* Package: sci-biology/velvet-1.2.10:0 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux openmp * FEATURES: network-sandbox preserve-libs sandbox 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=-O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp' 'OPT=-O3 -pipe -march=native -fno-diagnostics-color -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 -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -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 -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -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:877:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 877 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘scanBinaryReferenceSequences’: src/splayTable.c:933:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 933 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:949:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 949 | fgets(line, MAXLINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’: src/splayTable.c:1207:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1207 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/splayTable.c:1213:41: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1213 | fgets(line, MAXLINE, seqFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -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 -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -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 -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -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 -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -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 -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -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 -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o x86_64-pc-linux-gnu-gcc -O3 -pipe -march=native -fno-diagnostics-color -fPIC -fopenmp -fopenmp -O3 -pipe -march=native -fno-diagnostics-color -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: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 641 | file.gzFile = file.autoFile = NULL; | ^ src/readSet.c: In function ‘readFastXPair’: src/readSet.c:680:22: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 680 | file1.gzFile = file1.autoFile = NULL; | ^ src/readSet.c:681:22: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’} from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types] 681 | file2.gzFile = file2.autoFile = NULL; | ^ make: *** [Makefile:110: obj/readSet.o] Error 1 * ERROR: sci-biology/velvet-1.2.10::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/velvet-1.2.10::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/velvet-1.2.10::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:velvet-1.2.10:20231204-073620.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/velvet-1.2.10/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/velvet-1.2.10/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10' * S: '/var/tmp/portage/sci-biology/velvet-1.2.10/work/velvet_1.2.10'