39: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ AS_PER_gkLibrary.C:174:53: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ AS_PER_gkLibrary.C:183:50: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ AS_PER_gkLibrary.C:191:39: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ AS_PER_gkLibrary.C:199:46: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ AS_PER_gkLibrary.C:207:44: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ AS_PER_gkLibrary.C:216:46: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long long unsigned int’ AS_PER_gkStore.C: In member function ‘void gkStore::gkStore_open(int, int)’: AS_PER_gkStore.C:136:50: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘uint64’ AS_PER_gkStore_IID.C: In member function ‘void gkStore::gkStore_addIIDtoTypeMap(AS_IID, uint32, uint32)’: AS_PER_gkStore_IID.C:109:28: warning: comparison between signed and unsigned integer expressions AS_PER_gkStore_IID.C:116:28: warning: comparison between signed and unsigned integer expressions AS_PER_gkStore_IID.C:123:28: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_PLC.o AS_PER_gkStore_PLC.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_UID.o AS_PER_gkStore_UID.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_clearRange.o AS_PER_gkStore_clearRange.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_fragments.o AS_PER_gkStore_fragments.C AS_PER_gkStore_UID.C: In member function ‘void gkStore::gkStore_loadIIDtoUID()’: AS_PER_gkStore_UID.C:93:41: warning: missing braces around initializer for ‘HeapIterator_AS’ AS_PER_gkStore_UID.C: In member function ‘void gkStore::gkStore_loadSTRtoUID()’: AS_PER_gkStore_UID.C:201:37: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_load.o AS_PER_gkStore_load.C AS_PER_gkStore_load.C: In member function ‘void gkStore::gkStore_load(AS_IID, AS_IID, int)’: AS_PER_gkStore_load.C:76:18: warning: comparison between signed and unsigned integer expressions AS_PER_gkStore_load.C:79:19: warning: comparison between signed and unsigned integer expressions AS_PER_gkStore_load.C:98:18: warning: comparison between signed and unsigned integer expressions AS_PER_gkStore_load.C:101:19: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_partition.o AS_PER_gkStore_partition.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStream.o AS_PER_gkStream.C AS_PER_gkStore_partition.C: In member function ‘void gkStore::gkStore_buildPartitions(short int*, uint32)’: AS_PER_gkStore_partition.C:131:51: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_encodeSequenceQuality.o AS_PER_encodeSequenceQuality.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_asmStore.o AS_PER_asmStore.C ############################## AS_GKP ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_main.o AS_GKP_main.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_bench.o AS_GKP_bench.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_buildPartition.o AS_GKP_buildPartition.C AS_GKP_main.C: In function ‘char* constructIIDdump(char*, char*, uint32, uint32, uint32, double, uint64)’: AS_GKP_main.C:356:18: warning: comparison between signed and unsigned integer expressions AS_GKP_main.C:363:18: warning: comparison between signed and unsigned integer expressions AS_GKP_main.C: In function ‘int main(int, char**)’: AS_GKP_main.C:651:98: warning: format ‘%lld’ expects type ‘long long int’, but argument 3 has type ‘int32’ AS_GKP_main.C: In function ‘char* constructIIDdumpFromIDFile(char*, char*, char*, char*)’: AS_GKP_main.C:215:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_main.C:222:24: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_main.C:238:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_main.C:251:24: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_checkLibrary.o AS_GKP_checkLibrary.C AS_GKP_bench.C: In function ‘void printrusage(char*, double)’: AS_GKP_bench.C:62:27: warning: missing braces around initializer for ‘char [65]’ AS_GKP_bench.C:63:27: warning: missing braces around initializer for ‘timeval’ AS_GKP_bench.C: In function ‘void addRandomFrags(char*, uint32)’: AS_GKP_bench.C:118:15: warning: comparison between signed and unsigned integer expressions AS_GKP_bench.C: In function ‘void updateRandomMates(char*, uint32)’: AS_GKP_bench.C:170:15: warning: comparison between signed and unsigned integer expressions AS_GKP_bench.C:178:34: warning: comparison between signed and unsigned integer expressions AS_GKP_bench.C: In function ‘void readRandomFragments(char*, uint32)’: AS_GKP_bench.C:212:15: warning: comparison between signed and unsigned integer expressions AS_GKP_buildPartition.C: In function ‘int Build_Partition(char*, char*, int32)’: AS_GKP_buildPartition.C:61:15: warning: comparison between signed and unsigned integer expressions AS_GKP_buildPartition.C:71:1: warning: control reaches end of non-void function g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_checkFrag.o AS_GKP_checkFrag.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_checkLink.o AS_GKP_checkLink.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_checkPlace.o AS_GKP_checkPlace.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_dump.o AS_GKP_dump.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_edit.o AS_GKP_edit.C AS_GKP_dump.C: In function ‘void dumpGateKeeperLibraries(char*, AS_IID, AS_IID, char*, int, int)’: AS_GKP_dump.C:173:40: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C:179:21: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C: In function ‘void dumpGateKeeperFragments(char*, AS_IID, AS_IID, char*, int, int, int, int)’: AS_GKP_dump.C:228:40: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C: In function ‘void dumpGateKeeperAsFasta(char*, AS_IID, AS_IID, char*, int, int, int, int)’: AS_GKP_dump.C:329:40: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C:364:27: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C: In function ‘void dumpGateKeeperAsFRG(char*, int, AS_IID, AS_IID, char*, int, int, int)’: AS_GKP_dump.C:431:40: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C:436:23: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_errors.o AS_GKP_errors.C AS_GKP_dump.C: In function ‘void dumpGateKeeperAsNewbler(char*, char*, AS_IID, AS_IID, char*, int, int)’: AS_GKP_dump.C:713:40: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C:718:23: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C: In function ‘void dumpGateKeeperAsFastQ(char*, char*, AS_IID, AS_IID, char*, int, int)’: AS_GKP_dump.C:876:40: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C:881:23: warning: comparison between signed and unsigned integer expressions AS_GKP_dump.C: In function ‘int dumpGateKeeperIsFeatureSet(char*, AS_IID, char*)’: AS_GKP_dump.C:1112:61: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_illumina.o AS_GKP_illumina.C AS_GKP_edit.C: In function ‘void editStore(char*, char*, int)’: AS_GKP_edit.C:348:51: warning: comparison between signed and unsigned integer expressions AS_GKP_edit.C:449:51: warning: comparison between signed and unsigned integer expressions AS_GKP_edit.C:273:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_edit.C:655:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_edit.C: In function ‘void updateVectorClear(char*, char*)’: AS_GKP_edit.C:57:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_edit.C:112:24: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_illumina.C: In function ‘uint64 readSeq(FILE*, char*, ilFragment*, char, uint32, uint32)’: AS_GKP_illumina.C:298:45: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_illumina.C:299:45: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_illumina.C:300:45: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_illumina.C:301:45: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result AS_GKP_illumina.C: In function ‘uint64 readQSeq(FILE*, char*, ilFragment*, char, uint32, uint32)’: AS_GKP_illumina.C:253:45: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/sffToCA.o sffToCA.C sffToCA.C: In function ‘void readsff_manifest(FILE*, sffHeader*, sffManifest*)’: sffToCA.C:291:31: warning: comparison between signed and unsigned integer expressions sffToCA.C: In function ‘void readsff_read(FILE*, sffHeader*, sffRead*)’: sffToCA.C:427:18: warning: comparison between signed and unsigned integer expressions sffToCA.C: In function ‘int processRead(sffHeader*, sffRead*, gkFragment*)’: sffToCA.C:705:50: warning: comparison between signed and unsigned integer expressions sffToCA.C:706:50: warning: comparison between signed and unsigned integer expressions sffToCA.C: In function ‘int loadSFF(char*)’: sffToCA.C:806:21: warning: comparison between signed and unsigned integer expressions sffToCA.C: In function ‘int processMate(gkFragment*, gkFragment*, gkFragment*, char**, int*, int)’: sffToCA.C:1278:37: warning: comparison between signed and unsigned integer expressions sffToCA.C:1280:40: warning: comparison between signed and unsigned integer expressions sffToCA.C:1281:40: warning: comparison between signed and unsigned integer expressions sffToCA.C:1417:35: warning: comparison between signed and unsigned integer expressions sffToCA.C:1422:37: warning: comparison between signed and unsigned integer expressions sffToCA.C:1423:37: warning: comparison between signed and unsigned integer expressions sffToCA.C:1441:7: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fastqToCA.o fastqToCA.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fastqSample.o fastqSample.C fastqSample.C: In function ‘int main(int, char**)’: fastqSample.C:169:63: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 3 has type ‘uint32’ fastqSample.C:170:63: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 3 has type ‘uint32’ fastqSample.C:182:11: warning: comparison between signed and unsigned integer expressions fastqSample.C: In member function ‘void aRead::read(FILE*)’: fastqSample.C:39:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result fastqSample.C:40:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result fastqSample.C:41:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result fastqSample.C:42:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result ############################## AS_OBT ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/chimera.o chimera.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/consolidate.o consolidate.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/deduplicate.o deduplicate.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/initialTrim.o initialTrim.C chimera.C: In function ‘void process(AS_IID, const clear_t*, gkStore*, bool, const overlapList*)’: chimera.C:645:24: warning: large integer implicitly truncated to unsigned type chimera.C:661:26: warning: large integer implicitly truncated to unsigned type chimera.C:680:26: warning: large integer implicitly truncated to unsigned type chimera.C:1039:68: warning: comparison between signed and unsigned integer expressions chimera.C:1049:40: warning: comparison between signed and unsigned integer expressions chimera.C:1053:69: warning: comparison between signed and unsigned integer expressions chimera.C:1068:68: warning: comparison between signed and unsigned integer expressions chimera.C:1073:69: warning: comparison between signed and unsigned integer expressions consolidate.C: In function ‘void consolidate(OVSoverlap*, int32, obtConsolidate_t&)’: consolidate.C:114:22: warning: comparison between signed and unsigned integer expressions consolidate.C:126:19: warning: comparison between signed and unsigned integer expressions consolidate.C:149:22: warning: comparison between signed and unsigned integer expressions consolidate.C:157:19: warning: comparison between signed and unsigned integer expressions deduplicate.C: In function ‘void readOverlapsAndProcessFragments(gkStore*, OverlapStore*, OverlapStore*, uint32, fragT*)’: deduplicate.C:138:52: warning: comparison between signed and unsigned integer expressions deduplicate.C: In function ‘void processMatedFragments(gkStore*, fragT*)’: deduplicate.C:259:56: warning: comparison between signed and unsigned integer expressions deduplicate.C:273:20: warning: comparison between signed and unsigned integer expressions deduplicate.C: In function ‘void deleteFragments(gkStore*, fragT*)’: deduplicate.C:311:56: warning: comparison between signed and unsigned integer expressions deduplicate.C: In function ‘int main(int, char**)’: deduplicate.C:326:50: warning: operation on ‘errorLimit’ may be undefined deduplicate.C:390:52: warning: comparison between signed and unsigned integer expressions initialTrim.C: In function ‘int main(int, char**)’: initialTrim.C:110:61: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/merge-trimming.o merge-trimming.C merge-trimming.C: In function ‘mode5* findModeOfFivePrimeMode(gkStore*, char*)’: merge-trimming.C:102:52: warning: comparison between signed and unsigned integer expressions merge-trimming.C: In function ‘int main(int, char**)’: merge-trimming.C:570:47: warning: comparison between signed and unsigned integer expressions merge-trimming.C:608:64: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 4 has type ‘uint32’ merge-trimming.C:616:64: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 4 has type ‘uint32’ merge-trimming.C:624:64: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 4 has type ‘uint32’ merge-trimming.C: In function ‘bool readLine(FILE*)’: merge-trimming.C:38:26: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapMask.o overlapMask.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/trim.o trim.C overlapMask.C: In function ‘int main(int, char**)’: overlapMask.C:104:52: warning: comparison between signed and unsigned integer expressions overlapMask.C:142:7: warning: comparison between signed and unsigned integer expressions overlapMask.C:171:56: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/readOverlap.o readOverlap.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/removeMateOverlap.o removeMateOverlap.C readOverlap.C: In function ‘OVSoverlap* readOverlap(OverlapStore*, OverlapStore*)’: readOverlap.C:67:1: warning: control reaches end of non-void function g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/util++.o util++.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OBT_acceptableOverlap.o AS_OBT_acceptableOverlap.C removeMateOverlap.C: In function ‘int main(int, char**)’: removeMateOverlap.C:155:63: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long long int’ removeMateOverlap.C:155:63: warning: format ‘%d’ expects type ‘int’, but argument 6 has type ‘long long int’ removeMateOverlap.C:162:61: warning: comparison between signed and unsigned integer expressions ############################## AS_MER ############################## g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/meryl.o meryl.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/mercy.o mercy.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/mercy-regions.o mercy-regions.C mercy.C: In function ‘void compare(merylStreamReader*, merylStreamReader*, kMer&, u32bit, u32bit (*)[6])’: mercy.C:136:12: warning: suggest explicit braces to avoid ambiguous ‘else’ mercy.C:155:10: warning: suggest explicit braces to avoid ambiguous ‘else’ mercy.C:174:8: warning: suggest explicit braces to avoid ambiguous ‘else’ g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overmerry.o overmerry.C mercy-regions.C: In function ‘int main(int, char**)’: mercy-regions.C:983:79: warning: format ‘%u’ expects type ‘unsigned int’, but argument 3 has type ‘intervalNumber’ mercy-regions.C:983:79: warning: format ‘%u’ expects type ‘unsigned int’, but argument 4 has type ‘intervalNumber’ mercy-regions.C:983:79: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘intervalNumber’ mercy-regions.C:983:79: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘intervalNumber’ mercy-regions.C:986:87: warning: format ‘%u’ expects type ‘unsigned int’, but argument 3 has type ‘intervalNumber’ mercy-regions.C:986:87: warning: format ‘%u’ expects type ‘unsigned int’, but argument 4 has type ‘intervalNumber’ mercy-regions.C:986:87: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘intervalNumber’ mercy-regions.C:986:87: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘intervalNumber’ mercy-regions.C:1010:79: warning: format ‘%u’ expects type ‘unsigned int’, but argument 3 has type ‘intervalNumber’ mercy-regions.C:1010:79: warning: format ‘%u’ expects type ‘unsigned int’, but argument 4 has type ‘intervalNumber’ mercy-regions.C:1010:79: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘intervalNumber’ mercy-regions.C:1010:79: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘intervalNumber’ mercy-regions.C:1013:87: warning: format ‘%u’ expects type ‘unsigned int’, but argument 3 has type ‘intervalNumber’ mercy-regions.C:1013:87: warning: format ‘%u’ expects type ‘unsigned int’, but argument 4 has type ‘intervalNumber’ mercy-regions.C:1013:87: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘intervalNumber’ mercy-regions.C:1013:87: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘intervalNumber’ mercy-regions.C:1022:54: warning: format ‘%u’ expects type ‘unsigned int’, but argument 4 has type ‘intervalNumber’ mercy-regions.C:1022:54: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘intervalNumber’ mercy-regions.C: In function ‘void readBadMers(char*, std::map&)’: mercy-regions.C:838:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result mercy-regions.C:857:25: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result mercy-regions.C: In function ‘void readVariation(char*, std::map&)’: mercy-regions.C:803:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result mercy-regions.C:817:32: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result mercy-regions.C: In function ‘void readDepth(char*, std::map&)’: mercy-regions.C:755:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result mercy-regions.C:772:25: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/merTrim.o merTrim.C merTrim.C:214:2: warning: #warning not really replacing N with random ACGT overmerry.C: In function ‘u32bit ovmWorker_analyzeReadForThreshold(ovmGlobalData*, ovmThreadData*, ovmComputation*, merStream*, uint32*)’: overmerry.C:506:63: warning: format ‘%u’ expects type ‘unsigned int’, but argument 4 has type ‘u32bit’ overmerry.C:506:63: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘u32bit’ overmerry.C:506:63: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘u32bit’ overmerry.C:506:63: warning: format ‘%u’ expects type ‘unsigned int’, but argument 7 has type ‘u32bit’ overmerry.C:506:63: warning: format ‘%u’ expects type ‘unsigned int’, but argument 8 has type ‘u32bit’ overmerry.C:506:63: warning: format ‘%u’ expects type ‘unsigned int’, but argument 9 has type ‘u32bit’ overmerry.C:506:63: warning: format ‘%u’ expects type ‘unsigned int’, but argument 10 has type ‘u32bit’ In file included from merTrim.C:38:0: /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include/existDB.H: In member function ‘void existDB::insertMer(u64bit, u64bit, u64bit, u64bit*)’: /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include/existDB.H:83:8: warning: suggest explicit braces to avoid ambiguous ‘else’ g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/estimate-mer-threshold.o estimate-mer-threshold.C estimate-mer-threshold.C: In function ‘int main(int, char**)’: estimate-mer-threshold.C:103:70: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘u64bit’ estimate-mer-threshold.C:106:89: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘u64bit’ estimate-mer-threshold.C:106:89: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘u64bit’ estimate-mer-threshold.C:110:89: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘u64bit’ estimate-mer-threshold.C:110:89: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘u64bit’ estimate-mer-threshold.C:114:87: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘u64bit’ estimate-mer-threshold.C:114:87: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘u64bit’ estimate-mer-threshold.C:139:84: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 3 has type ‘uint32’ g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MER_gkpStore_to_FastABase.o AS_MER_gkpStore_to_FastABase.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/include -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MER_gkpStoreChain.o AS_MER_gkpStoreChain.C ############################## AS_OVL ############################## g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_overlap.o AS_OVL_overlap.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_driver.o AS_OVL_driver.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_overlap_ca.o AS_OVL_overlap_ca.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_driver_ca.o AS_OVL_driver_ca.C In file included from AS_OVL_overlap.C:70:0: AS_OVL_overlap_common.h: In function ‘int main(int, char**)’: AS_OVL_overlap_common.h:779:28: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘String_Ref_t Add_Extra_Hash_String(const char*)’: AS_OVL_overlap_common.h:1074:15: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘void Add_Ref(String_Ref_t, int, Work_Area_t*)’: AS_OVL_overlap_common.h:1273:64: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘int Build_Hash_Index(gkStream*, int32, gkFragment*)’: AS_OVL_overlap_common.h:1491:24: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h:1494:29: warning: comparison between signed and unsigned integer expressions In file included from AS_OVL_driver.C:45:0: AS_OVL_driver_common.h: In function ‘int OverlapDriver(int, char**)’: AS_OVL_driver_common.h:151:90: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘int64’ AS_OVL_driver_common.h:151:90: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘int64’ AS_OVL_driver_common.h:178:45: warning: comparison between signed and unsigned integer expressions AS_OVL_driver_common.h:180:61: warning: comparison between signed and unsigned integer expressions AS_OVL_driver_common.h: In function ‘int Choose_Hi_IID_Sub(uint32*, int, int)’: AS_OVL_driver_common.h:299:37: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘void Put_String_In_Hash(int)’: AS_OVL_overlap_common.h:4135:13: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘int Read_Next_Frag(char*, char*, gkStream*, gkFragment*, Screen_Info_t*, uint32*)’: AS_OVL_overlap_common.h:4258:58: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’ In file included from AS_OVL_overlap_ca.C:73:0: AS_OVL_overlap_common.h: In function ‘int main(int, char**)’: AS_OVL_overlap_common.h:641:33: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h:779:28: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘String_Ref_t Add_Extra_Hash_String(const char*)’: AS_OVL_overlap_common.h:1074:15: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘void Add_Ref(String_Ref_t, int, Work_Area_t*)’: AS_OVL_overlap_common.h:1273:64: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘int Build_Hash_Index(gkStream*, int32, gkFragment*)’: AS_OVL_overlap_common.h:1491:24: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h:1494:29: warning: comparison between signed and unsigned integer expressions In file included from AS_OVL_driver_ca.C:50:0: AS_OVL_driver_common.h: In function ‘int OverlapDriver(int, char**)’: AS_OVL_driver_common.h:151:90: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘int64’ AS_OVL_driver_common.h:151:90: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘int64’ AS_OVL_driver_common.h:178:45: warning: comparison between signed and unsigned integer expressions AS_OVL_driver_common.h:180:61: warning: comparison between signed and unsigned integer expressions AS_OVL_driver_common.h: In function ‘int Choose_Hi_IID_Sub(uint32*, int, int)’: AS_OVL_driver_common.h:299:37: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘void Put_String_In_Hash(int)’: AS_OVL_overlap_common.h:4135:13: warning: comparison between signed and unsigned integer expressions AS_OVL_overlap_common.h: In function ‘String_Ref_t Add_Extra_Hash_String(const char*)’: AS_OVL_overlap_common.h:1073:35: warning: ‘ref’ is used uninitialized in this function AS_OVL_overlap_common.h: In function ‘int Read_Next_Frag(char*, char*, gkStream*, gkFragment*, Screen_Info_t*, uint32*)’: AS_OVL_overlap_common.h:4258:58: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 4 has type ‘size_t’ AS_OVL_overlap_common.h: In function ‘String_Ref_t Add_Extra_Hash_String(const char*)’: AS_OVL_overlap_common.h:1073:35: warning: ‘ref’ is used uninitialized in this function g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o AS_OVL_delcher.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/OlapFromSeedsOVL.o OlapFromSeedsOVL.C AS_OVL_overlap_common.h: In function ‘String_Ref_t Hash_Find(uint64, int64, char*, int64*, int*)’: AS_OVL_overlap_common.h:2232:18: warning: ‘H_Ref’ may be used uninitialized in this function g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/FragCorrectOVL.o FragCorrectOVL.C AS_OVL_overlap_common.h: In function ‘String_Ref_t Hash_Find(uint64, int64, char*, int64*, int*)’: AS_OVL_overlap_common.h:2232:18: warning: ‘H_Ref’ may be used uninitialized in this function OlapFromSeedsOVL.C: In function ‘void Extract_Needed_Frags(gkStore*, int32, int32, Frag_List_t*, int*)’: OlapFromSeedsOVL.C:2505:53: warning: comparison between signed and unsigned integer expressions OlapFromSeedsOVL.C:2544:33: warning: comparison between signed and unsigned integer expressions OlapFromSeedsOVL.C:2580:52: warning: comparison between signed and unsigned integer expressions OlapFromSeedsOVL.C: In function ‘void Get_Seeds_From_Store(char*, int32, int32, Olap_Info_t**, int*)’: OlapFromSeedsOVL.C:2682:38: warning: format ‘%2u’ expects type ‘unsigned int’, but argument 4 has type ‘long long unsigned int’ OlapFromSeedsOVL.C:2682:38: warning: format ‘%5u’ expects type ‘unsigned int’, but argument 7 has type ‘long long unsigned int’ OlapFromSeedsOVL.C:2682:38: warning: format ‘%5u’ expects type ‘unsigned int’, but argument 8 has type ‘long long unsigned int’ OlapFromSeedsOVL.C:2682:38: warning: format ‘%4u’ expects type ‘unsigned int’, but argument 9 has type ‘long long unsigned int’ OlapFromSeedsOVL.C:2682:38: warning: format ‘%4u’ expects type ‘unsigned int’, but argument 10 has type ‘long long unsigned int’ OlapFromSeedsOVL.C:2682:38: warning: format ‘%2u’ expects type ‘unsigned int’, but argument 11 has type ‘long long unsigned int’ OlapFromSeedsOVL.C: In function ‘void Output_Olap(Olap_Info_t*, int, int, int, int, int, int, int)’: OlapFromSeedsOVL.C:3551:11: warning: enumeration value ‘OVL_STORE’ not handled in switch OlapFromSeedsOVL.C: In function ‘void Output_Olap_From_Diff(const Sequence_Diff_t*, int)’: OlapFromSeedsOVL.C:3646:11: warning: enumeration value ‘OVL_STORE’ not handled in switch OlapFromSeedsOVL.C: In function ‘void Set_Signature(Difference_Signature_t*, short int*, int, const Sequence_Diff_t*, const char*, int, int)’: OlapFromSeedsOVL.C:5201:81: warning: suggest parentheses around ‘&&’ within ‘||’ OlapFromSeedsOVL.C:5223:81: warning: suggest parentheses around ‘&&’ within ‘||’ OlapFromSeedsOVL.C: In function ‘void Stream_Old_Frags()’: OlapFromSeedsOVL.C:5583:42: warning: comparison between signed and unsigned integer expressions OlapFromSeedsOVL.C:5607:33: warning: comparison between signed and unsigned integer expressions OlapFromSeedsOVL.C:5614:48: warning: comparison between signed and unsigned integer expressions OlapFromSeedsOVL.C: In function ‘void Tidy_Up()’: OlapFromSeedsOVL.C:5863:11: warning: enumeration value ‘OVL_STORE’ not handled in switch FragCorrectOVL.C: In function ‘void Extract_Needed_Frags(gkStore*, int32, int32, Frag_List_t*, int*)’: FragCorrectOVL.C:992:32: warning: comparison between signed and unsigned integer expressions FragCorrectOVL.C:1026:35: warning: comparison between signed and unsigned integer expressions FragCorrectOVL.C:1059:52: warning: comparison between signed and unsigned integer expressions OlapFromSeedsOVL.C: In function ‘void Output_Correction_Header(FILE*, int)’: OlapFromSeedsOVL.C:3144:55: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result FragCorrectOVL.C: In function ‘void Stream_Old_Frags()’: FragCorrectOVL.C:2109:42: warning: comparison between signed and unsigned integer expressions FragCorrectOVL.C:2126:35: warning: comparison between signed and unsigned integer expressions FragCorrectOVL.C:2133:48: warning: comparison between signed and unsigned integer expressions OlapFromSeedsOVL.C: In function ‘void Determine_Homopoly_Corrections(FILE*, int, New_Vote_t*, char*, char*, int)’: OlapFromSeedsOVL.C:1773:61: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result OlapFromSeedsOVL.C: In function ‘void Determine_Standard_Corrections(FILE*, int, New_Vote_t*, char*, char*, int)’: OlapFromSeedsOVL.C:1926:61: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result FragCorrectOVL.C: In function ‘void Output_Corrections(FILE*)’: FragCorrectOVL.C:1308:58: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result FragCorrectOVL.C:1326:63: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result FragCorrectOVL.C:1400:71: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result FragCorrectOVL.C:1451:71: warning: ignoring return value of ‘size_t fwrite(const void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ShowCorrectsOVL.o ShowCorrectsOVL.C ShowCorrectsOVL.C: In function ‘int main(int, char**)’: ShowCorrectsOVL.C:96:56: warning: format ‘%8u’ expects type ‘unsigned int’, but argument 2 has type ‘long long unsigned int’ ShowCorrectsOVL.C:99:45: warning: format ‘%4u’ expects type ‘unsigned int’, but argument 2 has type ‘long long unsigned int’ g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CorrectOlapsOVL.o CorrectOlapsOVL.C CorrectOlapsOVL.C: In function ‘void Correct_Frags()’: CorrectOlapsOVL.C:736:23: warning: comparison between signed and unsigned integer expressions CorrectOlapsOVL.C:738:28: warning: comparison between signed and unsigned integer expressions CorrectOlapsOVL.C: In function ‘void Dump_Erate_File(char*, int32, int32, Olap_Info_t*, uint64)’: CorrectOlapsOVL.C:916:22: warning: comparison between signed and unsigned integer expressions CorrectOlapsOVL.C: In function ‘void Read_Frags()’: CorrectOlapsOVL.C:2045:35: warning: comparison between signed and unsigned integer expressions CorrectOlapsOVL.C: In function ‘void Redo_Olaps()’: CorrectOlapsOVL.C:2181:42: warning: comparison between signed and unsigned integer expressions CorrectOlapsOVL.C:2195:35: warning: comparison between signed and unsigned integer expressions CorrectOlapsOVL.C:2236:48: warning: comparison between signed and unsigned integer expressions g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CatCorrectsOVL.o CatCorrectsOVL.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CatEratesOVL.o CatEratesOVL.C g++ -pthread -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SharedOVL.o SharedOVL.C SharedOVL.C: In function ‘int Fwd_Banded_Homopoly_Prefix_Match(const char*, int, const char*, int, int, int, int, int*, int*, int*, int*, int*, int*, Alignment_Cell_t*, double, int)’: SharedOVL.C:192:39: warning: suggest parentheses around ‘&&’ within ‘||’ SharedOVL.C:287:67: warning: suggest parentheses around ‘&&’ within ‘||’ SharedOVL.C: In function ‘int Rev_Homopoly_Match_Start(const char*, int, const char*, int, int, int*, int*, int*, int*, Homopoly_Match_Entry_t**, double, int)’: SharedOVL.C:1260:9: warning: ‘best_end_d’ may be used uninitialized in this function SharedOVL.C:1260:21: warning: ‘best_end_e’ may be used uninitialized in this function SharedOVL.C: In function ‘void Set_Fwd_Banded_Delta(int*, int*, Alignment_Cell_t*, int, int, int*, int*)’: SharedOVL.C:1784:28: warning: ‘sign’ may be used uninitialized in this function SharedOVL.C: In function ‘int Fwd_Banded_Homopoly_Prefix_Match(const char*, int, const char*, int, int, int, int, int*, int*, int*, int*, int*, int*, Alignment_Cell_t*, double, int)’: SharedOVL.C:135:19: warning: ‘best_col’ may be used uninitialized in this function SharedOVL.C:135:41: warning: ‘best_errors’ may be used uninitialized in this function SharedOVL.C: In function ‘int Fwd_Homopoly_Prefix_Match(const char*, int, const char*, int, int, int*, int*, int*, int*, int*, int*, Homopoly_Match_Entry_t**)’: SharedOVL.C:404:9: warning: ‘best_end_d’ may be used uninitialized in this function SharedOVL.C:404:21: warning: ‘best_end_e’ may be used uninitialized in this function ############################## AS_OVS ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlap.o AS_OVS_overlap.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapFile.o AS_OVS_overlapFile.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStore.o AS_OVS_overlapStore.C AS_OVS_overlap.C: In function ‘int AS_OVS_convertOVLdumpToOVSoverlap(char*, OVSoverlap*)’: AS_OVS_overlap.C:134:24: warning: comparison between signed and unsigned integer expressions AS_OVS_overlap.C: In function ‘int AS_OVS_convertOBTdumpToOVSoverlap(char*, OVSoverlap*)’: AS_OVS_overlap.C:171:24: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStats.o AS_OVS_overlapStats.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore.o overlapStore.C AS_OVS_overlapStore.C: In function ‘OverlapStore* AS_OVS_openOverlapStorePrivate(const char*, int, int)’: AS_OVS_overlapStore.C:133:62: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘uint64’ AS_OVS_overlapStore.C:139:73: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘uint64’ AS_OVS_overlapStore.C:172:27: warning: comparison between signed and unsigned integer expressions AS_OVS_overlapStore.C: In function ‘void AS_OVS_restoreBackup(OverlapStore*)’: AS_OVS_overlapStore.C:219:27: warning: comparison between signed and unsigned integer expressions AS_OVS_overlapStore.C: In function ‘void AS_OVS_closeOverlapStore(OverlapStore*)’: AS_OVS_overlapStore.C:448:27: warning: comparison between signed and unsigned integer expressions AS_OVS_overlapStore.C: In function ‘void AS_OVS_writeOverlapToStore(OverlapStore*, OVSoverlap*)’: AS_OVS_overlapStore.C:624:41: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore_build.o overlapStore_build.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore_merge.o overlapStore_merge.C overlapStore.C: In function ‘int main(int, char**)’: overlapStore.C:236:73: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ overlapStore.C:146:35: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result overlapStore.C:153:37: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result overlapStore_build.C: In function ‘void writeToDumpFile(OVSoverlap*, BinaryOverlapFile**, uint32, uint64*, uint32, char*)’: overlapStore_build.C:69:13: warning: comparison between signed and unsigned integer expressions overlapStore_build.C:79:65: warning: format ‘%d’ expects type ‘int’, but argument 6 has type ‘long long unsigned int’ overlapStore_build.C:79:65: warning: format ‘%d’ expects type ‘int’, but argument 7 has type ‘long long unsigned int’ overlapStore_build.C:79:65: warning: format ‘%d’ expects type ‘int’, but argument 8 has type ‘long long unsigned int’ overlapStore_build.C: In function ‘void buildStore(char*, char*, uint64, uint32, uint32, uint32, char**, Ovl_Skip_Type_t)’: overlapStore_build.C:202:68: warning: format ‘%d’ expects type ‘int’, but argument 6 has type ‘long long unsigned int’ overlapStore_build.C:202:68: warning: format ‘%d’ expects type ‘int’, but argument 7 has type ‘long long unsigned int’ overlapStore_build.C:202:68: warning: format ‘%d’ expects type ‘int’, but argument 8 has type ‘long long unsigned int’ overlapStore_build.C:295:15: warning: comparison between signed and unsigned integer expressions overlapStore_build.C:305:15: warning: comparison between signed and unsigned integer expressions overlapStore_build.C:314:15: warning: comparison between signed and unsigned integer expressions overlapStore_build.C:328:70: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘time_t’ overlapStore_build.C:336:5: warning: comparison between signed and unsigned integer expressions overlapStore_build.C:337:5: warning: comparison between signed and unsigned integer expressions overlapStore_build.C:346:70: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘time_t’ overlapStore_build.C:349:70: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘time_t’ overlapStore_build.C:350:29: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore_dump.o overlapStore_dump.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore_erates.o overlapStore_erates.C overlapStore_dump.C: In function ‘void dumpStore(char*, uint32, double, uint32, uint32, uint32, uint32)’: overlapStore_dump.C:89:45: warning: format ‘%5d’ expects type ‘int’, but argument 6 has type ‘long long int’ overlapStore_dump.C:89:45: warning: format ‘%5d’ expects type ‘int’, but argument 7 has type ‘long long int’ overlapStore_dump.C:89:45: warning: format ‘%5d’ expects type ‘int’, but argument 10 has type ‘long long unsigned int’ overlapStore_dump.C:109:70: warning: format ‘%4d’ expects type ‘int’, but argument 6 has type ‘long long unsigned int’ overlapStore_dump.C:109:70: warning: format ‘%4d’ expects type ‘int’, but argument 7 has type ‘long long unsigned int’ overlapStore_dump.C:109:70: warning: format ‘%4d’ expects type ‘int’, but argument 8 has type ‘long long unsigned int’ overlapStore_dump.C:125:40: warning: format ‘%4d’ expects type ‘int’, but argument 6 has type ‘long long unsigned int’ overlapStore_dump.C:125:40: warning: format ‘%4d’ expects type ‘int’, but argument 7 has type ‘long long unsigned int’ overlapStore_dump.C:125:40: warning: format ‘%4d’ expects type ‘int’, but argument 8 has type ‘long long unsigned int’ overlapStore_dump.C:125:40: warning: format ‘%4d’ expects type ‘int’, but argument 9 has type ‘long long unsigned int’ g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStats.o overlapStats.C In file included from overlapStats.C:61:0: AS_UTL_histogram.h:344:2: warning: #warning not remembering the smallest/largest In file included from overlapStats.C:101:0: overlapStatsBoringStuff.h:282:2: warning: #warning bogus compute of repeatThreshold g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/convertOverlap.o convertOverlap.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/filterOverlap.o filterOverlap.C In file included from overlapStats.C:61:0: AS_UTL_histogram.h: In function ‘void AS_UTL_histogramShow(AS_UTL_histogram*, FILE*, char*)’: AS_UTL_histogram.h:186:30: warning: missing braces around initializer for ‘uint64 [3]’ AS_UTL_histogram.h:187:30: warning: missing braces around initializer for ‘uint64 [3]’ AS_UTL_histogram.h:208:18: warning: comparison between signed and unsigned integer expressions AS_UTL_histogram.h:241:18: warning: comparison between signed and unsigned integer expressions AS_UTL_histogram.h:252:15: warning: comparison between signed and unsigned integer expressions AS_UTL_histogram.h:252:31: warning: comparison between signed and unsigned integer expressions AS_UTL_histogram.h:253:13: warning: comparison between signed and unsigned integer expressions AS_UTL_histogram.h:260:13: warning: comparison between signed and unsigned integer expressions AS_UTL_histogram.h: In function ‘AS_UTL_histogram3d* AS_UTL_histogram3dAllocate(AS_UTL_histogram3d*, uint32, uint32)’: AS_UTL_histogram.h:306:31: warning: comparison between signed and unsigned integer expressions AS_UTL_histogram.h: In function ‘void AS_UTL_histogram3dAdd(AS_UTL_histogram3d*, uint64, uint64)’: AS_UTL_histogram.h:335:31: warning: comparison between signed and unsigned integer expressions In file included from overlapStats.C:101:0: overlapStatsBoringStuff.h: In function ‘RepeatModel* computeRepeatModels(OverlapStore*, gkStore*)’: overlapStatsBoringStuff.h:295:66: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘uint64’ overlapStats.C: In function ‘FragmentEndData* process_FragmentEnds(OVSoverlap*, uint64, gkStore*, RepeatModel*, FragmentEndData*, int)’: overlapStats.C:146:15: warning: comparison between signed and unsigned integer expressions overlapStats.C: In function ‘LibraryOverlapData* process_LibraryRandomness(OVSoverlap*, uint64, gkStore*, RepeatModel*, LibraryOverlapData*)’: overlapStats.C:287:19: warning: comparison between signed and unsigned integer expressions overlapStats.C: In function ‘void finalize_LibraryRandomness(gkStore*, RepeatModel*, LibraryOverlapData*)’: overlapStats.C:338:164: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘uint64’ overlapStats.C:338:164: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘uint64’ overlapStats.C:339:63: warning: unknown conversion type character ‘r’ in format overlapStats.C:358:96: warning: format ‘%d’ expects type ‘int’, but argument 6 has type ‘uint64’ overlapStats.C: In function ‘int main(int, char**)’: overlapStats.C:409:74: warning: too few arguments for format convertOverlap.C: In function ‘void convertOVLtoASCII()’: convertOverlap.C:155:66: warning: format ‘%5d’ expects type ‘int’, but argument 6 has type ‘long long int’ convertOverlap.C:155:66: warning: format ‘%5d’ expects type ‘int’, but argument 7 has type ‘long long int’ convertOverlap.C: In function ‘void convertOBTtoASCII()’: convertOverlap.C:175:61: warning: format ‘%4d’ expects type ‘int’, but argument 6 has type ‘long long unsigned int’ convertOverlap.C:175:61: warning: format ‘%4d’ expects type ‘int’, but argument 7 has type ‘long long unsigned int’ convertOverlap.C:175:61: warning: format ‘%4d’ expects type ‘int’, but argument 8 has type ‘long long unsigned int’ convertOverlap.C: In function ‘void convertMERtoASCII()’: convertOverlap.C:196:31: warning: format ‘%d’ expects type ‘int’, but argument 7 has type ‘long long unsigned int’ convertOverlap.C:196:31: warning: format ‘%4d’ expects type ‘int’, but argument 8 has type ‘long long unsigned int’ convertOverlap.C:196:31: warning: format ‘%4d’ expects type ‘int’, but argument 9 has type ‘long long unsigned int’ convertOverlap.C:196:31: warning: format ‘%4d’ expects type ‘int’, but argument 10 has type ‘long long unsigned int’ convertOverlap.C:196:31: warning: format ‘%4d’ expects type ‘int’, but argument 11 has type ‘long long unsigned int’ convertOverlap.C: In function ‘void convertOBTtoBinary()’: convertOverlap.C:84:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result convertOverlap.C:88:29: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result convertOverlap.C: In function ‘void convertOVLtoBinary()’: convertOverlap.C:66:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result convertOverlap.C:70:29: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result ############################## AS_ALN ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_dpaligner.o AS_ALN_dpaligner.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_qvaligner.o AS_ALN_qvaligner.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_loverlapper.o AS_ALN_loverlapper.