* Package: sci-biology/velvet-1.2.10 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: 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 recommendes using -O3 in CFLAGS * To adjust the MAXKMERLENGTH or CATEGORIES parameters as described in the manual, * please set the variables VELVET_MAXKMERLENGTH or VELVET_CATEGORIES in your * environment or /etc/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 -j1 -j1 CC=x86_64-pc-linux-gnu-gcc 'CFLAGS=-march=native -O2 -pipe -fPIC -fopenmp' 'OPT=-march=native -O2 -pipe -fPIC -fopenmp' 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 -march=native -O2 -pipe -fPIC -fopenmp -march=native -O2 -pipe -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -fPIC -fopenmp -march=native -O2 -pipe -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o In file included from src/run.h:34:0, from src/run.c:31: src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’ declared but never defined extern inline void setShortReadMarkerOffset(ShortReadMarker * marker, ^ src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’ declared but never defined extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker); ^ src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’ declared but never defined extern inline void setShortReadMarkerPosition(ShortReadMarker * marker, ^ src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’ declared but never defined extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker); ^ x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -fPIC -fopenmp -march=native -O2 -pipe -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o src/splay.c:25:17: fatal error: omp.h: No such file or directory compilation terminated. make: *** [Makefile:110: obj/splay.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-1.2.10:20160815-014831.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'