Building velvet-1.1.04.txz (origin /buildshare/ports/355755/biology/velvet) for powerpc-10-0 on XXX slot2: created x distfiles/ x distfiles/velvet_1.1.04.tgz x packages/ x packages/gmake-3.82_1.txz x packages/perl5-5.16.3_10.txz x packages/pkg-1.2.7_2.txz x packages/python27-2.7.6_4.txz x packages/gettext-0.18.3.1_1.txz ELF ldconfig path: /lib /usr/lib /usr/lib/compat Make depends ===> velvet-1.1.04 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /buildshare/ports/355755/ports-mgmt/pkg ===> Installing existing package /packages/pkg-1.2.7_2.txz Installing pkg-1.2.7_2... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of velvet-1.1.04 ===> velvet-1.1.04 depends on file: /usr/local/bin/python2.7 - not found ===> Verifying install for /usr/local/bin/python2.7 in /buildshare/ports/355755/lang/python27 ===> Installing existing package /packages/python27-2.7.6_4.txz Installing python27-2.7.6_4...Installing gettext-0.18.3.1_1... done done ==== Note that some of the standard modules are provided as separate ports since they require extra dependencies: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter Install them as needed. ==== ===> Returning to build of velvet-1.1.04 ===> velvet-1.1.04 depends on executable: gmake - not found ===> Verifying install for gmake in /buildshare/ports/355755/devel/gmake ===> Installing existing package /packages/gmake-3.82_1.txz Installing gmake-3.82_1... done ===> Returning to build of velvet-1.1.04 ===> velvet-1.1.04 depends on file: /usr/local/bin/python2.7 - found ===> velvet-1.1.04 depends on file: /usr/local/bin/perl5.16.3 - not found ===> Verifying install for /usr/local/bin/perl5.16.3 in /buildshare/ports/355755/lang/perl5.16 ===> Installing existing package /packages/perl5-5.16.3_10.txz Installing perl5-5.16.3_10... done ===> Returning to build of velvet-1.1.04 Make install ===> velvet-1.1.04 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by velvet-1.1.04 for building ===> Extracting for velvet-1.1.04 => SHA256 Checksum OK for velvet_1.1.04.tgz. ===> Patching for velvet-1.1.04 ===> Applying FreeBSD patches for velvet-1.1.04 /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/shuffleSequences_fasta.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/shuffleSequences_fastq.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/afg_handling/asmbly_splitter.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/afg_handling/snp_view.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/columbus_scripts/enlarge_exons.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/columbus_scripts/gff2fasta.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/columbus_scripts/merge_gtf_exons.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/extractContigReads/extractContigReads.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/fasta2agp/fasta2agp.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/observed-insert-length.pl/observed-insert-length.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/select_paired/select_paired.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/show_repeats/show_repeats.pl /usr/bin/sed -i.bak -e s,#!/usr/bin/perl,/usr/local/bin/perl, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py /usr/bin/sed -i.bak -e s,#!/usr/bin/python,/usr/local/bin/python2.7, /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py ===> velvet-1.1.04 depends on file: /usr/local/bin/python2.7 - found ===> velvet-1.1.04 depends on executable: gmake - found ===> Configuring for velvet-1.1.04 ===> FreeBSD 10 autotools fix applied to /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/third-party/zlib-1.2.3/configure ===> Building for velvet-1.1.04 gmake[1]: Entering directory `/obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04' rm obj/*.o obj/dbg/*.o rm: obj/*.o: No such file or directory rm: obj/dbg/*.o: No such file or directory gmake[1]: [cleanobj] Error 1 (ignored) mkdir -p obj cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o src/splayTable.c: In function 'computeClearHSPs': src/splayTable.c:627: warning: comparison is always true due to limited range of data type src/splayTable.c: In function 'inputSequenceArrayIntoSplayTableAndArchive': src/splayTable.c:1018: warning: format '%ld' expects type 'long int', but argument 2 has type 'time_t' cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o src/graph.c: In function 'importGraph': src/graph.c:2117: warning: comparison is always true due to limited range of data type src/graph.c:2145: warning: comparison is always true due to limited range of data type cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o src/readSet.c: In function 'velvetifySequence': src/readSet.c:189: warning: case label value is less than minimum value for type src/readSet.c: In function 'readFastQFile': src/readSet.c:394: warning: comparison is always true due to limited range of data type src/readSet.c: In function 'readFastQGZFile': src/readSet.c:505: warning: comparison is always true due to limited range of data type src/readSet.c: In function 'readFastAFile': src/readSet.c:663: warning: comparison is always true due to limited range of data type src/readSet.c: In function 'readFastAGZFile': src/readSet.c:736: warning: comparison is always true due to limited range of data type cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o src/graphReConstruction.c: In function 'referenceGraphKmers': src/graphReConstruction.c:504: warning: comparison is always true due to limited range of data type src/graphReConstruction.c:571: warning: comparison is always true due to limited range of data type src/graphReConstruction.c: In function 'fillUpGraph': src/graphReConstruction.c:1132: warning: format '%ld' expects type 'long int', but argument 2 has type 'time_t' src/graphReConstruction.c:1171: warning: format '%ld' expects type 'long int', but argument 2 has type 'time_t' cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o src/preGraphConstruction.c: In function 'createPreNodes': src/preGraphConstruction.c:441: warning: comparison is always false due to limited range of data type cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o src/scaffold.c: In function 'computeNodeToNodeMappings': src/scaffold.c:1642: warning: format '%ld' expects type 'long int', but argument 2 has type 'time_t' cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o cc -O2 -pipe -fno-strict-aliasing -Wall -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o cc -O2 -pipe -fno-strict-aliasing -Wall -lm -lz -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o cc -O2 -pipe -fno-strict-aliasing -Wall -lm -lz -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o gmake[1]: Leaving directory `/obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04' ===> Installing for velvet-1.1.04 ===> velvet-1.1.04 depends on file: /usr/local/bin/python2.7 - found ===> velvet-1.1.04 depends on file: /usr/local/bin/perl5.16.3 - found ===> Generating temporary packing list ===> Checking if biology/velvet already installed install -s -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/velvetg /usr/local/bin install -s -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/velveth /usr/local/bin install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/shuffleSequences_fasta.pl /usr/local/bin/shuffleSequences_fasta.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/shuffleSequences_fastq.pl /usr/local/bin/shuffleSequences_fastq.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/VelvetOptimiser-2.1.7/VelvetOptimiser.pl /usr/local/bin/VelvetOptimiser.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/afg_handling/asmbly_splitter.pl /usr/local/bin/asmbly_splitter.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/afg_handling/snp_view.pl /usr/local/bin/snp_view.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/columbus_scripts/enlarge_exons.pl /usr/local/bin/enlarge_exons.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/columbus_scripts/gff2fasta.pl /usr/local/bin/gff2fasta.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/columbus_scripts/merge_gtf_exons.pl /usr/local/bin/merge_gtf_exons.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/estimate-exp_cov/velvet-estimate-exp_cov.pl /usr/local/bin/velvet-estimate-exp_cov.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/extractContigReads/extractContigReads.pl /usr/local/bin/extractContigReads.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/fasta2agp/fasta2agp.pl /usr/local/bin/fasta2agp.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/observed-insert-length.pl/observed-insert-length.pl /usr/local/bin/observed-insert-length.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/select_paired/select_paired.pl /usr/local/bin/select_paired.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/show_repeats/show_repeats.pl /usr/local/bin/show_repeats.pl install -o root -g wheel -m 555 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/AssemblyAssembler1.3/AssemblyAssembler1.3.py /usr/local/bin/AssemblyAssembler1.3.py /bin/mkdir -p /usr/local/lib/perl5/site_perl/5.16/VelvetOpt install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/VelvetOptimiser-2.1.7/VelvetOpt/Assembly.pm /usr/local/lib/perl5/site_perl/5.16/VelvetOpt/Assembly.pm install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/VelvetOptimiser-2.1.7/VelvetOpt/Utils.pm /usr/local/lib/perl5/site_perl/5.16/VelvetOpt/Utils.pm install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/VelvetOptimiser-2.1.7/VelvetOpt/gwrap.pm /usr/local/lib/perl5/site_perl/5.16/VelvetOpt/gwrap.pm install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/contrib/VelvetOptimiser-2.1.7/VelvetOpt/hwrap.pm /usr/local/lib/perl5/site_perl/5.16/VelvetOpt/hwrap.pm /bin/mkdir -p /usr/local/share/doc/velvet install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/ChangeLog /usr/local/share/doc/velvet install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/Manual.pdf /usr/local/share/doc/velvet install -o root -g wheel -m 444 /obj/buildshare/ports/355755/biology/velvet/work/velvet_1.1.04/Columbus_manual.pdf /usr/local/share/doc/velvet ===> Registering installation for velvet-1.1.04 Installing velvet-1.1.04... done Make package ===> Building package for velvet-1.1.04 Creating package for velvet-1.1.04 slot2: removed