* Package: sci-biology/wgs-assembler-6.1 * Repository: gentoo * Maintainer: weaver@gentoo.org sci-biology@gentoo.org * USE: elibc_glibc kernel_linux test userland_GNU x86 * FEATURES: sandbox test userpriv usersandbox >>> 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 ../kmer/libutil/mt19937ar/mt19937ar.c: In function ‘mtRandomGaussian’: ../kmer/libutil/mt19937ar/mt19937ar.c:166:34: warning: variable ‘y2’ set but not used [-Wunused-but-set-variable] 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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wcpp] meryl/build.C: In function ‘void build(merylArgs*)’: meryl/build.C:765:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/build.C:766:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/build.C:767:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/build.C:771:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/build.C:776:22: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/build.C:783:41: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 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 [-Wcpp] 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 argument of type ‘int’, but argument 3 has type ‘u32bit’ [-Wformat] 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 [-Wcpp] ../kmer/libmeryl/libmeryl.C:6:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libmeryl/libmeryl.C:7:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libmeryl/libmeryl.C:8:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libmeryl/libmeryl.C:9:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libmeryl/libmeryl.C:10:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libmeryl/libmeryl.C:11:24: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libmeryl/libmeryl.C: In constructor ‘merylStreamReader::merylStreamReader(const char*, u32bit)’: ../kmer/libmeryl/libmeryl.C:42:11: warning: variable ‘Pmagic’ set but not used [-Wunused-but-set-variable] 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 argument of type ‘unsigned int’, but argument 5 has type ‘u32bit’ [-Wformat] ../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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 argument of type ‘long long unsigned int’, but argument 4 has type ‘long unsigned int’ [-Wformat] ../kmer/libseq/seqStore.C:321:199: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘long unsigned int’ [-Wformat] ../kmer/libseq/seqStore.C:322:199: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘long unsigned int’ [-Wformat] ../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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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:82:32: 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 [enabled by default] 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 argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat] ../kmer/libseq/seqStream.C:23:66: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘u32bit’ [-Wformat] ../kmer/libseq/seqStream.C: In member function ‘void seqStream::tradeSpaceForTime()’: ../kmer/libseq/seqStream.C:147:90: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘u64bit’ [-Wformat] 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 argument of type ‘int’, but argument 3 has type ‘u32bit’ [-Wformat] 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 argument of type ‘int’, but argument 3 has type ‘u32bit’ [-Wformat] 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? [-Wcpp] 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 argument of type ‘int’, but argument 3 has type ‘u32bit’ [-Wformat] ../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*’ [-Wwrite-strings] ../kmer/libseq/test-merStream.C:223:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libseq/test-merStream.C:225:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libseq/test-merStream.C:228:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libseq/test-merStream.C:239:90: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libseq/test-merStream.C:243:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libseq/test-merStream.C:245:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] ../kmer/libseq/test-merStream.C:248:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 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 ‘openFile’: ../kmer/libutil/file.c:390:9: warning: variable ‘isRW’ set but not used [-Wunused-but-set-variable] ../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 [-Wunused-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 ../kmer/libutil/qsort_mt.c: In function ‘qsort_algo’: ../kmer/libutil/qsort_mt.c:264:13: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] ../kmer/libutil/qsort_mt.c: In function ‘qsort_thread’: ../kmer/libutil/qsort_mt.c:370:13: warning: variable ‘id’ set but not used [-Wunused-but-set-variable] 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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wformat-extra-args] 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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 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+0x1c80): 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’ [-Wparentheses] meryl/asmMerQC.C:130:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses] meryl/asmMerQC.C:149:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses] meryl/asmMerQC.C: In function ‘int main(int, char**)’: meryl/asmMerQC.C:384:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/asmMerQC.C:385:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/asmMerQC.C:386:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/asmMerQC.C:387:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/asmMerQC.C:388:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/asmMerQC.C:389:81: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 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’ [-Wparentheses] meryl/mapMers.C: In function ‘int main(int, char**)’: meryl/mapMers.C:19:13: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] 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’ [-Wparentheses] 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’ [-Wparentheses] 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’ [-Wparentheses] ../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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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’ [-Wparentheses] 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’ [-Wunused-variable] 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 [-Wunused-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 [-Wunused-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 [-Wunused-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 ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘u64bit’ [-Wformat] ../kmer/libkmer/positionDB-sort.C:37:86: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘u64bit’ [-Wformat] ../kmer/libkmer/positionDB-sort.C:37:86: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘u64bit’ [-Wformat] 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’ [-Wparentheses] 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+0x1c80): 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’ [-Wparentheses] meryl/mapMers-depth.C: In function ‘int main(int, char**)’: meryl/mapMers-depth.C:86:67: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘int’ [-Wformat] meryl/mapMers-depth.C:91:65: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘int’ [-Wformat] meryl/mapMers-depth.C:17:13: warning: variable ‘beVerbose’ set but not used [-Wunused-but-set-variable] 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+0x1c80): 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*’ [-Wwrite-strings] meryl/testPositionBias.C:55:50: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/testPositionBias.C:56:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/testPositionBias.C: In function ‘double computeRMSD(u32bit)’: meryl/testPositionBias.C:83:43: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/testPositionBias.C:84:50: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] meryl/testPositionBias.C:85:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] 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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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 [-Wunused-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+0x1c80): 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’ [-Wparentheses] ../kmer/libkmer/driver-existDB.C: In function ‘int testExhaustive(char*, char*, u32bit)’: ../kmer/libkmer/driver-existDB.C:102:55: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘u64bit’ [-Wformat] ../kmer/libkmer/driver-existDB.C:104:63: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘u64bit’ [-Wformat] ../kmer/libkmer/driver-existDB.C:118:36: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘u64bit’ [-Wformat] 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+0x1c80): 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’ [-Wparentheses] 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+0x1c80): 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’ [-Wparentheses] 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+0x1c80): 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’ [-Wparentheses] 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+0x1c80): 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+0x1c80): 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+0x1c80): 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+0x1c80): 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' cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] * Make Target is objs ############################## AS_RUN ############################## cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] ############################## AS_UTL ############################## cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 [-Wsign-compare] 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 [-Wsign-compare] 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 [-Wsign-compare] 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_heap.C: In function ‘void* NextHeapIterator_AS(HeapIterator_AS*)’: AS_UTL_heap.C:78:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 [-Wsign-compare] 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 AS_UTL_Var.C: In function ‘void ReadVA(FILE*, VarArrayType*, FileVarArrayType*)’: AS_UTL_Var.C:343:58: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 4 has type ‘size_t’ [-Wformat] AS_UTL_Var.C:343:58: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 5 has type ‘size_t’ [-Wformat] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 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 [-Wunused-result] AS_UTL_fileIO.C:264:43: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 [-Wsign-compare] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] ############################## AS_UID ############################## cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] 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 cc1plus: warning: command line option ‘-Wimplicit’ is valid for C/ObjC but not for C++ [enabled by default] In file included from uidserver.C:24:0: uidserver_common.h:15:23: fatal error: rpc/types.h: No such file or directory compilation terminated. make[1]: *** [uidserver.o] Error 1 make[1]: *** Waiting for unfinished jobs.... 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 [-Wunused-result] make: *** [objs] Error 1 make: Leaving directory `/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1/src' emake failed * ERROR: sci-biology/wgs-assembler-6.1 failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 56: Called src_compile * environment, line 2343: Called die * The specific snippet of code: * emake -C src -j1 SITE_NAME=LOCAL || die * * If you need support, post the output of 'emerge --info =sci-biology/wgs-assembler-6.1', * the complete build log and the output of 'emerge -pqv =sci-biology/wgs-assembler-6.1'. * The complete build log is located at '/var/log/portage/build/sci-biology/wgs-assembler-6.1:20110708-122919.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/wgs-assembler-6.1/temp/environment'. * S: '/var/tmp/portage/sci-biology/wgs-assembler-6.1/work/wgs-6.1'