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_pieceOlap.o AS_ALN_pieceOlap.C AS_ALN_loverlapper.C: In function ‘void safe_suffix(char**, int*, char*, int)’: AS_ALN_loverlapper.C:103:3: warning: comparison between signed and unsigned integer expressions AS_ALN_loverlapper.C: In function ‘void print_piece(Local_Overlap*, int, char*, char*)’: AS_ALN_loverlapper.C:139:3: warning: comparison between signed and unsigned integer expressions AS_ALN_loverlapper.C:140:3: warning: comparison between signed and unsigned integer expressions AS_ALN_loverlapper.C: In function ‘int* AS_Local_Trace(Local_Overlap*, char*, char*)’: AS_ALN_loverlapper.C:818:5: warning: comparison between signed and unsigned integer expressions AS_ALN_loverlapper.C:819:5: warning: comparison between signed and unsigned integer expressions AS_ALN_loverlapper.C: In function ‘int _ZL13compressChainP13Local_Overlapi.clone.0(int*, Local_Chain**, int)’: AS_ALN_loverlapper.C:225:7: warning: ‘I’ may be used uninitialized in this function AS_ALN_pieceOlap.C: In function ‘void safe_substr(char**, int*, const char*, int, int)’: AS_ALN_pieceOlap.C:50:3: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_forcns.o AS_ALN_forcns.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_local.o CA_ALN_local.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_overlap.o CA_ALN_overlap.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_scafcomp.o CA_ALN_scafcomp.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_bruteforcedp.o AS_ALN_bruteforcedp.C AS_ALN_bruteforcedp.C: In function ‘void alignLinker(char*, char*, char*, char*, dpCell (*)[2048], alignLinker_s*, int, int, int, int)’: AS_ALN_bruteforcedp.C:184:12: warning: assuming signed overflow does not occur when assuming that (X + c) >= X is always true AS_ALN_bruteforcedp.C:185:12: warning: assuming signed overflow does not occur when assuming that (X + c) >= X is always true CA_ALN_overlap.C: In function ‘void _ZL25Print_Local_Overlap_PieceP8_IO_FILEPcS1_P13Local_Segment.clone.2(char*, char*, Local_Segment*)’: CA_ALN_overlap.C:1148:20: warning: array subscript is below array bounds CA_ALN_overlap.C:1148:20: warning: array subscript is below array bounds CA_ALN_scafcomp.C: In function ‘Segment* Align_Scaffold(Segment*, int, int, Scaffold*, Scaffold*, int*, int, int)’: CA_ALN_scafcomp.C:1455:9: warning: ‘beg’ may be used uninitialized in this function CA_ALN_scafcomp.C:1456:9: warning: ‘end’ may be used uninitialized in this function ############################## AS_CGB ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_unitigger.o AS_CGB_unitigger.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_FGB_main.o AS_FGB_main.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_FGB_io.o AS_FGB_io.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_histo.o AS_CGB_histo.C AS_CGB_unitigger.C: In function ‘void output_the_chunks(Tfragment*, Tedge*, TChunkFrag*, TChunkMesg*, float, int, char*, char*, gkStore*)’: AS_CGB_unitigger.C:80:28: warning: comparison between signed and unsigned integer expressions AS_CGB_unitigger.C:93:72: warning: format ‘%lld’ expects type ‘long long int’, but argument 6 has type ‘uint32’ AS_CGB_unitigger.C:95:31: warning: comparison between signed and unsigned integer expressions AS_CGB_unitigger.C:142:31: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_fga.o AS_CGB_fga.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_fgb.o AS_CGB_fgb.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_FGB_hanging_fragment.o AS_FGB_hanging_fragment.C AS_CGB_fgb.C: In function ‘void setup_segments(Tfragment*, Tedge*)’: AS_CGB_fgb.C:213:3: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_FGB_contained.o AS_FGB_contained.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_traversal.o AS_CGB_traversal.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_walk.o AS_CGB_walk.C AS_CGB_traversal.C: In function ‘void as_diagq(FILE*, IntFragment_ID*, int, IntFragment_ID, IntFragment_ID)’: AS_CGB_traversal.C:124:21: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_edgemate.o AS_CGB_edgemate.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_main.o AS_CGB_main.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_cgb.o AS_CGB_cgb.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_classify.o AS_CGB_classify.C AS_CGB_main.C: In function ‘int main_cgb(THeapGlobals*, UnitiggerGlobals*, gkStore*)’: AS_CGB_main.C:404:82: warning: suggest parentheses around ‘&&’ within ‘||’ AS_CGB_cgb.C: In function ‘IntEdge_ID find_intrachunk_edge(Tfragment*, Tedge*, IntFragment_ID, int, IntFragment_ID*, int*)’: AS_CGB_cgb.C:399:16: warning: comparison between signed and unsigned integer expressions AS_CGB_cgb.C: In function ‘int count_the_randomly_sampled_fragments_in_a_chunk(Tfragment*, TChunkFrag*, TChunkMesg*, IntChunk_ID, gkStore*)’: AS_CGB_cgb.C:986:15: warning: comparison between signed and unsigned integer expressions AS_CGB_cgb.C: In function ‘float compute_the_global_fragment_arrival_rate(int, float, FILE*, int64, Tfragment*, Tedge*, float, TChunkFrag*, TChunkMesg*, gkStore*)’: AS_CGB_cgb.C:1132:23: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_chimeras.o AS_CGB_chimeras.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_cga.o AS_CGB_cga.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble.o AS_CGB_Bubble.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_Graph.o AS_CGB_Bubble_Graph.C AS_CGB_Bubble.C: In function ‘AS_CGB_Bubble_List* _collect_bubbles(BubGraph*, BubVertexSet*, BubVertexSet*, IntFragment_ID*, int)’: AS_CGB_Bubble.C:114:19: warning: comparison between signed and unsigned integer expressions AS_CGB_Bubble.C:128:19: warning: comparison between signed and unsigned integer expressions AS_CGB_Bubble.C: In function ‘void _forward_collect_sets(BubGraph*, BubVertexSet*, IntFragment_ID*, int)’: AS_CGB_Bubble.C:200:19: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_VertexSet.o AS_CGB_Bubble_VertexSet.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_dfs.o AS_CGB_Bubble_dfs.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_Popper.o AS_CGB_Bubble_Popper.C AS_CGB_Bubble_Popper.C: In function ‘void BP_reset(BubblePopper*)’: AS_CGB_Bubble_Popper.C:112:23: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_PopperMethods.o AS_CGB_Bubble_PopperMethods.C AS_CGB_Bubble_PopperMethods.C: In function ‘void BP_transitive_closure(BubblePopper*)’: AS_CGB_Bubble_PopperMethods.C:151:41: warning: comparison between signed and unsigned integer expressions AS_CGB_Bubble_PopperMethods.C: In function ‘int BP_DAG_longest_path(BubblePopper*)’: AS_CGB_Bubble_PopperMethods.C:225:29: warning: comparison between signed and unsigned integer expressions AS_CGB_Bubble_PopperMethods.C:232:33: warning: comparison between signed and unsigned integer expressions ############################## AS_BOG ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BuildUnitigs.o BuildUnitigs.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_BestOverlapGraph.o AS_BOG_BestOverlapGraph.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_ChunkGraph.o AS_BOG_ChunkGraph.cc In file included from BuildUnitigs.cc:22:0: AS_BOG_Datatypes.hh:44:2: warning: #warning there is a comparison assuming fragment_end_type FIVE_PRIME < THREE_PRIME g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_MateChecker.o AS_BOG_MateChecker.cc In file included from AS_BOG_BestOverlapGraph.cc:24:0: AS_BOG_Datatypes.hh:44:2: warning: #warning there is a comparison assuming fragment_end_type FIVE_PRIME < THREE_PRIME In file included from AS_BOG_ChunkGraph.cc:24:0: AS_BOG_Datatypes.hh:44:2: warning: #warning there is a comparison assuming fragment_end_type FIVE_PRIME < THREE_PRIME AS_BOG_ChunkGraph.cc:89:5: warning: multi-line comment In file included from AS_BOG_MateChecker.cc:24:0: AS_BOG_Datatypes.hh:44:2: warning: #warning there is a comparison assuming fragment_end_type FIVE_PRIME < THREE_PRIME AS_BOG_MateChecker.cc:155:2: warning: #warning assumes innie mate pairs AS_BOG_MateChecker.cc:722:2: warning: #warning EMPTIED OUT A UNITIG In file included from BuildUnitigs.cc:26:0: AS_BOG_MateChecker.hh: In function ‘bool operator==(SeqInterval, SeqInterval)’: AS_BOG_MateChecker.hh:110:45: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_MateChecker.hh: In member function ‘void MateLocation::incrRange(int32*, int32, int32, int32)’: AS_BOG_MateChecker.hh:234:23: warning: comparison between signed and unsigned integer expressions AS_BOG_BestOverlapGraph.cc: In member function ‘uint32 BestOverlapGraph::BEnd(const OVSoverlap&)’: AS_BOG_BestOverlapGraph.cc:51:6: warning: suggest explicit braces to avoid ambiguous ‘else’ AS_BOG_BestOverlapGraph.cc:57:6: warning: suggest explicit braces to avoid ambiguous ‘else’ BuildUnitigs.cc: In function ‘int main(int, char**)’: BuildUnitigs.cc:280:67: warning: format ‘%lld’ expects type ‘long long int’, but argument 3 has type ‘long int’ In file included from AS_BOG_MateChecker.cc:26:0: AS_BOG_MateChecker.hh: In function ‘bool operator==(SeqInterval, SeqInterval)’: AS_BOG_MateChecker.hh:110:45: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_MateChecker.hh: In member function ‘void MateLocation::incrRange(int32*, int32, int32, int32)’: AS_BOG_MateChecker.hh:234:23: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc: In member function ‘void MateChecker::checkUnitigGraph(UnitigGraph&, int)’: AS_BOG_MateChecker.cc:72:47: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc: In member function ‘void MateChecker::computeGlobalLibStats(UnitigGraph&)’: AS_BOG_MateChecker.cc:227:45: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:258:51: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:259:44: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:270:51: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:271:44: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc: In member function ‘void MateChecker::evaluateMates(UnitigGraph&)’: AS_BOG_MateChecker.cc:303:45: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:385:60: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:389:37: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:395:60: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:399:37: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc: In member function ‘void MateChecker::moveContains(UnitigGraph&)’: AS_BOG_MateChecker.cc:432:45: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:611:14: warning: suggest explicit braces to avoid ambiguous ‘else’ AS_BOG_MateChecker.cc:711:57: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc: In member function ‘void MateChecker::splitDiscontinuousUnitigs(UnitigGraph&)’: AS_BOG_MateChecker.cc:754:45: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:854:58: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc: In member function ‘UnitigBreakPoints* MateChecker::computeMateCoverage(Unitig*, BestOverlapGraph*, int)’: AS_BOG_MateChecker.cc:985:52: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_MateChecker.cc:1060:51: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_MateChecker.cc:1063:30: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc: In member function ‘void MateLocation::buildHappinessGraphs(Unitig*, DistanceCompute*)’: AS_BOG_MateChecker.cc:1236:68: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:1264:39: warning: comparison between signed and unsigned integer expressions AS_BOG_MateChecker.cc:1265:39: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_Unitig.o AS_BOG_Unitig.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_UnitigGraph.o AS_BOG_UnitigGraph.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fixUnitigs.o fixUnitigs.C In file included from AS_BOG_Unitig.cc:24:0: AS_BOG_Datatypes.hh:44:2: warning: #warning there is a comparison assuming fragment_end_type FIVE_PRIME < THREE_PRIME AS_BOG_Unitig.cc:62:2: warning: #warning WHAT REALLLY HAPPENS IF NO BACKBONE NODE, OR NO PREVIOUS BACKBONE NODE AS_BOG_Unitig.cc:227:2: warning: #warning not knowing the overlap length really hurts. AS_BOG_Unitig.cc:282:2: warning: #warning not knowing the overlap length really hurts. AS_BOG_Unitig.cc:470:2: warning: #warning not knowing the overlap length really hurts. In file included from AS_BOG_UnitigGraph.cc:24:0: AS_BOG_Datatypes.hh:44:2: warning: #warning there is a comparison assuming fragment_end_type FIVE_PRIME < THREE_PRIME AS_BOG_UnitigGraph.cc:539:2: warning: #warning Reverse complement degrades assemblies AS_BOG_UnitigGraph.cc:809:2: warning: #warning possible bug AS_BOG_UnitigGraph.cc:1480:2: warning: #warning NEED TO SET AS_UTG_ERROR_RATE AS_BOG_UnitigGraph.cc:1481:2: warning: #warning NEED TO SET AS_UTG_ERROR_RATE AS_BOG_UnitigGraph.cc:1482:2: warning: #warning NEED TO SET AS_UTG_ERROR_RATE AS_BOG_UnitigGraph.cc:2029:2: warning: #warning THIS IS VALGRIND UNCLEAN fixUnitigs.C: In function ‘int updateFragmentWithParent(IntUnitigMesg*, int, OverlapStore*)’: fixUnitigs.C:138:21: warning: format ‘%d’ expects type ‘int’, but argument 8 has type ‘long long int’ fixUnitigs.C:138:21: warning: format ‘%d’ expects type ‘int’, but argument 9 has type ‘long long int’ fixUnitigs.C:153:21: warning: format ‘%d’ expects type ‘int’, but argument 8 has type ‘long long int’ fixUnitigs.C:153:21: warning: format ‘%d’ expects type ‘int’, but argument 9 has type ‘long long int’ fixUnitigs.C:176:25: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘long long unsigned int’ fixUnitigs.C:176:25: warning: format ‘%d’ expects type ‘int’, but argument 7 has type ‘long long int’ fixUnitigs.C:176:25: warning: format ‘%d’ expects type ‘int’, but argument 8 has type ‘long long int’ fixUnitigs.C:245:25: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘long long unsigned int’ fixUnitigs.C:245:25: warning: format ‘%d’ expects type ‘int’, but argument 7 has type ‘long long int’ fixUnitigs.C:245:25: warning: format ‘%d’ expects type ‘int’, but argument 8 has type ‘long long int’ AS_BOG_Unitig.cc: In member function ‘bool Unitig::placeFrag(DoveTailNode&, int32&, BestEdgeOverlap*, DoveTailNode&, int32&, BestEdgeOverlap*)’: AS_BOG_Unitig.cc:156:3: warning: comparison between signed and unsigned integer expressions AS_BOG_Unitig.cc:157:3: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/scoreOverlaps.o scoreOverlaps.C AS_BOG_Unitig.cc: In member function ‘bool Unitig::addAndPlaceFrag(int32, BestEdgeOverlap*, BestEdgeOverlap*, bool)’: AS_BOG_Unitig.cc:604:47: warning: comparison between signed and unsigned integer expressions AS_BOG_Unitig.cc: In member function ‘void Unitig::reverseComplement(bool)’: AS_BOG_Unitig.cc:746:47: warning: comparison between signed and unsigned integer expressions AS_BOG_Unitig.cc: In member function ‘void Unitig::sort()’: AS_BOG_Unitig.cc:816:45: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::checkUnitigMembership()’: AS_BOG_UnitigGraph.cc:65:43: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::reportOverlapsUsed(const char*)’: AS_BOG_UnitigGraph.cc:148:41: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:149:41: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:150:41: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::setParentAndHang(ChunkGraph*)’: AS_BOG_UnitigGraph.cc:262:36: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:273:52: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:283:52: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::breakUnitigs(ContainerMap&, char*)’: AS_BOG_UnitigGraph.cc:629:58: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:642:58: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::joinUnitigs()’: AS_BOG_UnitigGraph.cc:860:41: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1015:73: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1018:73: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1042:54: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1070:50: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1074:50: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::placeContains()’: AS_BOG_UnitigGraph.cc:1205:35: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::placeZombies()’: AS_BOG_UnitigGraph.cc:1240:36: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::popBubbles(OverlapStore*, OverlapStore*)’: AS_BOG_UnitigGraph.cc:1312:36: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1338:57: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1365:33: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1370:27: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1382:33: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1387:27: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1538:57: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1697:59: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘float UnitigGraph::getGlobalArrivalRate(long int, long int)’: AS_BOG_UnitigGraph.cc:1819:13: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:1846:34: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc: In member function ‘UnitigVector* UnitigGraph::breakUnitigAt(ContainerMap&, Unitig*, UnitigBreakPoints&)’: AS_BOG_UnitigGraph.cc:2104:46: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:2112:65: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_UnitigGraph.cc:2118:66: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_UnitigGraph.cc:2183:44: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:2235:63: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_UnitigGraph.cc:2254:64: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_UnitigGraph.cc: In member function ‘void UnitigGraph::writeIUMtoFile(char*, char*, int)’: AS_BOG_UnitigGraph.cc:2354:28: warning: comparison between signed and unsigned integer expressions AS_BOG_UnitigGraph.cc:2367:51: warning: format ‘%lld’ expects type ‘long long int’, but argument 6 has type ‘uint32’ AS_BOG_UnitigGraph.cc:2369:35: warning: comparison between signed and unsigned integer expressions In file included from scoreOverlaps.C:24:0: AS_BOG_Datatypes.hh:44:2: warning: #warning there is a comparison assuming fragment_end_type FIVE_PRIME < THREE_PRIME In file included from scoreOverlaps.C:28:0: AS_BOG_MateChecker.hh: In function ‘bool operator==(SeqInterval, SeqInterval)’: AS_BOG_MateChecker.hh:110:45: warning: suggest parentheses around ‘&&’ within ‘||’ AS_BOG_MateChecker.hh: In member function ‘void MateLocation::incrRange(int32*, int32, int32, int32)’: AS_BOG_MateChecker.hh:234:23: warning: comparison between signed and unsigned integer expressions scoreOverlaps.C: In function ‘int main(int, char**)’: scoreOverlaps.C:190:47: warning: format ‘%5d’ expects type ‘int’, but argument 10 has type ‘long long int’ scoreOverlaps.C:190:47: warning: format ‘%5d’ expects type ‘int’, but argument 11 has type ‘long long int’ scoreOverlaps.C:190:47: warning: too many arguments for format ############################## AS_REZ ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ConsistencyChecksREZ.o ConsistencyChecksREZ.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapFillREZ.o GapFillREZ.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapWalkerREZ.o GapWalkerREZ.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/StatisticsREZ.o StatisticsREZ.C GapFillREZ.C: In function ‘int Place_Closure_Chunk(Scaffold_Fill_t*, ContigT*, int, int, char, int)’: GapFillREZ.C:777:20: warning: comparison between signed and unsigned integer expressions GapFillREZ.C:802:131: warning: format ‘%f’ expects type ‘double’, but argument 4 has type ‘int’ GapFillREZ.C: In function ‘void Choose_Stones(Scaffold_Fill_t*, int, int, int)’: GapFillREZ.C:3785:63: warning: comparison between signed and unsigned integer expressions GapFillREZ.C:3796:61: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UpdateREZ.o UpdateREZ.C GapFillREZ.C: In function ‘void Print_Frag_Info(FILE*, int)’: GapFillREZ.C:8825:64: warning: format ‘%5.0f’ expects type ‘double’, but argument 4 has type ‘CDS_CID_t’ GapFillREZ.C:8825:64: warning: too many arguments for format GapFillREZ.C: In function ‘void Print_Potential_Fill_Chunks(FILE*, int (*)(ContigT*), int)’: GapFillREZ.C:8957:63: warning: comparison between signed and unsigned integer expressions GapFillREZ.C: In function ‘void Reverse_Positions(Gap_Fill_t*)’: GapFillREZ.C:9595:72: warning: operation on ‘this_gap->Gap_Fill_t::adjustment.LengthT::mean’ may be undefined StatisticsREZ.C: In function ‘void compute_scaffold_statistics(ScaffoldWalkStatisticsT*)’: StatisticsREZ.C:142:49: warning: comparison between signed and unsigned integer expressions StatisticsREZ.C: In function ‘void print_scaffold_walk_stat_struct(ScaffoldWalkStatisticsT*, FILE*, int)’: StatisticsREZ.C:243:53: warning: comparison between signed and unsigned integer expressions StatisticsREZ.C: In function ‘void compute_combined_walk_statistics(WalkStatisticsT*)’: StatisticsREZ.C:461:62: warning: comparison between signed and unsigned integer expressions StatisticsREZ.C: In function ‘void output_combined_celagram_files(WalkStatisticsT*)’: StatisticsREZ.C:565:63: warning: comparison between signed and unsigned integer expressions StatisticsREZ.C:572:56: warning: comparison between signed and unsigned integer expressions StatisticsREZ.C: In function ‘void free_walk_statistics(WalkStatisticsT*)’: StatisticsREZ.C:633:63: warning: comparison between signed and unsigned integer expressions StatisticsREZ.C: In function ‘void print_all_scaffold_walk_stat_struct(char*, WalkStatisticsT*, FILE*, int)’: StatisticsREZ.C:645:62: warning: comparison between signed and unsigned integer expressions StatisticsREZ.C:648:24: warning: format not a string literal and no format arguments StatisticsREZ.C: In function ‘int read_scaffold_walk_statistics(ScaffoldWalkStatisticsT*)’: StatisticsREZ.C:434:62: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UtilsREZ.o UtilsREZ.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MicroHetREZ.o MicroHetREZ.C GapFillREZ.C: In function ‘int _ZL19Place_Closure_ChunkP15Scaffold_Fill_tP9NodeCGW_Tiici.clone.31(Scaffold_Fill_t*, double*, double*, int, int, char, int)’: GapFillREZ.C:764:11: warning: ‘bestScfID’ may be used uninitialized in this function GapFillREZ.C:764:22: warning: ‘bestGap’ may be used uninitialized in this function ############################## AS_CNS ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Array_CNS.o Array_CNS.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlign.o MultiAlign.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignPrint.o MultiAlignPrint.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignStore.o MultiAlignStore.C MultiAlign.C: In function ‘size_t saveVARData(MultiAlignT*, char*&)’: MultiAlign.C:352:50: warning: comparison between signed and unsigned integer expressions MultiAlign.C: In function ‘void restoreVARData(char*&, MultiAlignT*)’: MultiAlign.C:381:50: warning: comparison between signed and unsigned integer expressions MultiAlign.C:396:50: warning: comparison between signed and unsigned integer expressions MultiAlign.C: In function ‘void DumpMultiAlignForHuman(FILE*, MultiAlignT*, bool)’: MultiAlign.C:653:50: warning: comparison between signed and unsigned integer expressions MultiAlign.C:665:51: warning: comparison between signed and unsigned integer expressions MultiAlign.C: In function ‘bool LoadMultiAlignFromHuman(MultiAlignT*, bool&, FILE*)’: MultiAlign.C:810:112: warning: format ‘%s’ expects type ‘char*’, but argument 4 has type ‘int32’ MultiAlign.C:810:112: warning: too many arguments for format MultiAlign.C:815:109: warning: too few arguments for format MultiAlign.C:829:121: warning: format ‘%s’ expects type ‘char*’, but argument 4 has type ‘int32’ MultiAlign.C:829:121: warning: too many arguments for format MultiAlign.C:855:75: warning: format ‘%s’ expects type ‘char*’, but argument 3 has type ‘int32’ MultiAlign.C:855:75: warning: too many arguments for format MultiAlign.C:860:100: warning: too few arguments for format MultiAlign.C:865:108: warning: format ‘%s’ expects type ‘char*’, but argument 4 has type ‘int32’ MultiAlign.C:865:108: warning: too many arguments for format MultiAlign.C:870:102: warning: too few arguments for format MultiAlign.C:875:110: warning: format ‘%s’ expects type ‘char*’, but argument 4 has type ‘int32’ MultiAlign.C:875:110: warning: too many arguments for format MultiAlign.C:886:30: warning: comparison between signed and unsigned integer expressions MultiAlign.C:915:130: warning: format ‘%s’ expects type ‘char*’, but argument 6 has type ‘int32’ MultiAlign.C:915:130: warning: too many arguments for format MultiAlign.C:931:30: warning: comparison between signed and unsigned integer expressions MultiAlign.C:949:91: warning: format ‘%s’ expects type ‘char*’, but argument 3 has type ‘int32’ MultiAlign.C:949:91: warning: too many arguments for format MultiAlign.C:973:130: warning: format ‘%s’ expects type ‘char*’, but argument 6 has type ‘int32’ MultiAlign.C:973:130: warning: too many arguments for format MultiAlignStore.C: In member function ‘void MultiAlignStore::insertMultiAlign(MultiAlignT*, bool, bool)’: MultiAlignStore.C:323:7: warning: comparison between signed and unsigned integer expressions MultiAlignStore.C:345:7: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignment_CNS.o MultiAlignment_CNS.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/RefreshMANode.o RefreshMANode.C MultiAlignment_CNS.C: In function ‘int GetMANodePositions(int32, MultiAlignT*)’: MultiAlignment_CNS.C:470:50: warning: comparison between signed and unsigned integer expressions MultiAlignment_CNS.C:531:50: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AbacusRefine.o AbacusRefine.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ApplyAlignment.o ApplyAlignment.C ApplyAlignment.C:521:2: warning: #warning assert skipped until contig consensus gets fixed AbacusRefine.C: In function ‘int32 RefineOrigAbacus(Abacus*, VarRegion)’: AbacusRefine.C:642:1: warning: no return statement in function returning non-void ApplyAlignment.C: In function ‘void CheckColumns()’: ApplyAlignment.C:104:44: warning: comparison between signed and unsigned integer expressions ApplyAlignment.C: In function ‘void ApplyAlignment(int32, int32, int32*, int32, int32, int32*)’: ApplyAlignment.C:362:21: warning: converting to non-pointer type ‘int’ from NULL g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BaseCall.o BaseCall.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GetAlignmentTrace.o GetAlignmentTrace.C GetAlignmentTrace.C:400:2: warning: #warning CNS_TIGHTSEMIBANDWIDTH relaxed to get around BOG placement problems BaseCall.C: In function ‘int BaseCall(int32, int, double*, VarRegion*, int, char*, int, int, CNS_Options*)’: BaseCall.C:58:11: warning: ‘bi_cons’ may be used uninitialized in this function g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeMultiAligns.o MergeMultiAligns.C AbacusRefine.C: In function ‘int _ZL12RefineWindowP6MANodeP6ColumniP11CNS_Options.clone.10(int32, int32, int, CNS_Options*)’: AbacusRefine.C:1972:63: warning: ‘score_reduction’ may be used uninitialized in this function g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeRefine.o MergeRefine.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignContig.o MultiAlignContig.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignUnitig.o MultiAlignUnitig.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/PrintAlignment.o PrintAlignment.C MultiAlignContig.C: In function ‘int MultiAlignContig(MultiAlignT*, gkStore*, CNS_PrintKey, CNS_Options*)’: MultiAlignContig.C:189:44: warning: comparison between signed and unsigned integer expressions MultiAlignContig.C:190:44: warning: comparison between signed and unsigned integer expressions MultiAlignContig.C:341:58: warning: comparison between signed and unsigned integer expressions MultiAlignUnitig.C: In member function ‘int unitigConsensus::computePositionFromLayout()’: MultiAlignUnitig.C:514:18: warning: comparison between signed and unsigned integer expressions MultiAlignUnitig.C: In member function ‘void unitigConsensus::rebuildFrankensteinFromConsensus()’: MultiAlignUnitig.C:693:21: warning: comparison between signed and unsigned integer expressions MultiAlignUnitig.C: In member function ‘int unitigConsensus::alignFragmentToFragments()’: MultiAlignUnitig.C:872:30: warning: comparison between signed and unsigned integer expressions MultiAlignUnitig.C:954:49: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ReplaceEndUnitigInContig.o ReplaceEndUnitigInContig.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/utgcns.o utgcns.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ctgcns.o ctgcns.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/tigStore.o tigStore.C tigStore.C: In function ‘void dumpConsensus(MultiAlignStore*, int32, int32, MultiAlignT*, bool)’: tigStore.C:216:113: warning: format ‘%llu’ expects type ‘long long unsigned int’, but argument 5 has type ‘size_t’ tigStore.C: In function ‘void changeProperties(MultiAlignStore*, char*)’: tigStore.C:55:34: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result tigStore.C:133:36: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result ############################## AS_LIN ############################## gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrf.o dpbtrf.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrs.o dpbtrs.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/daxpy.o daxpy.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemm.o dgemm.c dgemm.c: In function ‘dgemm_’: dgemm.c:239:5: warning: suggest parentheses around ‘&&’ within ‘||’ gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemv.o dgemv.c dgemv.c: In function ‘dgemv_’: dgemv.c:154:5: warning: suggest parentheses around ‘&&’ within ‘||’ gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dlamch.o dlamch.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtf2.o dpbtf2.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpotf2.o dpotf2.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dptrfs.o dptrfs.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpttrs.o dpttrs.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyr.o dsyr.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyrk.o dsyrk.c dsyrk.c: In function ‘dsyrk_’: dsyrk.c:205:5: warning: suggest parentheses around ‘&&’ within ‘||’ gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtbsv.o dtbsv.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtrsm.o dtrsm.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/idamax.o idamax.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ilaenv.o ilaenv.c ilaenv.c: In function ‘ilaenv_’: ilaenv.c:171:2: warning: suggest parentheses around ‘&&’ within ‘||’ ilaenv.c:172:3: warning: suggest parentheses around ‘&&’ within ‘||’ ilaenv.c:176:3: warning: suggest parentheses around ‘&&’ within ‘||’ ilaenv.c:177:4: warning: suggest parentheses around ‘&&’ within ‘||’ gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/lsame.o lsame.c lsame.c: In function ‘lsame_’: lsame.c:71:2: warning: suggest parentheses around ‘&&’ within ‘||’ lsame.c:72:3: warning: suggest parentheses around ‘&&’ within ‘||’ lsame.c:75:2: warning: suggest parentheses around ‘&&’ within ‘||’ lsame.c:76:3: warning: suggest parentheses around ‘&&’ within ‘||’ gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/xerbla.o xerbla.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_copy.o s_copy.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_cmp.o s_cmp.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ddot.o ddot.c gcc -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dscal.o dscal.c ############################## AS_CGW ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGW_main.o AS_CGW_main.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/eCR.o eCR.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/eCR-examineGap.o eCR-examineGap.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/eCR-diagnostic.o eCR-diagnostic.C eCR.C: In function ‘int findLastUnitig(ContigT*, int*)’: eCR.C:1389:45: warning: comparison between signed and unsigned integer expressions eCR.C: In function ‘fragPositions* getAlteredFragPositions(NodeCGW_T*, int, int)’: eCR.C:1499:45: warning: comparison between signed and unsigned integer expressions eCR.C:1505:23: warning: comparison between signed and unsigned integer expressions eCR.C:1539:51: warning: comparison between signed and unsigned integer expressions eCR.C: In function ‘int GetNewUnitigMultiAlign(NodeCGW_T*, fragPositions*, int, int)’: eCR.C:1654:26: warning: comparison between signed and unsigned integer expressions eCR.C:1665:26: warning: comparison between signed and unsigned integer expressions eCR.C:1705:27: warning: comparison between signed and unsigned integer expressions eCR-examineGap.C: In function ‘int examineGap(ContigT*, int, ContigT*, int, int, int*, int*, int*, int*, int*, int*, int*, int, int, int*, int*)’: eCR-examineGap.C:273:49: warning: comparison between signed and unsigned integer expressions eCR-examineGap.C:311:21: warning: comparison between signed and unsigned integer expressions eCR-diagnostic.C: In function ‘void DumpContigMultiAlignInfo(char*, MultiAlignT*, int)’: eCR-diagnostic.C:42:55: warning: format ‘%9ld’ expects type ‘long int’, but argument 4 has type ‘size_t’ eCR-diagnostic.C:44:49: warning: comparison between signed and unsigned integer expressions eCR-diagnostic.C:50:50: warning: comparison between signed and unsigned integer expressions eCR-diagnostic.C:61:51: warning: comparison between signed and unsigned integer expressions eCR-diagnostic.C: In function ‘void DumpUnitigInfo(char*, NodeCGW_T*)’: eCR-diagnostic.C:91:49: warning: comparison between signed and unsigned integer expressions eCR-diagnostic.C: In function ‘void DumpContigUngappedOffsets(char*, int)’: eCR-diagnostic.C:146:48: warning: comparison between signed and unsigned integer expressions eCR-diagnostic.C: In function ‘void DumpUnitigInfo(char*, NodeCGW_T*)’: eCR-diagnostic.C:84:39: warning: ‘i’ is used uninitialized in this function g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/eCR-partition.o eCR-partition.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/resolveSurrogates.o resolveSurrogates.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dumpCloneMiddles.o dumpCloneMiddles.C eCR-partition.C: In function ‘int main(int, char**)’: eCR-partition.C:110:55: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/exploreGapStructure.o exploreGapStructure.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/frgs2clones.o frgs2clones.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dumpSingletons.o dumpSingletons.C exploreGapStructure.C: In function ‘int main(int, char**)’: exploreGapStructure.C:82:11: warning: ‘varPrev’ may be used uninitialized in this function g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Globals_CGW.o Globals_CGW.C dumpSingletons.C: In function ‘int main(int, char**)’: dumpSingletons.C:122:64: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGW_EdgeDiagnostics.o AS_CGW_EdgeDiagnostics.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIEdgeT_CGW.o CIEdgeT_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Biconnected_CGW.o CIScaffoldT_Biconnected_CGW.C AS_CGW_EdgeDiagnostics.C: In function ‘int PopulateOrientHTFromArray(HashTable_AS*, VarArrayOrientHolder*)’: AS_CGW_EdgeDiagnostics.C:510:45: warning: comparison between signed and unsigned integer expressions AS_CGW_EdgeDiagnostics.C: In function ‘void ValidateAllContigEdges(ScaffoldGraphT*, int)’: AS_CGW_EdgeDiagnostics.C:850:59: warning: comparison between signed and unsigned integer expressions AS_CGW_EdgeDiagnostics.C: In function ‘int CountUniqueIDs(VarArrayCDS_CID_t*)’: AS_CGW_EdgeDiagnostics.C:1091:51: warning: comparison between signed and unsigned integer expressions CIEdgeT_CGW.C: In function ‘int CheckImplicitOverlaps_(GraphCGW_T*, CDS_CID_t, int)’: CIEdgeT_CGW.C:278:39: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_CGW.o CIScaffoldT_CGW.C CIScaffoldT_CGW.C: In function ‘int IsScaffoldInternallyConnected(ScaffoldGraphT*, CIScaffoldT*, int32)’: CIScaffoldT_CGW.C:737:52: warning: comparison between signed and unsigned integer expressions CIScaffoldT_CGW.C: In function ‘void killScaffoldIfOnlySurrogate(CDS_CID_t)’: CIScaffoldT_CGW.C:857:9: warning: comparison between signed and unsigned integer expressions CIScaffoldT_CGW.C:872:9: warning: comparison between signed and unsigned integer expressions CIScaffoldT_CGW.C:883:9: warning: comparison between signed and unsigned integer expressions CIScaffoldT_CGW.C: In function ‘void CheckCIScaffoldT(ScaffoldGraphT*, CIScaffoldT*)’: CIScaffoldT_CGW.C:1433:51: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Cleanup_CGW.o CIScaffoldT_Cleanup_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Merge_CGW.o CIScaffoldT_Merge_CGW.C CIScaffoldT_Cleanup_CGW.C: In function ‘void PropagateContainmentOverlapsToNewContig(ContigT*, VarArrayIntElementPos*, int32, int32)’: CIScaffoldT_Cleanup_CGW.C:80:54: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:240:39: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ CIScaffoldT_Cleanup_CGW.C: In function ‘void PropagateInternalOverlapsToNewContig(ContigT*, VarArrayIntElementPos*, CDS_CID_t, int32, int32)’: CIScaffoldT_Cleanup_CGW.C:375:54: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:534:30: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ CIScaffoldT_Cleanup_CGW.C:603:51: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:692:66: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:720:53: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:745:50: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:749:30: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ CIScaffoldT_Cleanup_CGW.C:771:32: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ CIScaffoldT_Cleanup_CGW.C: In function ‘void PropagateExtremalOverlapsToNewContig(CDS_CID_t, int, ContigT*, int, int32, int32)’: CIScaffoldT_Cleanup_CGW.C:975:37: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ CIScaffoldT_Cleanup_CGW.C: In function ‘void PropagateOverlapsToNewContig(ContigT*, VarArrayIntElementPos*, CDS_CID_t, int, CDS_CID_t, int, CDS_CID_t, int32)’: CIScaffoldT_Cleanup_CGW.C:1059:54: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C: In function ‘int DeleteAllSurrogateContigsFromFailedMerges(CIScaffoldT*, NodeCGW_T*)’: CIScaffoldT_Cleanup_CGW.C:1370:48: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:1397:50: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C: In function ‘int CleanupAScaffold(ScaffoldGraphT*, CIScaffoldT*, int, int, int)’: CIScaffoldT_Cleanup_CGW.C:1511:80: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:1512:80: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:1547:125: warning: too many arguments for format CIScaffoldT_Cleanup_CGW.C:1665:60: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C: In function ‘int CreateAContigInScaffold(CIScaffoldT*, VarArrayIntElementPos*, LengthT, LengthT)’: CIScaffoldT_Cleanup_CGW.C:1893:60: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:1955:62: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:1995:60: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:2030:60: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C: In function ‘void RepairContigNeighbors(ChunkInstanceT*)’: CIScaffoldT_Cleanup_CGW.C:2445:52: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:2448:25: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C: In function ‘void RemoveSurrogateDuplicates()’: CIScaffoldT_Cleanup_CGW.C:2550:92: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:2554:7: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Cleanup_CGW.C:2615:9: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Celamy_CGW.o Celamy_CGW.C CIScaffoldT_Merge_CGW.C: In function ‘int isLargeOverlapSize(LengthT*, int32)’: CIScaffoldT_Merge_CGW.C:614:40: warning: format ‘%f’ expects type ‘double’, but argument 9 has type ‘int’ CIScaffoldT_Merge_CGW.C: In function ‘int DoesScaffoldCFit(CIScaffoldT*, CIScaffoldT*, CIScaffoldT*, SEdgeT*, SEdgeT*, VarArrayPtrT*, VarArrayPtrT*, int32*, int, int32)’: CIScaffoldT_Merge_CGW.C:1292:45: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘void ZeroEdgeWeights(VarArrayPtrT*)’: CIScaffoldT_Merge_CGW.C:1466:35: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘int AssignEdgeWeights(VarArrayPtrT*, SEdgeT*, CIScaffoldT*, VarArrayPtrT*, CIScaffoldT*, VarArrayPtrT*, int, int)’: CIScaffoldT_Merge_CGW.C:1496:40: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C:1520:42: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C:1643:40: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘SEdgeT* FindMoreAttractiveMergeEdge(SEdgeT*, CIScaffoldT*, CIScaffoldT*, int32, int, int, int32)’: CIScaffoldT_Merge_CGW.C:1795:43: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘int isQualityScaffoldMergingEdge(SEdgeT*, CIScaffoldT*, CIScaffoldT*, ScaffoldInstrumenter*, VarArrayMateInstrumenterP*, float, float)’: CIScaffoldT_Merge_CGW.C:1926:78: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C:1927:78: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘void SaveBadScaffoldMergeEdge(SEdgeT*, ChunkOverlapperT*)’: CIScaffoldT_Merge_CGW.C:2035:33: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ CIScaffoldT_Merge_CGW.C: In function ‘void ExamineUsableSEdgeSet(VarArrayPtrT*, int, InterleavingSpec*, int)’: CIScaffoldT_Merge_CGW.C:2721:37: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘void ExamineUsableSEdges(VarArrayPtrT*, int, InterleavingSpec*, int)’: CIScaffoldT_Merge_CGW.C:2746:43: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C:2756:43: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘int BuildSEdgesForMerging(ScaffoldGraphT*, VarArrayPtrT**, VarArrayPtrT**, float*, int, InterleavingSpec*, int32)’: CIScaffoldT_Merge_CGW.C:2811:45: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘void MergeScaffoldsAggressive(ScaffoldGraphT*, char*, int)’: CIScaffoldT_Merge_CGW.C:3301:42: warning: comparison between signed and unsigned integer expressions CIScaffoldT_Merge_CGW.C: In function ‘int TouchesMarkedScaffolds(SEdgeT*)’: CIScaffoldT_Merge_CGW.C:598:1: warning: control reaches end of non-void function Celamy_CGW.C: In function ‘void drawSurrogateFrags(FILE*, ContigT*, int, int)’: Celamy_CGW.C:197:53: warning: comparison between signed and unsigned integer expressions Celamy_CGW.C:208:56: warning: comparison between signed and unsigned integer expressions Celamy_CGW.C:251:31: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long int’ Celamy_CGW.C:263:34: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long int’ Celamy_CGW.C: In function ‘void drawFrags(FILE*, ContigT*, int, int)’: Celamy_CGW.C:277:52: warning: comparison between signed and unsigned integer expressions Celamy_CGW.C: In function ‘void CelamyScaffold(FILE*, CIScaffoldT*, int64, int64)’: Celamy_CGW.C:450:25: warning: too few arguments for format g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ChunkOverlap_CGW.o ChunkOverlap_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ContigT_CGW.o ContigT_CGW.C ChunkOverlap_CGW.C: In function ‘void printChunkOverlapCheckT(char*, ChunkOverlapCheckT*)’: ChunkOverlap_CGW.C:190:97: warning: format ‘%d’ expects type ‘int’, but argument 20 has type ‘double’ ChunkOverlap_CGW.C: In function ‘void CreateChunkOverlapFromEdge(GraphCGW_T*, EdgeCGW_T*)’: ChunkOverlap_CGW.C:382:32: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ ChunkOverlap_CGW.C: In function ‘void FillChunkOverlapWithOVL(GraphCGW_T*, OverlapMesg*)’: ChunkOverlap_CGW.C:455:32: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ ChunkOverlap_CGW.C: In function ‘void CollectChunkOverlap(GraphCGW_T*, CDS_CID_t, CDS_CID_t, PairOrient, float, float, float, int, int, int)’: ChunkOverlap_CGW.C:712:32: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ ChunkOverlap_CGW.C: In function ‘ChunkOverlapCheckT OverlapChunks(GraphCGW_T*, CDS_CID_t, CDS_CID_t, PairOrient, int32, int32, float, int)’: ChunkOverlap_CGW.C:1076:31: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ ContigT_CGW.C: In function ‘void dumpContigInfo(ChunkInstanceT*)’: ContigT_CGW.C:138:89: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘size_t’ ContigT_CGW.C:151:65: warning: comparison between signed and unsigned integer expressions ContigT_CGW.C: In function ‘int BuildContigEdges(ScaffoldGraphT*)’: ContigT_CGW.C:527:59: warning: comparison between signed and unsigned integer expressions ContigT_CGW.C: In function ‘void CheckAllContigFragments()’: ContigT_CGW.C:987:49: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/DemoteUnitigsWithRBP_CGW.o DemoteUnitigsWithRBP_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragmentPlacement.o fragmentPlacement.C fragmentPlacement.C:197:2: warning: #warning INNIE mate pairs assumed g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GraphCGW_T.o GraphCGW_T.