* Package: sci-biology/velvet-1.2.10 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux openmp userland_GNU * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox >>> Unpacking source... >>> Unpacking velvet_1.2.10.tgz to /var/tmp/portage/sci-biology/velvet-1.2.10/work >>> Source unpacked in /var/tmp/portage/sci-biology/velvet-1.2.10/work >>> Preparing source in /var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10 ... * Upstream recommends using -O3 in CFLAGS * To adjust the MAXKMERLENGTH, CATEGORIES, BIGASSEMBLY, LONGSEQUENCES parameters * as described in the PDF manual, please set the variables by prepending VELVET_ in * front of it. For example VELVET_MAXKMERLENGTH, VELVET_CATEGORIES, ... * Set them either in your environment or in /etc/portage/make.conf, then re-emerge * the package. For example: * VELVET_MAXKMERLENGTH=NN emerge [options] velvet >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10 ... make -j4 CC=x86_64-pc-linux-gnu-gcc 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp' 'OPT=-O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp' OPENMP=1 -j1 rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/*.o': No such file or directory rm: cannot remove 'obj/dbg/*.o': No such file or directory make: [Makefile:51: cleanobj] Error 1 (ignored) mkdir -p obj x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:4: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:6: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:6: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 681 | file2.gzFile = file2.autoFile = NULL; | ^ In file included from /usr/include/string.h:495, from src/readSet.c:23: In function ‘strncpy’, inlined from ‘importReadSet’ at src/readSet.c:1613:4: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c: In function ‘importReadSet’: src/readSet.c:1612:17: note: length computed here 1612 | lineLength = strlen(line) - 1; | ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: At top level: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:8: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:3: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 28 | dup(out[1]); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fopenmp -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fopenmp -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm make -j4 CC=x86_64-pc-linux-gnu-gcc 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp' 'OPT=-O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp' OPENMP=1 -j1 color rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make: [Makefile:51: cleanobj] Error 1 (ignored) mkdir -p obj x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/tightString.c -o obj/tightString.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splay.c -o obj/splay.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:4: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:6: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:6: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graph.c -o obj/graph.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fibHeap.c -o obj/fibHeap.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/fib.c -o obj/fib.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfib.c -o obj/dfib.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/recycleBin.c -o obj/recycleBin.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 681 | file2.gzFile = file2.autoFile = NULL; | ^ In file included from /usr/include/string.h:495, from src/readSet.c:23: In function ‘strncpy’, inlined from ‘importReadSet’ at src/readSet.c:1613:4: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c: In function ‘importReadSet’: src/readSet.c:1612:17: note: length computed here 1612 | lineLength = strlen(line) - 1; | ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/binarySequences.c -o obj/binarySequences.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: At top level: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/utility.c -o obj/utility.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:8: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/allocArray.c -o obj/allocArray.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D COLOR -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:3: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 28 | dup(out[1]); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fopenmp -o velveth_de obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fopenmp -o velvetg_de obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm >>> Source compiled. >>> Test phase: sci-biology/velvet-1.2.10 make -j4 CC=x86_64-pc-linux-gnu-gcc 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp' 'OPT=-O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp' OPENMP=1 -j1 test rm obj/*.o obj/dbg/*.o rm: cannot remove 'obj/dbg/*.o': No such file or directory make: [Makefile:51: cleanobj] Error 1 (ignored) mkdir -p obj x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function ‘scanReferenceSequences’: src/splayTable.c:877:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:4: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:6: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:6: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o In file included from src/run.h:34, from src/run2.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o In file included from src/concatenatedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o In file included from src/passageMarker.c:29: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o In file included from src/graphStats.c:28: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o In file included from src/correctedGraph.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function ‘readFastXFile’: src/readSet.c:641:21: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: warning: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wincompatible-pointer-types-Wincompatible-pointer-types]8;;] 681 | file2.gzFile = file2.autoFile = NULL; | ^ In file included from /usr/include/string.h:495, from src/readSet.c:23: In function ‘strncpy’, inlined from ‘importReadSet’ at src/readSet.c:1613:4: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/readSet.c: In function ‘importReadSet’: src/readSet.c:1612:17: note: length computed here 1612 | lineLength = strlen(line) - 1; | ^~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o In file included from src/shortReadPairs.