>>> Emerging (1 of 1) sci-biology/bcftools-1.10.2::gentoo * bcftools-1.10.2.tar.bz2 BLAKE2B SHA512 size ;-) ... [ ok ] * Using python3.6 to build >>> Unpacking source... >>> Unpacking bcftools-1.10.2.tar.bz2 to /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work >>> Source unpacked in /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work >>> Preparing source in /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work/bcftools-1.10.2 ... * Fixing shebang in misc/guess-ploidy.py. * Fixing shebang in misc/plot-roh.py. >>> Source prepared. >>> Configuring source in /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work/bcftools-1.10.2 ... ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --docdir=/usr/share/doc/bcftools-1.10.2 --htmldir=/usr/share/doc/bcftools-1.10.2/html --libdir=/usr/lib64 --enable-bcftools-plugins --enable-libgsl --enable-perl-filters --with-htslib=system checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... -ldl checking if the compiler accepts -rdynamic... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for gsl/gsl_version.h... yes checking for library containing cblas_dgemm... -lcblas checking for gsl_multifit_gradient in -lgsl... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h configure: License has been changed to GPL. Linking against the GNU scientific library requires that the resulting binary is licensed using the GNU General Public License. In particular, this means you will have to follow the terms of this license in order to distribute binary copies. For more information see the INSTALL file. Text of the GNU General Public License can be found in the LICENSE file, or at http://www.gnu.org/copyleft/gpl.html Information on the GNU Scientific Library, including the rationale for its choice of license can be found at https://www.gnu.org/software/gsl/ >>> Source configured. >>> Compiling source in /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/work/bcftools-1.10.2 ... make -j5 echo '#define BCFTOOLS_VERSION "1.10.2"' > version.h x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfindex.o vcfindex.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o tabix.o tabix.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfstats.o vcfstats.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfisec.o vcfisec.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfmerge.o vcfmerge.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfquery.o vcfquery.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcffilter.o vcffilter.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -fwrapv -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/5.30.3/x86_64-linux/CORE -c -o filter.o filter.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfsom.o vcfsom.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfnorm.o vcfnorm.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfgtcheck.o vcfgtcheck.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfview.o vcfview.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfannotate.o vcfannotate.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfroh.o vcfroh.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfconcat.o vcfconcat.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfcall.o vcfcall.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o mcall.o mcall.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcmp.o vcmp.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o gvcf.o gvcf.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o reheader.o reheader.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o convert.o convert.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfconvert.o vcfconvert.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o tsv2vcf.o tsv2vcf.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfcnv.o vcfcnv.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o HMM.o HMM.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o consensus.o consensus.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o ploidy.o ploidy.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o bin.o bin.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o hclust.o hclust.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o version.o version.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o regidx.o regidx.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o smpl_ilist.o smpl_ilist.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o csq.o csq.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfbuf.o vcfbuf.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o mpileup.o mpileup.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o bam2bcf.o bam2bcf.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o bam2bcf_indel.o bam2bcf_indel.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o bam_sample.o bam_sample.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o vcfsort.o vcfsort.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o cols.o cols.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o ccall.o ccall.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o em.o em.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o prob1.o prob1.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o kmin.o kmin.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o polysomy.o polysomy.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o peakfit.o peakfit.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -DPLUGINPATH='"/usr/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o test/test-rbuf.o test/test-rbuf.c x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -c -o test/test-regidx.o test/test-regidx.c x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/GTisec.so version.c plugins/GTisec.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/GTsubset.so version.c plugins/GTsubset.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/allele-length.so version.c plugins/allele-length.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/contrast.so version.c plugins/contrast.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/counts.so version.c plugins/counts.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/dosage.so version.c plugins/dosage.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -fwrapv -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/lib64/perl5/5.30.3/x86_64-linux/CORE -Wl,-O1 -Wl,--as-needed -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/fill-tags.so version.c plugins/fill-tags.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/fixref.so version.c plugins/fixref.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/frameshifts.so version.c plugins/frameshifts.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/gvcfz.so version.c plugins/gvcfz.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/impute-info.so version.c plugins/impute-info.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/indel-stats.so version.c plugins/indel-stats.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/mendelian.so version.c plugins/mendelian.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/missing2ref.so version.c plugins/missing2ref.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/parental-origin.so version.c plugins/parental-origin.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/prune.so version.c plugins/prune.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/setGT.so version.c plugins/setGT.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/split-vep.so version.c plugins/split-vep.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/split.so version.c plugins/split.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/tag2tag.so version.c plugins/tag2tag.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/trio-dnm.so version.c plugins/trio-dnm.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/trio-stats.so version.c plugins/trio-stats.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -ldl x86_64-pc-linux-gnu-gcc -fPIC -shared -Wall -O2 -pipe -march=native -ftree-vectorize -I. -Wl,-O1 -Wl,--as-needed -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -ldl x86_64-pc-linux-gnu-gcc -Wall -O2 -pipe -march=native -ftree-vectorize -I. -DUSE_GPL -c -o main.o main.c x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o test/test-rbuf test/test-rbuf.o -lz -ldl -ldl x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -ldl -ldl x86_64-pc-linux-gnu-gcc -rdynamic -pthread -Wl,-O1 -Wl,--as-needed -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o ccall.o em.o prob1.o kmin.o polysomy.o peakfit.o vcfplugin.o -lhts -lm -lz -ldl -ldl -lgsl -lcblas -Wl,-E -Wl,-O1 -Wl,--as-needed -L/usr/lib64/perl5/5.30.3/x86_64-linux/CORE -lperl -ldl -lm -lcrypt -lutil -lc >>> Source compiled. >>> Test phase [not enabled]: sci-biology/bcftools-1.10.2 >>> Install sci-biology/bcftools-1.10.2 into /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image make -j5 DESTDIR=/scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image install mkdir -p -m 755 /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image/usr/bin /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image/usr/share/man/man1 /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image/usr/libexec/bcftools install -p bcftools /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image/usr/bin install -p misc/color-chrs.pl misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image/usr/bin install -p -m 644 doc/bcftools.1 /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image/usr/share/man/man1 install -p plugins/*.so /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image/usr/libexec/bcftools >>> Completed installing sci-biology/bcftools-1.10.2 into /scratch/var/tmp/portage/sci-biology/bcftools-1.10.2/image * Final size of build directory: 20708 KiB (20.2 MiB) * Final size of installed tree: 2580 KiB ( 2.5 MiB) >>> Installing (1 of 1) sci-biology/bcftools-1.10.2::gentoo >>> Auto-cleaning packages...