Build log

velvet-0.7.42:20090715-002427.log (text/plain), 18.84 KB, created by Diego Elio Pettenò (RETIRED) on 2009-07-15 13:40:32 UTC

>>> Unpacking source...
>>> Unpacking velvet_0.7.42.tgz to /var/tmp/portage/sci-biology/velvet-0.7.42/work
>>> Source unpacked in /var/tmp/portage/sci-biology/velvet-0.7.42/work
>>> Preparing source in /var/tmp/portage/sci-biology/velvet-0.7.42/work/velvet_0.7.42 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/velvet-0.7.42/work/velvet_0.7.42 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/velvet-0.7.42/work/velvet_0.7.42 ...
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)
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o 
src/tightString.c: In function 'exportTightString':
src/tightString.c:511: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o 
src/splay.c: In function 'displaySplayTreeMemory':
src/splay.c:422: warning: format '%li' expects type 'long int', but argument 2 has type 'size_t'
src/splay.c:422: warning: format '%li' expects type 'long int', but argument 3 has type 'size_t'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o 
src/splayTable.c: In function 'inputSequenceIntoSplayTable':
src/splayTable.c:156: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/splayTable.c:156: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/splayTable.c:156: warning: format '%ld' expects type 'long int', but argument 6 has type 'Coordinate'
src/splayTable.c:190: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/splayTable.c:190: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/splayTable.c:190: warning: format '%ld' expects type 'long int', but argument 6 has type 'Coordinate'
src/splayTable.c:206: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/splayTable.c:206: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/splayTable.c:206: warning: format '%ld' expects type 'long int', but argument 6 has type 'Coordinate'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o 
src/graph.c: In function 'exportNode':
src/graph.c:1780: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graph.c:1780: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graph.c: In function 'exportGraph':
src/graph.c:2141: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graph.c: In function 'importGraph':
src/graph.c:2196: warning: format '%ld' expects type 'long int *', but argument 3 has type 'Coordinate *'
src/graph.c:2199: warning: format '%ld' expects type 'long int *', but argument 3 has type 'Coordinate *'
src/graph.c:2292: warning: format '%ld' expects type 'long int *', but argument 4 has type 'Coordinate *'
src/graph.c:2292: warning: format '%ld' expects type 'long int *', but argument 5 has type 'Coordinate *'
src/graph.c:2292: warning: format '%ld' expects type 'long int *', but argument 6 has type 'Coordinate *'
src/graph.c:2292: warning: format '%ld' expects type 'long int *', but argument 7 has type 'Coordinate *'
src/graph.c:2328: warning: format '%ld' expects type 'long int *', but argument 4 has type 'Coordinate *'
src/graph.c: In function 'displayArcMemory':
src/graph.c:3631: warning: format '%ld' expects type 'long int', but argument 2 has type 'size_t'
src/graph.c:3631: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
src/graph.c: In function 'displayNodeMemory':
src/graph.c:3638: warning: format '%ld' expects type 'long int', but argument 2 has type 'size_t'
src/graph.c:3638: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o 
src/run2.c: In function 'main':
src/run2.c:144: warning: format '%li' expects type 'long int *', but argument 3 has type 'Coordinate *'
src/run2.c:147: warning: format '%li' expects type 'long int', but argument 2 has type 'Coordinate'
src/run2.c:151: warning: format '%li' expects type 'long int *', but argument 3 has type 'Coordinate *'
src/run2.c:154: warning: format '%li' expects type 'long int', but argument 2 has type 'Coordinate'
src/run2.c:165: warning: format '%li' expects type 'long int *', but argument 3 has type 'Coordinate *'
src/run2.c:168: warning: format '%li' expects type 'long int', but argument 2 has type 'Coordinate'
src/run2.c:178: warning: format '%li' expects type 'long int *', but argument 3 has type 'Coordinate *'
src/run2.c:181: warning: format '%li' expects type 'long int', but argument 2 has type 'Coordinate'
src/run2.c:185: warning: format '%li' expects type 'long int *', but argument 3 has type 'Coordinate *'
src/run2.c:187: warning: format '%li' expects type 'long int *', but argument 3 has type 'Coordinate *'
src/run2.c:198: warning: format '%li' expects type 'long int *', but argument 3 has type 'Coordinate *'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o 
src/passageMarker.c: In function 'readPassageMarker':