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o In file included from src/locallyCorrectedGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o In file included from src/graphReConstruction.c:33: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o In file included from src/roadMap.c:26: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o src/preGraph.c: In function ‘addPreArcToPreNode_pg’: src/preGraph.c:165:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 165 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:167:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 167 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c: In function ‘removePreArcFromList_pg’: src/preGraph.c:285:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 285 | preArcPtr = &(preNode->preArcRight); | ^~~~~~~~~~~~~~~~~~~~~~~ src/preGraph.c:287:15: warning: taking address of packed member of ‘struct preNode_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 287 | preArcPtr = &(preNode->preArcLeft); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/run.h:34, from src/preGraph.c:35: src/preGraph.c: At top level: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o In file included from src/readCoherentGraph.c:25: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o src/kmer.c: In function ‘pushNucleotide’: src/kmer.c:419:8: warning: taking address of packed member of ‘struct kmer_st’ may result in an unaligned pointer value []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Waddress-of-packed-member-Waddress-of-packed-member]8;;] 419 | ptr = kmer->longlongs; | ^~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o In file included from src/scaffold.c:32: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o In file included from src/kmerOccurenceTable.c:27: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined 173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o src/autoOpen.c: In function ‘popenNoStderr’: src/autoOpen.c:28:3: warning: ignoring return value of ‘dup’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 28 | dup(out[1]); | ^~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fopenmp -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o -lz -lm x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -fopenmp -O2 -pipe -march=native -frecord-gcc-switches -fPIC -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fopenmp -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm cd tests && ./run-tests.sh [Mon May 25 14:40:36 2020] Running Velvet Test Suite [Mon May 25 14:40:36 2020] Found ../velveth, ok [Mon May 25 14:40:36 2020] Found ../velvetg, ok [Mon May 25 14:40:36 2020] Found Sequences.31, ok [Mon May 25 14:40:36 2020] Found Roadmaps.31, ok [Mon May 25 14:40:36 2020] Found read1.fq.gz, ok [Mon May 25 14:40:36 2020] Found read2.fq.gz, ok [Mon May 25 14:40:36 2020] Found reads.fq.gz, ok [Mon May 25 14:40:36 2020] Found read1.fa.gz, ok [Mon May 25 14:40:36 2020] Found read2.fa.gz, ok [Mon May 25 14:40:36 2020] Found reads.fa.gz, ok [Mon May 25 14:40:36 2020] making test folder: velvet.test.v0VSgn [Mon May 25 14:40:36 2020] running test 1 of 5: fasta_eq_fastq_ascii.t [Mon May 25 14:40:39 2020] ok [Mon May 25 14:40:39 2020] ok [Mon May 25 14:40:39 2020] ok [Mon May 25 14:40:39 2020] ok [Mon May 25 14:40:39 2020] passed test 1 [Mon May 25 14:40:39 2020] running test 2 of 5: fasta_eq_fastq_binary.t [Mon May 25 14:40:41 2020] ok [Mon May 25 14:40:41 2020] ok [Mon May 25 14:40:41 2020] passed test 2 [Mon May 25 14:40:41 2020] running test 3 of 5: fmt_auto_mode.t [Mon May 25 14:40:43 2020] ok [Mon May 25 14:40:43 2020] ok [Mon May 25 14:40:43 2020] passed test 3 [Mon May 25 14:40:43 2020] running test 4 of 5: interleaved_eq_separate.t [Mon May 25 14:40:48 2020] ok [Mon May 25 14:40:48 2020] ok [Mon May 25 14:40:48 2020] passed test 4 [Mon May 25 14:40:48 2020] running test 5 of 5: mismatched_separates.t [Mon May 25 14:40:48 2020] ok [Mon May 25 14:40:48 2020] ok [Mon May 25 14:40:48 2020] passed test 5 [Mon May 25 14:40:48 2020] removing test folder: velvet.test.v0VSgn [Mon May 25 14:40:48 2020] passed all 5 tests [Mon May 25 14:40:48 2020] hooray! >>> Completed testing sci-biology/velvet-1.2.10 >>> Install sci-biology/velvet-1.2.10 into /var/tmp/portage/sci-biology/velvet-1.2.10/image/ >>> Completed installing sci-biology/velvet-1.2.10 into /var/tmp/portage/sci-biology/velvet-1.2.10/image/ * Final size of build directory: 62532 KiB (61.0 MiB) * Final size of installed tree: 3660 KiB ( 3.5 MiB) strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/bin/velveth /usr/bin/velvetg /usr/bin/velveth_de /usr/bin/velvetg_de /usr/share/velvet/contrib/MetaVelvet-1.2.01/ISGraph/ISGraph.o /usr/share/velvet/contrib/MetaVelvet-1.2.01/ISGraph/libISGraph.a >>> Done. * QA Notice: Symbolic link /usr/share/velvet/contrib/read_prepare/read2.fq.gz points to /usr/share/velvet/tests/read2.fq.gz which does not exist. * QA Notice: Symbolic link /usr/share/velvet/contrib/read_prepare/read1.fq.gz points to /usr/share/velvet/tests/read1.fq.gz which does not exist. emerge --info: Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r3, 5.4.0-1009-aws x86_64) ================================================================= System uname: Linux-5.4.0-1009-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 KiB Mem: 16011344 total, 1832892 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 25 May 2020 12:35:49 +0000 sh bash 5.0_p17 ld GNU ld (Gentoo 2.34 p4) 2.34.0 app-shells/bash: 5.0_p17::gentoo dev-lang/perl: 5.30.2-r2::gentoo dev-lang/python: 2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.18::gentoo sys-devel/autoconf: 2.69-r5::gentoo sys-devel/automake: 1.16.2::gentoo sys-devel/binutils: 2.34-r1::gentoo sys-devel/gcc: 10.1.0::gentoo sys-devel/gcc-config: 2.3::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers) sys-libs/glibc: 2.31-r3::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXX="x86_64-pc-linux-gnu-g++" CXXFLAGS="-O2 -pipe -march=native 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MAKEOPTS="-j4" PKGDIR="/root/.packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS