printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild vcftools 2>&1 The package 'vcftools' will be built without being installed. Reading build dependency for vcftools-0.1.12a-1... Reading dependency for vcftools-0.1.12a-1... Reading build conflict for vcftools-0.1.12a-1... The following package will be rebuilt: vcftools curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/vcftools_0.1.12a.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 30 606k 30 182k 0 0 209k 0 0:00:02 --:--:-- 0:00:02 209k 100 606k 100 606k 0 0 357k 0 0:00:01 0:00:01 --:--:-- 358k Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-vcftools-0.1.12a-1 /sw/build.build dpkg-deb: building package `fink-buildlock-vcftools-0.1.12a-1' in `/sw/build.build/fink-buildlock-vcftools-0.1.12a-1_2014.07.29-14.31.37_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-vcftools-0.1.12a-1_2014.07.29-14.31.37_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-vcftools-0.1.12a-1. (Reading database ... 4296 files and directories currently installed.) Unpacking fink-buildlock-vcftools-0.1.12a-1 (from .../fink-buildlock-vcftools-0.1.12a-1_2014.07.29-14.31.37_darwin-x86_64.deb) ... Setting up fink-buildlock-vcftools-0.1.12a-1 (2014.07.29-14.31.37) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.8SPsA env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/vcftools_0.1.12a.tar.gz vcftools_0.1.12a/ vcftools_0.1.12a/cpp/ vcftools_0.1.12a/cpp/variant_file_output.cpp vcftools_0.1.12a/cpp/entry_filters.cpp vcftools_0.1.12a/cpp/dgeev.h vcftools_0.1.12a/cpp/header.h vcftools_0.1.12a/cpp/variant_file.h vcftools_0.1.12a/cpp/khash.h vcftools_0.1.12a/cpp/variant_file_diff.cpp vcftools_0.1.12a/cpp/vcf_file.h vcftools_0.1.12a/cpp/bgzf.h vcftools_0.1.12a/cpp/Makefile vcftools_0.1.12a/cpp/bcf_entry_setters.cpp vcftools_0.1.12a/cpp/vcftools.h vcftools_0.1.12a/cpp/variant_file_format_convert.cpp vcftools_0.1.12a/cpp/bcf_entry.cpp vcftools_0.1.12a/cpp/parameters.cpp vcftools_0.1.12a/cpp/output_log.h vcftools_0.1.12a/cpp/gamma.h vcftools_0.1.12a/cpp/bcf_file.cpp vcftools_0.1.12a/cpp/gamma.cpp vcftools_0.1.12a/cpp/entry.cpp vcftools_0.1.12a/cpp/vcf_file.cpp vcftools_0.1.12a/cpp/bcf_file.h vcftools_0.1.12a/cpp/entry_getters.cpp vcftools_0.1.12a/cpp/knetfile.c vcftools_0.1.12a/cpp/knetfile.h vcftools_0.1.12a/cpp/variant_file_filters.cpp vcftools_0.1.12a/cpp/output_log.cpp vcftools_0.1.12a/cpp/vcf_entry_setters.cpp vcftools_0.1.12a/cpp/header.cpp vcftools_0.1.12a/cpp/dgeev.cpp vcftools_0.1.12a/cpp/entry.h vcftools_0.1.12a/cpp/variant_file.cpp vcftools_0.1.12a/cpp/parameters.h vcftools_0.1.12a/cpp/vcf_entry.cpp vcftools_0.1.12a/cpp/entry_setters.cpp vcftools_0.1.12a/cpp/vcf_entry.h vcftools_0.1.12a/cpp/vcftools.1.gz vcftools_0.1.12a/cpp/bgzf.c vcftools_0.1.12a/cpp/bcf_entry.h vcftools_0.1.12a/cpp/vcftools.cpp vcftools_0.1.12a/Makefile vcftools_0.1.12a/README.txt vcftools_0.1.12a/website/ vcftools_0.1.12a/website/README vcftools_0.1.12a/website/vcf_poster_051513.pdf vcftools_0.1.12a/website/img/ vcftools_0.1.12a/website/img/top_bg_blue.png vcftools_0.1.12a/website/img/bullet.gif vcftools_0.1.12a/website/Makefile vcftools_0.1.12a/website/VCF-poster.pdf vcftools_0.1.12a/website/bcf.pdf vcftools_0.1.12a/website/src/ vcftools_0.1.12a/website/src/specs.inc