build.log

build2.log (text/plain), 17.23 KB, created by Martin Mokrejš on 2020-09-10 16:48:37 UTC

>>> 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...