src/passageMarker.c:239: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/passageMarker.c:239: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/passageMarker.c: In function 'isInitial':
src/passageMarker.c:479: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/passageMarker.c: In function 'newPassageMarker':
src/passageMarker.c:606: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/passageMarker.c:606: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/passageMarker.c:606: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/passageMarker.c: In function 'exportMarker':
src/passageMarker.c:637: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/passageMarker.c:637: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/passageMarker.c:637: warning: format '%ld' expects type 'long int', but argument 6 has type 'Coordinate'
src/passageMarker.c:637: warning: format '%ld' expects type 'long int', but argument 7 has type 'Coordinate'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o 
src/graphStats.c: In function 'surveyPath':
src/graphStats.c:54: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:54: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c: In function 'nodeStatistics':
src/graphStats.c:320: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c: In function 'isSNP':
src/graphStats.c:449: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
src/graphStats.c: In function 'displayGeneralStatistics':
src/graphStats.c:831: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c: In function 'displayStrainOnlySequences':
src/graphStats.c:949: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c: In function 'displayLocalBreakpoint':
src/graphStats.c:1020: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
src/graphStats.c:1020: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:1065: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
src/graphStats.c:1065: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:1082: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:1082: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c:1082: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/graphStats.c:1090: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:1090: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c:1090: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/graphStats.c: In function 'exportLongNodeSequences':
src/graphStats.c:1314: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c: In function 'destroyDisconnectedElements':
src/graphStats.c:1704: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
src/graphStats.c: In function 'measureTangleSizes':
src/graphStats.c:1768: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
src/graphStats.c: In function 'contigStats':
src/graphStats.c:1894: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
src/graphStats.c:1911: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
src/graphStats.c:1911: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c: In function 'exportAMOSLib':
src/graphStats.c:2105: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:2106: warning: format '%ld' expects type 'long int', but argument 3 has type 'long long int'
src/graphStats.c: In function 'exportAMOSMarker':
src/graphStats.c:2148: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:2151: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:2151: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c: In function 'exportAMOSShortMarker':
src/graphStats.c:2173: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:2174: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c: In function 'exportAMOSReverseShortMarker':
src/graphStats.c:2201: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:2202: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c: In function 'exportAMOSNode':
src/graphStats.c:2308: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:2310: warning: format '%ld' expects type 'long int', but argument 3 has type 'long long int'
src/graphStats.c:2317: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c:2318: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/graphStats.c: In function 'logFinalStats':
src/graphStats.c:2643: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/graphStats.c:2643: warning: format '%ld' expects type 'long int', but argument 5 has type 'Coordinate'
src/graphStats.c:2643: warning: format '%ld' expects type 'long int', but argument 6 has type 'Coordinate'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o 
src/readSet.c: In function 'readFastQFile':
src/readSet.c:523: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
src/readSet.c:534: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
src/readSet.c:535: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
src/readSet.c: In function 'exportRead':
src/readSet.c:913: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o 
src/shortReadPairs.c: In function 'printConnections':
src/shortReadPairs.c:1938: warning: format '%ld' expects type 'long int', but argument 6 has type 'Coordinate'
src/shortReadPairs.c:1938: warning: format '%ld' expects type 'long int', but argument 7 has type 'Coordinate'
src/shortReadPairs.c:1938: warning: format '%ld' expects type 'long int', but argument 8 has type 'Coordinate'
src/shortReadPairs.c:1952: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
src/shortReadPairs.c:1952: warning: format '%ld' expects type 'long int', but argument 3 has type 'Coordinate'
src/shortReadPairs.c:1952: warning: format '%ld' expects type 'long int', but argument 4 has type 'Coordinate'
src/shortReadPairs.c:1956: warning: format '%ld' expects type 'long int', but argument 2 has type 'Coordinate'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o 
src/graphReConstruction.c: In function 'referenceGraphKmers':
src/graphReConstruction.c:202: warning: format '%li' expects type 'long int', but argument 2 has type 'Coordinate'
src/graphReConstruction.c: In function 'ghostThreadSequenceThroughGraph':
src/graphReConstruction.c:386: warning: format '%li' expects type 'long int', but argument 2 has type 'Coordinate'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o 
src/roadMap.c: In function 'importRoadMapArray':
src/roadMap.c:137: warning: format '%ld' expects type 'long int *', but argument 4 has type 'Coordinate *'
src/roadMap.c:137: warning: format '%ld' expects type 'long int *', but argument 5 has type 'Coordinate *'
src/roadMap.c:137: warning: format '%ld' expects type 'long int *', but argument 6 has type 'Coordinate *'
src/roadMap.c:113: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
src/roadMap.c:130: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o 
src/preGraph.c: In function 'displayPreArcMemory_pg':
src/preGraph.c:1105: warning: format '%ld' expects type 'long int', but argument 2 has type 'size_t'
src/preGraph.c:1105: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
src/preGraphConstruction.c: In function 'createPreNodes':
src/preGraphConstruction.c:336: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
src/preGraphConstruction.c:347: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
src/preGraphConstruction.c:392: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
src/preGraphConstruction.c:498: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/crc.c -o obj/crc.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o 
gcc -O2 -pipe -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o 
src/kmer.c: In function 'printKmer':
src/kmer.c:280: warning: format '%lx' expects type 'long unsigned int', but argument 2 has type 'uint64_t'
src/kmer.c: In function 'testKmers':
src/kmer.c:294: warning: format '%lx' expects type 'long unsigned int', but argument 5 has type 'long long unsigned int'
src/kmer.c:295: warning: format '%lx' expects type 'long unsigned int', but argument 5 has type 'uint64_t'
gcc -O2 -pipe -Wall -O3 -Wl,-O1 -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/readSet.o: In function `convertConfidenceScores':
readSet.c:(.text+0x1732): undefined reference to `pow'
readSet.c:(.text+0x176e): undefined reference to `pow'
obj/readSet.o: In function `readMAQGZFile':
readSet.c:(.text+0x1bd5): undefined reference to `gzopen'
readSet.c:(.text+0x1c4c): undefined reference to `gzgets'
readSet.c:(.text+0x1edc): undefined reference to `gzclose'
obj/readSet.o: In function `readFastAGZFile':
readSet.c:(.text+0x1f95): undefined reference to `gzopen'
readSet.c:(.text+0x200c): undefined reference to `gzgets'
readSet.c:(.text+0x2259): undefined reference to `gzclose'
obj/readSet.o: In function `readFastQGZFile':
readSet.c:(.text+0x2315): undefined reference to `gzopen'
readSet.c:(.text+0x237e): undefined reference to `gzgets'
readSet.c:(.text+0x243e): undefined reference to `gzgets'
readSet.c:(.text+0x2564): undefined reference to `gzgets'
readSet.c:(.text+0x257e): undefined reference to `gzgets'
readSet.c:(.text+0x26a6): undefined reference to `gzclose'
collect2: ld returned 1 exit status
make: *** [velveth] Error 1
 [31;01m*[0m 
 [31;01m*[0m ERROR: sci-biology/velvet-0.7.42 failed.
 [31;01m*[0m Call stack:
 [31;01m*[0m               ebuild.sh, line   49:  Called src_compile
 [31;01m*[0m             environment, line  296:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       emake -j1 || die;
 [31;01m*[0m  The die message:
 [31;01m*[0m   (no error message)
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the topmost build error, and the call stack if relevant.
 [31;01m*[0m A complete build log is located at '/var/log/portage/sci-biology/velvet-0.7.42:20090715-002427.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/velvet-0.7.42/temp/environment'.
 [31;01m*[0m