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Gentoo's Bugzilla – Attachment 848084 Details for
Bug 890344
sci-biology/velvet-1.2.10 - Fatal error: cant create obj/readCoherentGraph.o: No such file or directory
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sci-biology:velvet-1.2.10:20230110-054002.log
sci-biology:velvet-1.2.10:20230110-054002.log (text/plain), 3.64 KB, created by
Toralf Förster
on 2023-01-10 13:04:01 UTC
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sci-biology:velvet-1.2.10:20230110-054002.log
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Creator:
Toralf Förster
Created:
2023-01-10 13:04:01 UTC
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3.64 KB
patch
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> * 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 userland_GNU > * 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=-pipe -march=native -fno-diagnostics-color -O2 -fPIC -fopenmp' 'OPT=-pipe -march=native -fno-diagnostics-color -O2 -fPIC -fopenmp' OPENMP=1 -j1 >x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fopenmp -fopenmp -pipe -march=native -fno-diagnostics-color -O2 -fPIC -fopenmp -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o >Assembler messages: >Fatal error: can't create obj/readCoherentGraph.o: No such file or directory >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); > | ^~~~~~~~~~~~~~~~~~~~~~~~~~ >src/readCoherentGraph.c:557:1: fatal error: error writing to -: Broken pipe > 557 | } > | ^ >compilation terminated. >make: *** [Makefile:110: obj/readCoherentGraph.o] Error 1 shuffle=1674694162 > * 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-1.2.10:20230110-054002.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' >
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