vcftools_0.1.12a/website/src/perl_module.inc vcftools_0.1.12a/website/src/license.inc vcftools_0.1.12a/website/src/index.php vcftools_0.1.12a/website/src/links.inc vcftools_0.1.12a/website/src/examples.inc vcftools_0.1.12a/website/src/documentation.inc vcftools_0.1.12a/website/src/man_latest.inc vcftools_0.1.12a/website/src/perl_examples.inc vcftools_0.1.12a/website/src/htslib.inc vcftools_0.1.12a/website/src/index.inc vcftools_0.1.12a/website/src/downloads.inc vcftools_0.1.12a/website/favicon.ico vcftools_0.1.12a/website/favicon.png vcftools_0.1.12a/website/style.css vcftools_0.1.12a/examples/ vcftools_0.1.12a/examples/consensus.out2 vcftools_0.1.12a/examples/concat-b.vcf vcftools_0.1.12a/examples/merge-test-a.vcf vcftools_0.1.12a/examples/consensus.out vcftools_0.1.12a/examples/cmp-test-a-3.3.vcf vcftools_0.1.12a/examples/indel-stats.vcf vcftools_0.1.12a/examples/subset.indels.out vcftools_0.1.12a/examples/fix-ploidy.vcf vcftools_0.1.12a/examples/valid-4.1.vcf vcftools_0.1.12a/examples/subset.SNPs.out vcftools_0.1.12a/examples/consensus.fa vcftools_0.1.12a/examples/fix-ploidy.samples vcftools_0.1.12a/examples/parse-test.vcf vcftools_0.1.12a/examples/annotate-test.vcf vcftools_0.1.12a/examples/concat-a.vcf vcftools_0.1.12a/examples/query-test.out vcftools_0.1.12a/examples/filters.txt vcftools_0.1.12a/examples/cmp-test.out vcftools_0.1.12a/examples/contrast.out vcftools_0.1.12a/examples/concat-c.vcf vcftools_0.1.12a/examples/fix-ploidy.txt vcftools_0.1.12a/examples/contrast.vcf vcftools_0.1.12a/examples/shuffle-test.vcf vcftools_0.1.12a/examples/merge-test.vcf.out vcftools_0.1.12a/examples/fill-an-ac.out vcftools_0.1.12a/examples/invalid-4.0.vcf vcftools_0.1.12a/examples/annotate3.out vcftools_0.1.12a/examples/cmp-test-b-3.3.vcf vcftools_0.1.12a/examples/concat.out vcftools_0.1.12a/examples/valid-4.0.vcf.stats vcftools_0.1.12a/examples/annotate.out vcftools_0.1.12a/examples/fix-ploidy.out vcftools_0.1.12a/examples/isec-n2-test.vcf.out vcftools_0.1.12a/examples/perl-api-1.pl vcftools_0.1.12a/examples/merge-test-c.vcf vcftools_0.1.12a/examples/merge-test-b.vcf vcftools_0.1.12a/examples/annotate.txt vcftools_0.1.12a/examples/subset.vcf vcftools_0.1.12a/examples/valid-4.0.vcf vcftools_0.1.12a/examples/consensus.vcf vcftools_0.1.12a/examples/valid-3.3.vcf vcftools_0.1.12a/examples/indel-stats.out vcftools_0.1.12a/examples/annotate2.out vcftools_0.1.12a/examples/cmp-test-a.vcf vcftools_0.1.12a/examples/cmp-test-b.vcf vcftools_0.1.12a/examples/floats.vcf vcftools_0.1.12a/examples/indel-stats.tab vcftools_0.1.12a/perl/ vcftools_0.1.12a/perl/vcf-concat vcftools_0.1.12a/perl/test.t vcftools_0.1.12a/perl/fill-fs vcftools_0.1.12a/perl/vcf-query vcftools_0.1.12a/perl/vcf-annotate vcftools_0.1.12a/perl/vcf-convert vcftools_0.1.12a/perl/tab-to-vcf vcftools_0.1.12a/perl/VcfStats.pm vcftools_0.1.12a/perl/vcf-validator vcftools_0.1.12a/perl/ChangeLog vcftools_0.1.12a/perl/vcf-stats vcftools_0.1.12a/perl/Makefile vcftools_0.1.12a/perl/fill-aa vcftools_0.1.12a/perl/Vcf.pm vcftools_0.1.12a/perl/vcf-merge vcftools_0.1.12a/perl/fill-ref-md5 vcftools_0.1.12a/perl/FaSlice.pm vcftools_0.1.12a/perl/vcf-shuffle-cols vcftools_0.1.12a/perl/vcf-contrast vcftools_0.1.12a/perl/vcf-fix-ploidy vcftools_0.1.12a/perl/vcf-consensus vcftools_0.1.12a/perl/vcf-fix-newlines vcftools_0.1.12a/perl/vcf-sort vcftools_0.1.12a/perl/vcf-compare vcftools_0.1.12a/perl/vcf-tstv vcftools_0.1.12a/perl/vcf-indel-stats vcftools_0.1.12a/perl/vcf-to-tab vcftools_0.1.12a/perl/fill-an-ac vcftools_0.1.12a/perl/vcf-isec vcftools_0.1.12a/perl/vcf-phased-join vcftools_0.1.12a/perl/vcf-subset sudo -u fink-bld [ENV] sh -c /tmp/fink.9vsUY [ -r /sw/fink/dists/stable/main/finkinfo/sci/vcftools.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.szGxN patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/vcftools.patch patching file Makefile patching file cpp/Makefile patching file perl/Makefile sudo -u fink-bld [ENV] sh -c /tmp/fink.iU_55 make CPP=clang++ PREFIX=/sw for dir in cpp perl; do cd $dir && /Applications/Xcode.app/Contents/Developer/usr/bin/make && cd ..; done clang++ -c -O2 -D_FILE_OFFSET_BITS=64 vcftools.cpp -o vcftools.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 bcf_file.cpp -o bcf_file.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 vcf_file.cpp -o vcf_file.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file.cpp -o variant_file.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 header.cpp -o header.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 bcf_entry.cpp -o bcf_entry.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 vcf_entry.cpp -o vcf_entry.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 entry.cpp -o entry.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file.cpp > variant_file.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcftools.cpp > vcftools.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 entry.cpp > entry.d clang++ -c -O2 -D_FILE_OFFSET_BITS=64 entry_getters.cpp -o entry_getters.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 entry_setters.cpp -o entry_setters.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 vcf_entry_setters.cpp -o vcf_entry_setters.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 header.cpp > header.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcf_file.cpp > vcf_file.d clang++ -c -O2 -D_FILE_OFFSET_BITS=64 bcf_entry_setters.cpp -o bcf_entry_setters.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 entry_filters.cpp -o entry_filters.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 bcf_file.cpp > bcf_file.d clang++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_filters.cpp -o variant_file_filters.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 bcf_entry.cpp > bcf_entry.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcf_entry.cpp > vcf_entry.d clang++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_output.cpp -o variant_file_output.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 entry_setters.cpp > entry_setters.d clang++ -c -O2 -D_FILE_OFFSET_BITS=64 parameters.cpp -o parameters.o clang++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_format_convert.cpp -o variant_file_format_convert.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 entry_getters.cpp > entry_getters.d clang++ -c -O2 -D_FILE_OFFSET_BITS=64 variant_file_diff.cpp -o variant_file_diff.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 vcf_entry_setters.cpp > vcf_entry_setters.d clang++ -c -O2 -D_FILE_OFFSET_BITS=64 output_log.cpp -o output_log.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_filters.cpp > variant_file_filters.d gcc -O2 -m64 -O2 -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 bcf_entry_setters.cpp > bcf_entry_setters.d clang++ -c -O2 -D_FILE_OFFSET_BITS=64 gamma.cpp -o gamma.o clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 entry_filters.cpp > entry_filters.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 gamma.cpp > gamma.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 output_log.cpp > output_log.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 parameters.cpp > parameters.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_format_convert.cpp > variant_file_format_convert.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_diff.cpp > variant_file_diff.d clang++ -MM -O2 -D_FILE_OFFSET_BITS=64 variant_file_output.cpp > variant_file_output.d clang++ -O2 -D_FILE_OFFSET_BITS=64 vcftools.o bcf_file.o vcf_file.o variant_file.o header.o bcf_entry.o vcf_entry.o entry.o entry_getters.o entry_setters.o vcf_entry_setters.o bcf_entry_setters.o entry_filters.o variant_file_filters.o variant_file_output.o parameters.o variant_file_format_convert.o variant_file_diff.o output_log.o bgzf.o gamma.o -o vcftools -lz make[1]: Nothing to be done for `vcftools'. /bin/rm -rf /sw/build.build/root-vcftools-0.1.12a-1 /bin/mkdir -p /sw/build.build/root-vcftools-0.1.12a-1/sw /bin/mkdir -p /sw/build.build/root-vcftools-0.1.12a-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-vcftools-0.1.12a-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.OXOyh /tmp/fink.4FgZW #!/bin/sh -ev make install PREFIX=/sw DESTDIR=/sw/build.build/root-vcftools-0.1.12a-1 mkdir -p /sw/build.build/root-vcftools-0.1.12a-1/sw/bin; mkdir -p /sw/build.build/root-vcftools-0.1.12a-1/sw/lib/perl5; mkdir -p /sw/build.build/root-vcftools-0.1.12a-1/sw/share/man1; \ cp cpp/vcftools.1.gz /sw/build.build/root-vcftools-0.1.12a-1/sw/share/man1; \ for dir in cpp perl; do cd $dir && /Applications/Xcode.app/Contents/Developer/usr/bin/make install && cd ..; done cp /sw/build.build/vcftools-0.1.12a-1/vcftools_0.1.12a/cpp/vcftools /sw/build.build/root-vcftools-0.1.12a-1/sw/bin/vcftools mkdir -p /sw/build.build/root-vcftools-0.1.12a-1/sw/share/vcftools/examples cp -p examples/* /sw/build.build/root-vcftools-0.1.12a-1/sw/share/vcftools/examples chmod 755 /sw/build.build/root-vcftools-0.1.12a-1/sw/bin/* sudo -u fink-bld [ENV] sh -c /tmp/fink.9jWaw /usr/bin/install -d -m 700 /sw/build.build/root-vcftools-0.1.12a-1/sw/share/doc/vcftools /bin/cp -r README.txt /sw/build.build/root-vcftools-0.1.12a-1/sw/share/doc/vcftools/ /bin/chmod -R go=u-w /sw/build.build/root-vcftools-0.1.12a-1/sw/share/doc/vcftools /bin/rm -f /sw/build.build/root-vcftools-0.1.12a-1/sw/info/dir /sw/build.build/root-vcftools-0.1.12a-1/sw/info/dir.old /sw/build.build/root-vcftools-0.1.12a-1/sw/share/info/dir /sw/build.build/root-vcftools-0.1.12a-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-vcftools-0.1.12a-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `vcftools' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/vcftools_0.1.12a-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-vcftools-0.1.12a-1 (Reading database ... 4297 files and directories currently installed.) Removing fink-buildlock-vcftools-0.1.12a-1 ...