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Gentoo's Bugzilla – Attachment 641714 Details for
Bug 725308
sci-biology/velvet-1.2.10 installs files with broken symlink
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build.log
build.log (text/plain), 94.23 KB, created by
Agostino Sarubbo
on 2020-05-25 13:10:34 UTC
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-05-25 13:10:34 UTC
Size:
94.23 KB
patch
obsolete
> * 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âscanReferenceSequencesâ: >src/splayTable.c:877:3: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âscanBinaryReferenceSequencesâ: >src/splayTable.c:933:3: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âfgetsâ declared with attribute âwarn_unused_resultâ []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 âinputSequenceArrayIntoSplayTableAndArchiveâ: >src/splayTable.c:1207:6: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âfgetsâ declared with attribute âwarn_unused_resultâ []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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âreadFastXFileâ: >src/readSet.c:641:21: warning: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âreadFastXPairâ: >src/readSet.c:680:22: warning: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âstrncpyâ, > inlined from âimportReadSetâ at src/readSet.c:1613:4: >/usr/include/bits/string_fortified.h:106:10: warning: â__builtin_strncpyâ 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 âimportReadSetâ: >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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âaddPreArcToPreNode_pgâ: >src/preGraph.c:165:15: warning: taking address of packed member of âstruct preNode_stâ 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 âstruct preNode_stâ 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 âremovePreArcFromList_pgâ: >src/preGraph.c:285:15: warning: taking address of packed member of âstruct preNode_stâ 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 âstruct preNode_stâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âpushNucleotideâ: >src/kmer.c:419:8: warning: taking address of packed member of âstruct kmer_stâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âpopenNoStderrâ: >src/autoOpen.c:28:3: warning: ignoring return value of âdupâ declared with attribute âwarn_unused_resultâ []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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âscanReferenceSequencesâ: >src/splayTable.c:877:3: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âscanBinaryReferenceSequencesâ: >src/splayTable.c:933:3: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âfgetsâ declared with attribute âwarn_unused_resultâ []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 âinputSequenceArrayIntoSplayTableAndArchiveâ: >src/splayTable.c:1207:6: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âfgetsâ declared with attribute âwarn_unused_resultâ []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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âreadFastXFileâ: >src/readSet.c:641:21: warning: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âreadFastXPairâ: >src/readSet.c:680:22: warning: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âstrncpyâ, > inlined from âimportReadSetâ at src/readSet.c:1613:4: >/usr/include/bits/string_fortified.h:106:10: warning: â__builtin_strncpyâ 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 âimportReadSetâ: >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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âaddPreArcToPreNode_pgâ: >src/preGraph.c:165:15: warning: taking address of packed member of âstruct preNode_stâ 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 âstruct preNode_stâ 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 âremovePreArcFromList_pgâ: >src/preGraph.c:285:15: warning: taking address of packed member of âstruct preNode_stâ 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 âstruct preNode_stâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âpushNucleotideâ: >src/kmer.c:419:8: warning: taking address of packed member of âstruct kmer_stâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âpopenNoStderrâ: >src/autoOpen.c:28:3: warning: ignoring return value of âdupâ declared with attribute âwarn_unused_resultâ []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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âscanReferenceSequencesâ: >src/splayTable.c:877:3: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âscanBinaryReferenceSequencesâ: >src/splayTable.c:933:3: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âfgetsâ declared with attribute âwarn_unused_resultâ []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 âinputSequenceArrayIntoSplayTableAndArchiveâ: >src/splayTable.c:1207:6: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ []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 âfgetsâ declared with attribute âwarn_unused_resultâ []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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âreadFastXFileâ: >src/readSet.c:641:21: warning: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âreadFastXPairâ: >src/readSet.c:680:22: warning: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â []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 âstrncpyâ, > inlined from âimportReadSetâ at src/readSet.c:1613:4: >/usr/include/bits/string_fortified.h:106:10: warning: â__builtin_strncpyâ 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 âimportReadSetâ: >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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âaddPreArcToPreNode_pgâ: >src/preGraph.c:165:15: warning: taking address of packed member of âstruct preNode_stâ 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 âstruct preNode_stâ 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 âremovePreArcFromList_pgâ: >src/preGraph.c:285:15: warning: taking address of packed member of âstruct preNode_stâ 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 âstruct preNode_stâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âpushNucleotideâ: >src/kmer.c:419:8: warning: taking address of packed member of âstruct kmer_stâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âsetShortReadMarkerOffsetâ declared but never defined > 178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:177:27: warning: inline function âgetShortReadMarkerOffsetâ declared but never defined > 177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); > | ^~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:174:20: warning: inline function âsetShortReadMarkerPositionâ declared but never defined > 174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/graph.h:173:26: warning: inline function âgetShortReadMarkerPositionâ 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 âpopenNoStderrâ: >src/autoOpen.c:28:3: warning: ignoring return value of âdupâ declared with attribute âwarn_unused_resultâ []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 -frecord-gcc-switches" >DISTDIR="/usr/portage/distfiles" >EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k" >ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" >FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" >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 >
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bug 725308
: 641714