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Input_CGW.o Input_CGW.C fragmentPlacement.C: In function ‘int NextCIFragTInChunkIterator(CGWFragIterator*, CIFragT**)’: fragmentPlacement.C:277:69: warning: comparison between signed and unsigned integer expressions fragmentPlacement.C: In function ‘void ReallyAssignFragsToResolvedCI(CDS_CID_t, CDS_CID_t, VarArrayCDS_CID_t*)’: fragmentPlacement.C:528:47: warning: comparison between signed and unsigned integer expressions fragmentPlacement.C:560:75: warning: comparison between signed and unsigned integer expressions fragmentPlacement.C:561:29: warning: comparison between signed and unsigned integer expressions fragmentPlacement.C: In function ‘int getChunkInstanceID(ChunkInstanceT*, int)’: fragmentPlacement.C:667:3: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void SaveGraphCGWToStream(GraphCGW_T*, FILE*)’: GraphCGW_T.C:100:7: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘GraphCGW_T* LoadGraphCGWFromStream(FILE*)’: GraphCGW_T.C:136:5: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void DeleteGraphNode(GraphCGW_T*, NodeCGW_T*)’: GraphCGW_T.C:712:38: warning: comparison between signed and unsigned integer expressions Input_CGW.C: In function ‘int ProcessInput(int, int, char**)’: Input_CGW.C:111:57: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void MergeNodeGraphEdges(GraphCGW_T*, NodeCGW_T*, int, int, int)’: GraphCGW_T.C:1400:52: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:1438:44: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void CheckEdgesAgainstOverlapper(GraphCGW_T*)’: GraphCGW_T.C:1474:31: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ Input_CGW.C: In function ‘void ProcessInputUnitig(MultiAlignT*)’: Input_CGW.C:234:52: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void UpdateNodeFragments(GraphCGW_T*, CDS_CID_t, int, int)’: GraphCGW_T.C:1601:47: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:1617:47: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:1635:30: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:1640:30: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘CDS_CID_t SplitUnresolvedCI(GraphCGW_T*, CDS_CID_t, VarArrayCDS_CID_t*)’: GraphCGW_T.C:2356:5: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:2381:5: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void ComputeMatePairDetailedStatus()’: GraphCGW_T.C:2756:7: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:2768:7: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void ComputeMatePairStatisticsRestricted(int, int32, char*)’: GraphCGW_T.C:3074:51: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:3141:7: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:3166:33: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:3401:52: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:3554:48: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:3670:50: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void CheckUnitigs(CDS_CID_t)’: GraphCGW_T.C:3847:49: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C: In function ‘void CheckSurrogateUnitigs()’: GraphCGW_T.C:3874:90: warning: comparison between signed and unsigned integer expressions GraphCGW_T.C:3878:5: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Instrument_CGW.o Instrument_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/InterleavedMerging.o InterleavedMerging.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/LeastSquaresGaps_CGW.o LeastSquaresGaps_CGW.C Instrument_CGW.C: In function ‘int DetectBreakpointType(ScaffoldGraphT*, VarArrayInstrumenterBreakpoint*, int32, int32, VarArrayMateDetail*, InstBreakpointType)’: Instrument_CGW.C:1555:60: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void InstrumentFloatStatistics(VarArrayfloat*, InstrumenterStatistics*, int)’: Instrument_CGW.C:1736:35: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void InstrumentCoordStatistics(VarArrayint32*, InstrumenterStatistics*, int)’: Instrument_CGW.C:1785:35: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void AddFragDetailsToMateStats(MateStats*, VarArrayFragDetail*)’: Instrument_CGW.C:1827:41: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void AddMateDetailsToMateStatsSet(MateStats*, VarArrayMateDetail*)’: Instrument_CGW.C:1850:41: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintExternalMateDetailAndDist(MateDetail*, DistT*, char*, FILE*, int)’: Instrument_CGW.C:2188:4: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintMateDetailsAndDists(ScaffoldGraphT*, VarArrayMateDetail*, char*, FILE*)’: Instrument_CGW.C:2229:41: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintExternalMateDetailsAndDists(ScaffoldGraphT*, VarArrayMateDetail*, char*, FILE*, int)’: Instrument_CGW.C:2250:41: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintMateComparison(int32, int32, int32, int32, char*, int, int, FILE*)’: Instrument_CGW.C:2274:26: warning: format not a string literal and no format arguments Instrument_CGW.C: In function ‘void PrintBreakpoints(VarArrayInstrumenterBreakpoint*, char*, FILE*)’: Instrument_CGW.C:2482:57: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintUnitigInstrumenter(ScaffoldGraphT*, UnitigInstrumenter*, InstrumenterVerbosity, char*, FILE*)’: Instrument_CGW.C:2551:66: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintContigInstrumenter(ScaffoldGraphT*, ContigInstrumenter*, InstrumenterVerbosity, char*, FILE*)’: Instrument_CGW.C:2628:66: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintInferredStddevs(VarArrayfloat*, char*, FILE*)’: Instrument_CGW.C:2658:45: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintUnanchoredContigIDs(ScaffoldInstrumenter*, char*, FILE*)’: Instrument_CGW.C:2720:54: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void AddInstrumenterBreakpoints(VarArrayInstrumenterBreakpoint*, VarArrayInstrumenterBreakpoint*)’: Instrument_CGW.C:2889:53: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void AddFragDetails(VarArrayFragDetail*, VarArrayFragDetail*)’: Instrument_CGW.C:2900:41: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void AddMateDetails(VarArrayMateDetail*, VarArrayMateDetail*)’: Instrument_CGW.C:2910:41: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘int AddMateInstrumenters(MateInstrumenter*, MateInstrumenter*)’: Instrument_CGW.C:2962:49: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘int AddInstrumenterBookkeeping(ScaffoldGraphT*, InstrumenterBookkeeping*, InstrumenterBookkeeping*, int)’: Instrument_CGW.C:2988:55: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C:2999:56: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C:3009:56: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘int AddContigInstrumenters(ScaffoldGraphT*, ContigInstrumenter*, ContigInstrumenter*)’: Instrument_CGW.C:3097:49: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C:3102:52: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘int AddScaffoldInstrumenters(ScaffoldGraphT*, ScaffoldInstrumenter*, ScaffoldInstrumenter*)’: Instrument_CGW.C:3485:54: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C:3491:49: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘int AppendContigPairSets(ScaffoldGraphT*, VarArrayCP_Index*, VarArrayInstrumenterContigPair*, MateStatusPositions*)’: Instrument_CGW.C:3625:39: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintScaffoldMateDetailArray(HashTable_AS*, VarArrayMateDetail*, PairOrient, PairOrient, char*, CDS_CID_t, FILE*, int)’: Instrument_CGW.C:4169:41: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintUnmatedDetails(ScaffoldInstrumenter*, FILE*, int)’: Instrument_CGW.C:4269:56: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void CheckFragmentMatePairs(ScaffoldGraphT*, InstrumenterBookkeeping*, SurrogateTracker*, ScaffoldInstrumenter*, MateStatusPositionsSet*, uint32, int32*, int32*, int32*, CDS_CID_t)’: Instrument_CGW.C:4326:62: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C:4338:62: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘int InstrumentUnitig(ScaffoldGraphT*, ScaffoldInstrumenter*, ChunkInstanceT*, float, float, UnitigInstrumenter*)’: Instrument_CGW.C:4743:56: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C:4764:54: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PopulateICP(IntContigPairs*, CDS_CID_t, CIEdgeT*)’: Instrument_CGW.C:4928:67: warning: format ‘%ld’ expects type ‘long int’, but argument 3 has type ‘CDS_CID_t’ Instrument_CGW.C:4928:67: warning: format ‘%ld’ expects type ‘long int’, but argument 4 has type ‘IntContig_ID’ Instrument_CGW.C:4934:6: warning: suggest explicit braces to avoid ambiguous ‘else’ Instrument_CGW.C:4940:6: warning: suggest explicit braces to avoid ambiguous ‘else’ Instrument_CGW.C: In function ‘int AddContigPlacementToScaffoldInstrumenter(ScaffoldInstrumenter*, ContigPlacement*)’: Instrument_CGW.C:5160:62: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘int InstrumentScaffoldGraph(ScaffoldGraphT*, ScaffoldGraphInstrumenter*, int32, int32, InstrumenterVerbosity, FILE*)’: Instrument_CGW.C:5579:44: warning: comparison between signed and unsigned integer expressions InterleavedMerging.C: In function ‘void PrintContigElements(FILE*, VarArrayContigElement*)’: InterleavedMerging.C:207:48: warning: comparison between signed and unsigned integer expressions InterleavedMerging.C: In function ‘void PrintLocal_Overlaps(FILE*, VarArrayLocal_Overlap*)’: InterleavedMerging.C:225:44: warning: comparison between signed and unsigned integer expressions InterleavedMerging.C: In function ‘Overlap* LookForChunkOverlapFromContigElements(ContigElement*, ContigElement*, SEdgeT*)’: InterleavedMerging.C:766:39: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ InterleavedMerging.C: In function ‘int PopulateScaffoldAlignmentInterface(CIScaffoldT*, CIScaffoldT*, SEdgeT*, ScaffoldAlignmentInterface*)’: InterleavedMerging.C:975:68: warning: comparison between signed and unsigned integer expressions InterleavedMerging.C: In function ‘SEdgeT* MakeScaffoldAlignmentAdjustments(CIScaffoldT*, CIScaffoldT*, SEdgeT*, ScaffoldAlignmentInterface*)’: InterleavedMerging.C:2182:44: warning: comparison between signed and unsigned integer expressions LeastSquaresGaps_CGW.C: In function ‘EdgeCGW_T* FindOverlapEdgeChiSquare(ScaffoldGraphT*, NodeCGW_T*, CDS_CID_t, PairOrient, double, double, float*, float, int*, int)’: LeastSquaresGaps_CGW.C:298:23: warning: NULL used in arithmetic InterleavedMerging.C: In function ‘void PopulateScaffoldStuff(ScaffoldStuff*, CIScaffoldT*, SEdgeT*, LengthT)’: InterleavedMerging.C:476:11: warning: ‘lastRight.LengthT::mean’ may be used uninitialized in this function InterleavedMerging.C:476:11: warning: ‘lastRight.LengthT::variance’ may be used uninitialized in this function LeastSquaresGaps_CGW.C: In function ‘void CheckInternalEdgeStatus(ScaffoldGraphT*, CIScaffoldT*, float, float, int, int)’: LeastSquaresGaps_CGW.C:369:15: warning: ‘gapDistance.LengthT::mean’ may be used uninitialized in this function LeastSquaresGaps_CGW.C:369:15: warning: ‘gapDistance.LengthT::variance’ may be used uninitialized in this function LeastSquaresGaps_CGW.C: In function ‘void MarkInternalEdgeStatus(ScaffoldGraphT*, CIScaffoldT*, float, float, int, int, int, int)’: LeastSquaresGaps_CGW.C:1727:15: warning: ‘gapDistance.LengthT::mean’ may be used uninitialized in this function LeastSquaresGaps_CGW.C:1727:15: warning: ‘gapDistance.LengthT::variance’ may be used uninitialized in this function LeastSquaresGaps_CGW.C: In function ‘int IsInternalEdgeStatusVaguelyOK(EdgeCGW_T*, CDS_CID_t)’: LeastSquaresGaps_CGW.C:1970:11: warning: ‘gapDistance.LengthT::variance’ may be used uninitialized in this function LeastSquaresGaps_CGW.C:1970:11: warning: ‘gapDistance.LengthT::mean’ may be used uninitialized in this function g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeEdges_CGW.o MergeEdges_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Output_CGW.o Output_CGW.C Output_CGW.C: In function ‘void OutputContigsFromMultiAligns(int32)’: Output_CGW.C:178:96: warning: too few arguments for format Output_CGW.C:186:96: warning: too few arguments for format g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SEdgeT_CGW.o SEdgeT_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ScaffoldGraph_CGW.o ScaffoldGraph_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitChunks_CGW.o SplitChunks_CGW.C SplitChunks_CGW.C:310:2: warning: #warning not setting the mate pair orientation correctly ScaffoldGraph_CGW.C: In function ‘void LoadScaffoldGraphFromCheckpoint(char*, int32, int)’: ScaffoldGraph_CGW.C:108:54: warning: comparison between signed and unsigned integer expressions ScaffoldGraph_CGW.C: In function ‘void CheckpointScaffoldGraph(const char*, const char*)’: ScaffoldGraph_CGW.C:198:54: warning: comparison between signed and unsigned integer expressions ScaffoldGraph_CGW.C: In function ‘void DestroyScaffoldGraph(ScaffoldGraphT*)’: ScaffoldGraph_CGW.C:331:54: warning: comparison between signed and unsigned integer expressions SplitChunks_CGW.C: In function ‘void IncrementMapInterval(char*, VarArrayuint16*, int32, int32)’: SplitChunks_CGW.C:75:41: warning: comparison between signed and unsigned integer expressions Instrument_CGW.C: In function ‘void PrintScaffoldMateDetail(HashTable_AS*, MateDetail*, PairOrient, PairOrient, char*, CDS_CID_t, FILE*, int)’: Instrument_CGW.C:4109:9: warning: ‘row’ may be used uninitialized in this function g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitScaffolds_CGW.o SplitScaffolds_CGW.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Stats_CGW.o Stats_CGW.C Stats_CGW.C: In function ‘void GenerateLinkStats(GraphCGW_T*, char*, int)’: Stats_CGW.C:597:39: warning: missing braces around initializer for ‘ChunkOverlapSpecT’ Stats_CGW.C: In function ‘int32 ApproximateUnitigCoverage(NodeCGW_T*)’: Stats_CGW.C:631:47: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/TransitiveReduction_CGW.o TransitiveReduction_CGW.C TransitiveReduction_CGW.C: In function ‘int FoundTransitiveEdgePath(ScaffoldGraphT*, CIEdgeT*, CIEdgeT*, ChunkInstanceT*, ChunkInstanceT*, ChunkInstanceT*, uint32, uint64)’: TransitiveReduction_CGW.C:168:22: warning: comparison between signed and unsigned integer expressions TransitiveReduction_CGW.C:171:21: warning: comparison between signed and unsigned integer expressions TransitiveReduction_CGW.C:213:32: warning: comparison between signed and unsigned integer expressions ############################## AS_TER ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/terminator.o terminator.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/asmOutputFasta.o asmOutputFasta.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/asmOutputStatistics.o asmOutputStatistics.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragsInVars.o fragsInVars.C asmOutputFasta.C: In function ‘void processIUM(IntUnitigMesg*)’: asmOutputFasta.C:128:3: warning: comparison between signed and unsigned integer expressions asmOutputFasta.C: In function ‘void processUTG(SnapUnitigMesg*)’: asmOutputFasta.C:162:3: warning: comparison between signed and unsigned integer expressions asmOutputFasta.C: In function ‘void processCCO(SnapConConMesg*)’: asmOutputFasta.C:197:3: warning: comparison between signed and unsigned integer expressions asmOutputFasta.C:225:31: warning: comparison between signed and unsigned integer expressions asmOutputStatistics.C:341:2: warning: #warning should be a library function fragsInVars.C: In function ‘int main(int, char**)’: fragsInVars.C:313:45: warning: comparison between signed and unsigned integer expressions fragsInVars.C:346:75: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘long long unsigned int’ fragsInVars.C:346:75: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘long long unsigned int’ fragsInVars.C:353:75: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘long long unsigned int’ fragsInVars.C:353:75: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘long long unsigned int’ fragsInVars.C:360:75: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘long long unsigned int’ fragsInVars.C:360:75: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘long long unsigned int’ fragsInVars.C:367:75: warning: format ‘%u’ expects type ‘unsigned int’, but argument 5 has type ‘long long unsigned int’ fragsInVars.C:367:75: warning: format ‘%u’ expects type ‘unsigned int’, but argument 6 has type ‘long long unsigned int’ fragsInVars.C: In function ‘void readVars(FILE*, var**, uint32*, uint32*, char**, uint32*, uint32*)’: fragsInVars.C:122:26: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result fragsInVars.C:192:28: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result terminator.C: In member function ‘void IIDtoUIDmap::add(AS_IID, AS_UID)’: terminator.C:63:16: warning: comparison between signed and unsigned integer expressions terminator.C:71:16: warning: comparison between signed and unsigned integer expressions terminator.C: In member function ‘AS_UID IIDtoUIDmap::lookup(AS_IID)’: terminator.C:78:15: warning: comparison between signed and unsigned integer expressions fragsInVars.C: In function ‘void readFrags(FILE*, frag**, uint32*, uint32*)’: fragsInVars.C:85:25: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result fragsInVars.C:104:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result terminator.C: In function ‘void writeMDI(FILE*, bool)’: terminator.C:118:54: warning: comparison between signed and unsigned integer expressions terminator.C: In function ‘void writeAFG(FILE*, bool)’: terminator.C:173:58: warning: comparison between signed and unsigned integer expressions terminator.C:182:5: warning: comparison between signed and unsigned integer expressions terminator.C: In function ‘void writeAMP(FILE*, bool)’: terminator.C:214:58: warning: comparison between signed and unsigned integer expressions terminator.C: In function ‘int main(int, char**)’: terminator.C:976:90: warning: too few arguments for format asmOutputStatistics.C: In function ‘void generateStatisticsFromGKPStore(char*, char*)’: asmOutputStatistics.C:701:55: warning: comparison between signed and unsigned integer expressions g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/buildPosMap.o buildPosMap.C buildPosMap.C:235:2: warning: #warning not remembering surrogate fragments buildPosMap.C:402:2: warning: #warning should be a library function buildPosMap.C:571:2: warning: #warning this function will overflow on large (bogus) var sequences buildPosMap.C: In function ‘void processULK(SnapUnitigLinkMesg*)’: buildPosMap.C:261:83: warning: comparison between signed and unsigned integer expressions buildPosMap.C: In function ‘void processCLK(SnapContigLinkMesg*)’: buildPosMap.C:392:83: warning: comparison between signed and unsigned integer expressions buildPosMap.C: In function ‘void processSLK(SnapScaffoldLinkMesg*)’: buildPosMap.C:505:27: warning: comparison between signed and unsigned integer expressions buildPosMap.C: In function ‘void transferVar(FILE*, FILE*)’: buildPosMap.C:582:28: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result buildPosMap.C:619:30: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result ############################## AS_ENV ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/greedyFragmentTiling.o greedyFragmentTiling.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/chimChe.o chimChe.C g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/metagenomics_ovl_analyses.o metagenomics_ovl_analyses.C In file included from chimChe.C:28:0: kmer_utils.h: In function ‘void spellOutPacked(int, char*, int)’: kmer_utils.h:99:3: warning: comparison between signed and unsigned integer expressions chimChe.C: In function ‘char* get_sequence(FILE*, char**, char**)’: chimChe.C:186:24: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C: In function ‘void print_olap(OVSoverlap)’: greedyFragmentTiling.C:100:61: warning: format ‘%5d’ expects type ‘int’, but argument 5 has type ‘long long int’ greedyFragmentTiling.C:100:61: warning: format ‘%5d’ expects type ‘int’, but argument 6 has type ‘long long int’ greedyFragmentTiling.C: In function ‘int isDeadEnd(int, int, double, int, int, int, int)’: greedyFragmentTiling.C:286:5: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C: In function ‘OVSoverlap better_olap(OVSoverlap, OVSoverlap, int, int, BestMeasure, int, int, int, int, int, double)’: greedyFragmentTiling.C:324:5: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:325:5: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:369:24: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:381:24: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C: In function ‘int setupolaps(int, int, BestMeasure, double, int, int, int, int, int, OVSoverlap**, double, double)’: greedyFragmentTiling.C:481:5: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C: In function ‘int ovlThickness(OVSoverlap, int, int, int)’: greedyFragmentTiling.C:707:17: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C: In function ‘int main(int, char**)’: greedyFragmentTiling.C:916:53: warning: format ‘%s’ expects type ‘char*’, but argument 3 has type ‘char (*)[16777216]’ greedyFragmentTiling.C:944:54: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:1011:38: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:1014:47: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:1023:30: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:1025:16: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:1119:38: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:1122:47: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C:1131:16: warning: comparison between signed and unsigned integer expressions greedyFragmentTiling.C: In function ‘OVSoverlap better_olap(OVSoverlap, OVSoverlap, int, int, BestMeasure, int, int, int, int, int, double)’: greedyFragmentTiling.C:431:1: warning: control reaches end of non-void function metagenomics_ovl_analyses.C: In function ‘int main(int, char**)’: metagenomics_ovl_analyses.C:706:3: warning: comparison between signed and unsigned integer expressions metagenomics_ovl_analyses.C:742:69: warning: format ‘%5d’ expects type ‘int’, but argument 6 has type ‘long long int’ metagenomics_ovl_analyses.C:742:69: warning: format ‘%5d’ expects type ‘int’, but argument 7 has type ‘long long int’ metagenomics_ovl_analyses.C:745:20: warning: comparison between signed and unsigned integer expressions metagenomics_ovl_analyses.C:751:25: warning: comparison between signed and unsigned integer expressions metagenomics_ovl_analyses.C:769:69: warning: format ‘%5d’ expects type ‘int’, but argument 8 has type ‘long long int’ metagenomics_ovl_analyses.C:769:69: warning: format ‘%5d’ expects type ‘int’, but argument 9 has type ‘long long int’ metagenomics_ovl_analyses.C:772:26: warning: comparison between signed and unsigned integer expressions metagenomics_ovl_analyses.C:776:104: warning: comparison between signed and unsigned integer expressions metagenomics_ovl_analyses.C:838:17: warning: comparison between signed and unsigned integer expressions ############################## AS_ARD ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/loadAssembly.o loadAssembly.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/getAssembly.o getAssembly.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Sybase.o Sybase.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ARD_database.o AS_ARD_database.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/DBTextOutput.o DBTextOutput.cc AS_ARD_database.cc:106:2: warning: #warning source is unused in MPS AS_ARD_database.cc:222:2: warning: #warning source is unused in mps In file included from AS_ARD_database.hh:29:0, from loadAssembly.cc:34: IAssemblyDB.hh: In constructor ‘AS_ARD::IAssemblyDB::IAssemblyDB(AS_ARD::IDBOutput*)’: IAssemblyDB.hh:48:22: warning: ‘AS_ARD::IAssemblyDB::db’ will be initialized after IAssemblyDB.hh:39:14: warning: ‘int AS_ARD::IAssemblyDB::numMDI’ IAssemblyDB.hh:51:10: warning: when initialized here g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BCPOutput.o BCPOutput.cc g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SQLOutput.o SQLOutput.cc In file included from AS_ARD_database.hh:29:0, from AS_ARD_database.cc:30: IAssemblyDB.hh: In constructor ‘AS_ARD::IAssemblyDB::IAssemblyDB(AS_ARD::IDBOutput*)’: IAssemblyDB.hh:48:22: warning: ‘AS_ARD::IAssemblyDB::db’ will be initialized after IAssemblyDB.hh:39:14: warning: ‘int AS_ARD::IAssemblyDB::numMDI’ IAssemblyDB.hh:51:10: warning: when initialized here AS_ARD_database.cc: In member function ‘bool AS_ARD::AS_ARD_database::addSCF2SDB(SnapScaffoldMesg*)’: AS_ARD_database.cc:376:20: warning: comparison between signed and unsigned integer expressions ############################## AS_REF ############################## g++ -O2 -pipe -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -DANSI_C -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fPIC -pthread -O2 -Wall -Wimplicit -Wno-write-strings -Wno-unused -Wno-char-subscripts -march=i686 -DX86_GCC_LINUX -c -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_RUN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UTL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_UID -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MSG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_PER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_GKP -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OBT -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_MER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVL -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_OVS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ALN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGB -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_BOG -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REZ -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CNS -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_LIN -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_CGW -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_TER -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ENV -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_ARD -I/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src/AS_REF -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/buildRefContigs.o buildRefContigs.C buildRefContigs.C:258:2: warning: #warning stddev computation is bogus buildRefContigs.C: In function ‘void outputDistances()’: buildRefContigs.C:188:19: warning: comparison between signed and unsigned integer expressions buildRefContigs.C:200:19: warning: comparison between signed and unsigned integer expressions buildRefContigs.C: In function ‘void outputFragments()’: buildRefContigs.C:289:15: warning: comparison between signed and unsigned integer expressions buildRefContigs.C: In function ‘void outputMates()’: buildRefContigs.C:321:15: warning: comparison between signed and unsigned integer expressions buildRefContigs.C: In function ‘void readMapping(char*)’: buildRefContigs.C:63:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result buildRefContigs.C:78:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result ################### libCA.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a AS_global.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a a - AS_global.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a AS_global.o r - AS_global.o * Make Target is libs ############################## AS_RUN ############################## make[1]: Nothing to be done for `libs'. ############################## AS_UTL ############################## ################### libAS_UTL.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_UTL.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Hash.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_heap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Var.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_rand.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_interval.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UnionFind_AS.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_skiplist.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_alloc.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fileIO.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_qsort_mt.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fasta.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_UID.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_reverseComplement.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_UTL.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Hash.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_heap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Var.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_rand.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_interval.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UnionFind_AS.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_skiplist.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_alloc.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fileIO.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_qsort_mt.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fasta.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_UID.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_reverseComplement.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Hash.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_heap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Var.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_rand.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_interval.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UnionFind_AS.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_skiplist.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_alloc.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fileIO.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_qsort_mt.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fasta.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_UID.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_reverseComplement.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Hash.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_heap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_Var.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_rand.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_interval.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UnionFind_AS.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_skiplist.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_alloc.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fileIO.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_qsort_mt.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_fasta.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_UID.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_UTL_reverseComplement.o ############################## AS_UID ############################## ################### libAS_UID.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_UID.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SYS_UIDclient_LOCAL.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_UID.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SYS_UIDclient_LOCAL.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SYS_UIDclient_LOCAL.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SYS_UIDclient_LOCAL.o ############################## AS_MSG ############################## ################### libAS_MSG.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_MSG.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg1.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg2.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_MSG.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg1.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg2.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg1.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg2.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg1.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MSG_pmesg2.o ############################## AS_PER ############################## ################### libAS_PER.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_PER.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_genericStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkLibrary.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_IID.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_PLC.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_UID.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_clearRange.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_fragments.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_load.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_partition.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStream.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_encodeSequenceQuality.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_asmStore.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_PER.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_genericStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkLibrary.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_IID.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_PLC.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_UID.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_clearRange.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_fragments.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_load.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_partition.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStream.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_encodeSequenceQuality.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_asmStore.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_genericStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkLibrary.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_IID.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_PLC.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_UID.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_clearRange.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_fragments.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_load.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_partition.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStream.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_encodeSequenceQuality.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_asmStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_genericStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkLibrary.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_IID.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_PLC.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_UID.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_clearRange.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_fragments.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_load.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStore_partition.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_gkStream.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_encodeSequenceQuality.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_PER_asmStore.o ############################## AS_GKP ############################## make[1]: Nothing to be done for `libs'. ############################## AS_OBT ############################## ################### libAS_OBT.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_OBT.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OBT_acceptableOverlap.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_OBT.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OBT_acceptableOverlap.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OBT_acceptableOverlap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OBT_acceptableOverlap.o ############################## AS_MER ############################## make[1]: Nothing to be done for `libs'. ############################## AS_OVL ############################## ################### libAS_OVL.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_OVL.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SharedOVL.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_OVL.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SharedOVL.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SharedOVL.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SharedOVL.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o ############################## AS_OVS ############################## ################### libAS_OVS.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_OVS.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapFile.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStats.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_OVS.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapFile.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStats.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapFile.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStats.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapFile.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVS_overlapStats.o ############################## AS_ALN ############################## ################### libAS_ALN.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_ALN.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_dpaligner.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_qvaligner.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_loverlapper.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_pieceOlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_forcns.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_local.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_overlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_scafcomp.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_bruteforcedp.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_ALN.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_dpaligner.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_qvaligner.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_loverlapper.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_pieceOlap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_forcns.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_local.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_overlap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_scafcomp.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_bruteforcedp.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_dpaligner.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_qvaligner.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_loverlapper.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_pieceOlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_forcns.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_local.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_overlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_scafcomp.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_bruteforcedp.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_dpaligner.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_qvaligner.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_loverlapper.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_pieceOlap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_forcns.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_local.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_overlap.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CA_ALN_scafcomp.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ALN_bruteforcedp.o ############################## AS_CGB ############################## ################### libAS_CGB.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_CGB.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_histo.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_CGB.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_histo.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_histo.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_histo.o ############################## AS_BOG ############################## make[1]: Nothing to be done for `libs'. ############################## AS_REZ ############################## ################### libAS_REZ.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_REZ.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ConsistencyChecksREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapFillREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapWalkerREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/StatisticsREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UpdateREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UtilsREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MicroHetREZ.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_REZ.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ConsistencyChecksREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapFillREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapWalkerREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/StatisticsREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UpdateREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UtilsREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MicroHetREZ.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ConsistencyChecksREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapFillREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapWalkerREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/StatisticsREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UpdateREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UtilsREZ.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MicroHetREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ConsistencyChecksREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapFillREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GapWalkerREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/StatisticsREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UpdateREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/UtilsREZ.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MicroHetREZ.o ############################## AS_CNS ############################## ################### libAS_CNS.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_CNS.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Array_CNS.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlign.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignPrint.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignment_CNS.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/RefreshMANode.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AbacusRefine.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ApplyAlignment.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BaseCall.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GetAlignmentTrace.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeMultiAligns.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeRefine.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignContig.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignUnitig.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/PrintAlignment.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ReplaceEndUnitigInContig.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_CNS.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Array_CNS.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlign.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignPrint.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignment_CNS.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/RefreshMANode.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AbacusRefine.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ApplyAlignment.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BaseCall.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GetAlignmentTrace.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeMultiAligns.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeRefine.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignContig.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignUnitig.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/PrintAlignment.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ReplaceEndUnitigInContig.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Array_CNS.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlign.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignPrint.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignment_CNS.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/RefreshMANode.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AbacusRefine.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ApplyAlignment.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BaseCall.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GetAlignmentTrace.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeMultiAligns.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeRefine.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignContig.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignUnitig.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/PrintAlignment.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ReplaceEndUnitigInContig.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Array_CNS.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlign.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignPrint.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignStore.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignment_CNS.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/RefreshMANode.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AbacusRefine.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ApplyAlignment.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BaseCall.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GetAlignmentTrace.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeMultiAligns.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeRefine.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignContig.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MultiAlignUnitig.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/PrintAlignment.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ReplaceEndUnitigInContig.o ############################## AS_LIN ############################## ################### libAS_LIN.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_LIN.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrf.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/daxpy.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemm.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemv.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dlamch.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtf2.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpotf2.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dptrfs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpttrs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyr.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyrk.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtbsv.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtrsm.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/idamax.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ilaenv.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/lsame.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/xerbla.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_copy.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_cmp.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ddot.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dscal.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_LIN.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrf.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrs.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/daxpy.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemm.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemv.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dlamch.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtf2.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpotf2.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dptrfs.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpttrs.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyr.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyrk.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtbsv.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtrsm.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/idamax.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ilaenv.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/lsame.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/xerbla.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_copy.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_cmp.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ddot.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dscal.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrf.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/daxpy.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemm.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemv.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dlamch.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtf2.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpotf2.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dptrfs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpttrs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyr.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyrk.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtbsv.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtrsm.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/idamax.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ilaenv.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/lsame.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/xerbla.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_copy.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_cmp.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ddot.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dscal.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrf.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtrs.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/daxpy.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemm.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dgemv.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dlamch.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpbtf2.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpotf2.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dptrfs.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dpttrs.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyr.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dsyrk.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtbsv.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dtrsm.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/idamax.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ilaenv.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/lsame.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/xerbla.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_copy.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/s_cmp.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ddot.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dscal.o ############################## AS_CGW ############################## ################### libAS_CGW.a ##################### cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_CGW.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Globals_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGW_EdgeDiagnostics.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIEdgeT_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Biconnected_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Cleanup_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Merge_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Celamy_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ChunkOverlap_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ContigT_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/DemoteUnitigsWithRBP_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragmentPlacement.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GraphCGW_T.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Input_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Instrument_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/InterleavedMerging.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/LeastSquaresGaps_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeEdges_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Output_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SEdgeT_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ScaffoldGraph_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitChunks_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitScaffolds_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Stats_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/TransitiveReduction_CGW.o ar: creating /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_CGW.a a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Globals_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGW_EdgeDiagnostics.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIEdgeT_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Biconnected_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Cleanup_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Merge_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Celamy_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ChunkOverlap_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ContigT_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/DemoteUnitigsWithRBP_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragmentPlacement.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GraphCGW_T.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Input_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Instrument_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/InterleavedMerging.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/LeastSquaresGaps_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeEdges_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Output_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SEdgeT_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ScaffoldGraph_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitChunks_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitScaffolds_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Stats_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/TransitiveReduction_CGW.o cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ ar rvs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Globals_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGW_EdgeDiagnostics.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIEdgeT_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Biconnected_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Cleanup_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Merge_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Celamy_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ChunkOverlap_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ContigT_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/DemoteUnitigsWithRBP_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragmentPlacement.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GraphCGW_T.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Input_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Instrument_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/InterleavedMerging.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/LeastSquaresGaps_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeEdges_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Output_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SEdgeT_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ScaffoldGraph_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitChunks_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitScaffolds_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Stats_CGW.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/TransitiveReduction_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Globals_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGW_EdgeDiagnostics.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIEdgeT_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Biconnected_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Cleanup_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CIScaffoldT_Merge_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Celamy_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ChunkOverlap_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ContigT_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/DemoteUnitigsWithRBP_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragmentPlacement.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/GraphCGW_T.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Input_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Instrument_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/InterleavedMerging.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/LeastSquaresGaps_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/MergeEdges_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Output_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SEdgeT_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ScaffoldGraph_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitChunks_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SplitScaffolds_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Stats_CGW.o a - /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/TransitiveReduction_CGW.o ############################## AS_TER ############################## make[1]: Nothing to be done for `libs'. ############################## AS_ENV ############################## make[1]: Nothing to be done for `libs'. ############################## AS_ARD ############################## make[1]: Nothing to be done for `libs'. ############################## AS_REF ############################## make[1]: Nothing to be done for `libs'. * Make Target is progs ############################## AS_RUN ############################## ++++++++++++++++++++ fragmentDepth ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/fragmentDepth /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragmentDepth.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ markUniqueUnique ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/markUniqueUnique /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/markUniqueUnique.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_UTL ############################## make[1]: Nothing to be done for `progs'. ############################## AS_UID ############################## ++++++++++++++++++++ uidclient ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/uidclient /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/uidclient.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_UID.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_UTL.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ uidserver ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/uidserver /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/uidserver.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_UID.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libAS_UTL.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_MSG ############################## ++++++++++++++++++++ remove_fragment ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/remove_fragment /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/remove_fragment.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ extractmessages ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/extractmessages /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ExtractMessages.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_PER ############################## make[1]: Nothing to be done for `progs'. ############################## AS_GKP ############################## ++++++++++++++++++++ gatekeeper ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/gatekeeper /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_main.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_buildPartition.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_checkLibrary.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_checkFrag.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_checkLink.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_checkPlace.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_dump.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_edit.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_errors.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_illumina.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ gatekeeperbench ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/gatekeeperbench /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_GKP_bench.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ sffToCA ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/sffToCA /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/sffToCA.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ fastqToCA ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/fastqToCA /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fastqToCA.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ fastqSample ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/fastqSample /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fastqSample.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_OBT ############################## ++++++++++++++++++++ initialTrim ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/initialTrim /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/initialTrim.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/trim.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ merge-trimming ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/merge-trimming /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/merge-trimming.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/trim.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ overlapMask ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/overlapMask /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapMask.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/util++.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/readOverlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ consolidate ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/consolidate /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/consolidate.