Build log

velvet-1.0.18:20110413-102018.log (text/plain), 7.82 KB, created by Diego Elio Pettenò (RETIRED) on 2011-04-13 12:14:25 UTC

 * Package:    sci-biology/velvet-1.0.18
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        elibc_glibc kernel_linux test userland_GNU x86
 * FEATURES:   sandbox test userpriv usersandbox
>>> Unpacking source...
>>> Unpacking velvet_1.0.18.tgz to /var/tmp/portage/sci-biology/velvet-1.0.18/work
>>> Source unpacked in /var/tmp/portage/sci-biology/velvet-1.0.18/work
>>> Preparing source in /var/tmp/portage/sci-biology/velvet-1.0.18/work/velvet_1.0.18 ...
 * Applying velvet-1.0.18-gentoo.diff ...
 [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/velvet-1.0.18/work/velvet_1.0.18 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/velvet-1.0.18/work/velvet_1.0.18 ...
make -j14 -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: [cleanobj] Error 1 (ignored)
echo "unbundled zlib"
unbundled zlib
mkdir -p obj
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o 
src/run.c: In function ‘main’:
src/run.c:195:10: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/crc.c -o obj/crc.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o 
i686-pc-linux-gnu-gcc -O2 -pipe -O3  -Wl,-O1 -Wl,--hash-style=gnu -lm -lz -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o 
obj/readSet.o: In function `readFastAGZFile':
readSet.c:(.text+0x170): undefined reference to `gzdopen'
readSet.c:(.text+0x19c): undefined reference to `gzgetc'
readSet.c:(.text+0x1c4): undefined reference to `gzungetc'
readSet.c:(.text+0x1ec): undefined reference to `gzgets'
readSet.c:(.text+0x430): undefined reference to `gzclose'
readSet.c:(.text+0x46b): undefined reference to `gzopen'
obj/readSet.o: In function `readFastQGZFile':
readSet.c:(.text+0xf6c): undefined reference to `gzdopen'
readSet.c:(.text+0xf98): undefined reference to `gzgetc'
readSet.c:(.text+0xfb7): undefined reference to `gzungetc'
readSet.c:(.text+0xfec): undefined reference to `gzgets'
readSet.c:(.text+0x10a3): undefined reference to `gzgets'
readSet.c:(.text+0x110f): undefined reference to `gzgets'
readSet.c:(.text+0x1127): undefined reference to `gzgets'
readSet.c:(.text+0x118e): undefined reference to `gzclose'
readSet.c:(.text+0x11c9): undefined reference to `gzopen'
obj/readSet.o: In function `readRawGZFile':
readSet.c:(.text+0x1265): undefined reference to `gzdopen'
readSet.c:(.text+0x12ac): undefined reference to `gzgets'
readSet.c:(.text+0x13e8): undefined reference to `gzclose'
readSet.c:(.text+0x1424): undefined reference to `gzopen'
obj/readSet.o: In function `readMAQGZFile':
readSet.c:(.text+0x14c0): undefined reference to `gzdopen'
readSet.c:(.text+0x1523): undefined reference to `gzgets'
readSet.c:(.text+0x1651): undefined reference to `gzclose'
readSet.c:(.text+0x168c): undefined reference to `gzopen'
obj/readSet.o: In function `readBAMFile':
readSet.c:(.text+0x2114): undefined reference to `gzdopen'
readSet.c:(.text+0x214c): undefined reference to `gzread'
readSet.c:(.text+0x2188): undefined reference to `gzread'
readSet.c:(.text+0x21d8): undefined reference to `gzseek'
readSet.c:(.text+0x21f9): undefined reference to `gzread'
readSet.c:(.text+0x2280): undefined reference to `gzread'
readSet.c:(.text+0x22c0): undefined reference to `gzread'
readSet.c:(.text+0x23dc): undefined reference to `gzread'
readSet.c:(.text+0x2427): undefined reference to `gzread'
readSet.c:(.text+0x2c8b): undefined reference to `gzclose'
readSet.c:(.text+0x2ce3): undefined reference to `gzopen'
obj/readSet.o: In function `convertConfidenceScores':
readSet.c:(.text+0x3b4f): undefined reference to `pow'
readSet.c:(.text+0x3b93): undefined reference to `pow'
collect2: ld returned 1 exit status
make: *** [velveth] Error 1
emake failed
 * ERROR: sci-biology/velvet-1.0.18 failed (compile phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  56:  Called src_compile
 *   environment, line 2630:  Called die
 * The specific snippet of code:
 *       emake -j1 $MAKE_XOPTS || die;
 * 
 * If you need support, post the output of 'emerge --info =sci-biology/velvet-1.0.18',
 * the complete build log and the output of 'emerge -pqv =sci-biology/velvet-1.0.18'.
 * The complete build log is located at '/var/log/portage/build/sci-biology/velvet-1.0.18:20110413-102018.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/velvet-1.0.18/temp/environment'.
 * S: '/var/tmp/portage/sci-biology/velvet-1.0.18/work/velvet_1.0.18'