Attachment 877124 Details for Bug 919223 – sci-biology:velvet-1.2.10:20231204-073620.log

sci-biology:velvet-1.2.10:20231204-073620.log

sci-biology:velvet-1.2.10:20231204-073620.log (text/plain), 14.28 KB, created by Toralf Förster on 2023-12-04 20:16:01 UTC

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Creator: Toralf Förster

Created: 2023-12-04 20:16:01 UTC

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obsolete

> * 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 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 -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 âscanReferenceSequencesâ:
>src/splayTable.c:877:17: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
>  877 |                 fgets(line, MAXLINE, file);
>      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~
>src/splayTable.c: In function âscanBinaryReferenceSequencesâ:
>src/splayTable.c:933:17: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
>  933 |                 fgets(line, MAXLINE, file);
>      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~
>src/splayTable.c:949:25: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
>  949 |                         fgets(line, MAXLINE, file);
>      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~
>src/splayTable.c: In function âinputSequenceArrayIntoSplayTableAndArchiveâ:
>src/splayTable.c:1207:41: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
> 1207 |                                         fgets(line, MAXLINE, seqFile);
>      |                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>src/splayTable.c:1213:41: warning: ignoring return value of âfgetsâ declared with attribute âwarn_unused_resultâ [-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 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 -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 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 -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 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 -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 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 -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 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 -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 âreadFastXFileâ:
>src/readSet.c:641:21: error: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â [-Wincompatible-pointer-types]
>  641 |         file.gzFile = file.autoFile = NULL;
>      |                     ^
>src/readSet.c: In function âreadFastXPairâ:
>src/readSet.c:680:22: error: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â [-Wincompatible-pointer-types]
>  680 |         file1.gzFile = file1.autoFile = NULL;
>      |                      ^
>src/readSet.c:681:22: error: assignment to âgzFileâ {aka âstruct gzFile_s *â} from incompatible pointer type âAutoFile *â [-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'
>

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Attachments on bug 919223: 877118 | 877119 | 877120 | 877121 | 877122 | 877123 | 877124 | 877125