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/util++.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/readOverlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ chimera ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/chimera /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/chimera.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/util++.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/readOverlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ deduplicate ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/deduplicate /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/deduplicate.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/util++.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/readOverlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ removeMateOverlap ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/removeMateOverlap /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/removeMateOverlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/util++.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/readOverlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_MER ############################## ++++++++++++++++++++ meryl ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/meryl /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/meryl.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MER_gkpStore_to_FastABase.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MER_gkpStoreChain.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmerylguts.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libkmer.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmeryl.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libbio.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libutil.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ mercy ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/mercy /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/mercy.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmerylguts.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libkmer.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmeryl.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libbio.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libutil.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters ++++++++++++++++++++ overmerry ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/overmerry /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overmerry.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MER_gkpStore_to_FastABase.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmerylguts.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libkmer.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmeryl.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libbio.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libutil.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ merTrim ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/merTrim /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/merTrim.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MER_gkpStore_to_FastABase.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmerylguts.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libkmer.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmeryl.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libbio.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libutil.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters ++++++++++++++++++++ estimate-mer-threshold ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/estimate-mer-threshold /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/estimate-mer-threshold.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_MER_gkpStore_to_FastABase.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmerylguts.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libkmer.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libmeryl.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libbio.a /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libutil.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/kmer/Linux-i686/lib/libseq.a(seqStore.o): In function `constructSeqStore(char*, seqCache*)': seqStore.C:(.text+0x1f90): warning: memset used with constant zero length parameter; this could be due to transposed parameters ############################## AS_OVL ############################## ++++++++++++++++++++ overlap ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/overlap /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_overlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_driver.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ overlap_ca ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/overlap_ca /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_overlap_ca.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_driver_ca.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ olap-from-seeds ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/olap-from-seeds /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/OlapFromSeedsOVL.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ correct-frags ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/correct-frags /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/FragCorrectOVL.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ show-corrects ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/show-corrects /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ShowCorrectsOVL.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ correct-olaps ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/correct-olaps /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CorrectOlapsOVL.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ cat-corrects ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/cat-corrects /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CatCorrectsOVL.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ++++++++++++++++++++ cat-erates ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/cat-erates /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/CatEratesOVL.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_OVL_delcher.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 -lpthread ############################## AS_OVS ############################## ++++++++++++++++++++ overlapStore ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/overlapStore /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore_build.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore_merge.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore_dump.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStore_erates.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ overlapStats ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/overlapStats /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/overlapStats.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ convertOverlap ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/convertOverlap /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/convertOverlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ filterOverlap ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/filterOverlap /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/filterOverlap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_ALN ############################## make[1]: Nothing to be done for `progs'. ############################## AS_CGB ############################## ++++++++++++++++++++ unitigger ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/unitigger /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_unitigger.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_FGB_main.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_FGB_io.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_histo.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_fga.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_fgb.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_FGB_hanging_fragment.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_FGB_contained.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_traversal.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_walk.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_edgemate.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_main.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_cgb.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_classify.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_chimeras.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_cga.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_Graph.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_VertexSet.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_dfs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_Popper.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGB_Bubble_PopperMethods.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_BOG ############################## ++++++++++++++++++++ buildUnitigs ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/buildUnitigs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BuildUnitigs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_BestOverlapGraph.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_ChunkGraph.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_MateChecker.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_Unitig.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_BOG_UnitigGraph.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ fixUnitigs ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/fixUnitigs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fixUnitigs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ scoreOverlaps ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/scoreOverlaps /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/scoreOverlaps.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_REZ ############################## make[1]: Nothing to be done for `progs'. ############################## AS_CNS ############################## ++++++++++++++++++++ utgcns ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/utgcns /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/utgcns.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ ctgcns ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/ctgcns /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/ctgcns.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ tigStore ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/tigStore /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/tigStore.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_LIN ############################## make[1]: Nothing to be done for `progs'. ############################## AS_CGW ############################## ++++++++++++++++++++ cgw ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/cgw /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_CGW_main.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ extendClearRanges ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/extendClearRanges /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/eCR.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/eCR-examineGap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/eCR-diagnostic.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ extendClearRangesPartition ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/extendClearRangesPartition /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/eCR-partition.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ resolveSurrogates ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/resolveSurrogates /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/resolveSurrogates.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ dumpCloneMiddles ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/dumpCloneMiddles /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dumpCloneMiddles.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ dumpSingletons ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/dumpSingletons /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/dumpSingletons.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ exploreGapStructure ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/exploreGapStructure /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/exploreGapStructure.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ frgs2clones ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/frgs2clones /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/frgs2clones.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_TER ############################## ++++++++++++++++++++ terminator ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/terminator /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/terminator.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ asmOutputFasta ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/asmOutputFasta /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/asmOutputFasta.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ asmOutputStatistics ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/asmOutputStatistics /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/asmOutputStatistics.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ fragsInVars ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/fragsInVars /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/fragsInVars.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ buildPosMap ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/buildPosMap /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/buildPosMap.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_ENV ############################## ++++++++++++++++++++ greedyFragmentTiling ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/greedyFragmentTiling /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/greedyFragmentTiling.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ metagenomics_ovl_analyses ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/metagenomics_ovl_analyses /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/metagenomics_ovl_analyses.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ chimChe ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/chimChe /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/chimChe.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_ARD ############################## ++++++++++++++++++++ loadAssembly ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/loadAssembly /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/loadAssembly.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Sybase.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/AS_ARD_database.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/DBTextOutput.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/BCPOutput.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/SQLOutput.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ++++++++++++++++++++ getAssembly ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/getAssembly /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/getAssembly.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/Sybase.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 ############################## AS_REF ############################## ++++++++++++++++++++ buildRefContigs ++++++++++++++++++++++ cd /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj; \ g++ -o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/bin/buildRefContigs /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/obj/buildRefContigs.o /var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib/libCA.a -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/Linux-i686/lib -L/usr/X11R6/lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -pthread -lm -Wl,-O1 -march=i686 -pthread -lm -Wl,-O1 -march=i686 * Make Target is all ############################## AS_RUN ############################## ############################## AS_UTL ############################## ############################## AS_UID ############################## ############################## AS_MSG ############################## ############################## AS_PER ############################## ############################## AS_GKP ############################## ############################## AS_OBT ############################## ############################## AS_MER ############################## ############################## AS_OVL ############################## ############################## AS_OVS ############################## ############################## AS_ALN ############################## ############################## AS_CGB ############################## ############################## AS_BOG ############################## ############################## AS_REZ ############################## ############################## AS_CNS ############################## ############################## AS_LIN ############################## ############################## AS_CGW ############################## ############################## AS_TER ############################## ############################## AS_ENV ############################## ############################## AS_ARD ############################## ############################## AS_REF ############################## make: Leaving directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src' >>> Source compiled. >>> Test phase [none]: sci-biology/wgs-assembler-6.1 >>> Install wgs-assembler-6.1 into /var/tmp/portage/sci-biology/wgs-assembler-6.1/image/ category sci-biology >>> Completed installing wgs-assembler-6.1 into /var/tmp/portage/sci-biology/wgs-assembler-6.1/image/ weaver@gentoo.org Andrey Kislyuk sci-biology strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment usr/bin/utgcns usr/bin/buildPosMap usr/bin/overlap usr/bin/fastqToCA usr/bin/estimate-mer-threshold usr/bin/removeMateOverlap usr/bin/percentCovered usr/bin/filterOverlap usr/bin/terminator usr/bin/chimChe usr/bin/tigStore usr/bin/extendClearRanges usr/bin/gatekeeper usr/bin/chimera usr/bin/buildUnitigs usr/bin/test-merStream usr/bin/cat-erates usr/bin/show-corrects usr/bin/extendClearRangesPartition usr/bin/dumpCloneMiddles usr/bin/maskMers usr/bin/mask usr/bin/existDB usr/bin/fragmentDepth usr/bin/gatekeeperbench usr/bin/olap-from-seeds usr/bin/mapMers-depth usr/bin/scoreOverlaps usr/bin/test-seqStream usr/bin/mapMers usr/bin/getAssembly usr/bin/sffToCA usr/bin/remove_fragment usr/bin/metagenomics_ovl_analyses usr/bin/mercy usr/bin/ctgcns usr/bin/resolveSurrogates usr/bin/asmOutputFasta usr/bin/asmMerQC usr/bin/loadAssembly usr/bin/buildRefContigs usr/bin/test-seqCache usr/bin/extractmessages usr/bin/overlapMask usr/bin/overlapStats usr/bin/overlapStore usr/bin/greedyFragmentTiling usr/bin/merge-trimming usr/bin/correct-frags usr/bin/fragsInVars usr/bin/overlap_ca usr/bin/unitigger usr/bin/deduplicate usr/bin/cgw usr/bin/overmerry usr/bin/consolidate usr/bin/meryl usr/bin/asmOutputStatistics usr/bin/convertOverlap usr/bin/merTrim usr/bin/fixUnitigs usr/bin/mt19937ar-test usr/bin/uidclient usr/bin/fastqSample usr/bin/exploreGapStructure usr/bin/dumpSingletons usr/bin/cat-corrects usr/bin/positionDB usr/bin/frgs2clones usr/bin/markUniqueUnique usr/bin/correct-olaps usr/bin/testPositionBias usr/bin/initialTrim usr/bin/uidserver usr/lib/libAS_CNS.a usr/lib/libAS_UTL.a usr/lib/libAS_LIN.a usr/lib/libAS_PER.a usr/lib/libAS_MSG.a usr/lib/libCA.a usr/lib/libAS_ALN.a usr/lib/libAS_OBT.a usr/lib/libAS_OVS.a usr/lib/libAS_OVL.a usr/lib/libAS_REZ.a usr/lib/libAS_CGB.a usr/lib/libAS_CGW.a usr/lib/libAS_UID.a usr/lib/wgs-assembler/libkmer.a usr/lib/wgs-assembler/libkaz.a usr/lib/wgs-assembler/libmeryl.a usr/lib/wgs-assembler/libutil.a usr/lib/wgs-assembler/libseq.a usr/lib/wgs-assembler/libmt19937ar.a usr/lib/wgs-assembler/libbio.a usr/lib/wgs-assembler/libmerylguts.a  * QA Notice: Files built without respecting LDFLAGS have been detected * Please include the following list of files in your report: * /usr/bin/percentCovered * /usr/bin/test-merStream * /usr/bin/maskMers * /usr/bin/mask * /usr/bin/existDB * /usr/bin/mapMers-depth * /usr/bin/test-seqStream * /usr/bin/mapMers * /usr/bin/asmMerQC * /usr/bin/test-seqCache * /usr/bin/mt19937ar-test * /usr/bin/positionDB * /usr/bin/testPositionBias  * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq * owners / ` to identify the installed package that owns a * file. If portageq reports that only one package owns a file then do * NOT file a bug report. A bug report is only useful if it identifies at * least two or more packages that are known to install the same file(s). * If a collision occurs and you can not explain where the file came from * then you should simply ignore the collision since there is not enough * information to determine if a real problem exists. Please do NOT file * a bug report at http://bugs.gentoo.org unless you report exactly which * two packages install the same file(s). Once again, please do NOT file * a bug report unless you have completely understood the above message. * * Detected file collision(s): * * /usr/bin/terminator * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * x11-terms/terminator-0.94 * /usr/bin/terminator * * Package 'sci-biology/wgs-assembler-6.1' NOT merged due to file * collisions. If necessary, refer to your elog messages for the whole * content of the above message.