------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.53.txz ===== Message from ca_root_nss-3.53: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/curl-7.70.0_1.txz Installing /packages/All/htslib-1.9.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.30.3.txz ===== Message from perl5-5.30.3: -- The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.2.txz Installing /packages/All/gsl-2.6.txz SUCCEEDED 00:00:11 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> bcftools-1.9_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> bcftools-1.9_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bcftools-1.9_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> bcftools-1.9_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bcftools-1.9_1 for building => SHA256 Checksum OK for samtools-bcftools-1.9_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> bcftools-1.9_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bcftools-1.9_1 for building ===> Extracting for bcftools-1.9_1 => SHA256 Checksum OK for samtools-bcftools-1.9_GH0.tar.gz. Extracted Memory Use: 12.09M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for bcftools-1.9_1 ===> Applying ports patches for bcftools-1.9_1 from /xports/biology/bcftools/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> bcftools-1.9_1 depends on package: htslib>=1.6 - found ===> bcftools-1.9_1 depends on package: gmake>=4.3 - found ===> bcftools-1.9_1 depends on package: autoconf>=2.69 - found ===> bcftools-1.9_1 depends on package: automake>=1.16.1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> bcftools-1.9_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.9_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> bcftools-1.9_1 depends on package: htslib>=1.6 - found ===> bcftools-1.9_1 depends on package: gmake>=4.3 - found ===> bcftools-1.9_1 depends on package: autoconf>=2.69 - found ===> bcftools-1.9_1 depends on package: automake>=1.16.1 - found ===> bcftools-1.9_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.9_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Configuring for bcftools-1.9_1 configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure: loading site script /xports/Templates/config.site checking for gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for grep that handles long lines and -e... (cached) /usr/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 location of HTSlib source tree... none found checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... (cached) yes checking for inflate in -lz... yes configure: creating ./config.status config.status: creating config.mk config.status: creating config.h SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for bcftools-1.9_1 gmake[1]: Entering directory '/construction/biology/bcftools/bcftools-1.9' echo '#define BCFTOOLS_VERSION "1.9"' > version.h cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfindex.o vcfindex.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tabix.o tabix.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfstats.o vcfstats.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfisec.o vcfisec.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfmerge.o vcfmerge.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfquery.o vcfquery.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcffilter.o vcffilter.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o filter.o filter.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsom.o vcfsom.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfnorm.o vcfnorm.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfgtcheck.o vcfgtcheck.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfview.o vcfview.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfannotate.o vcfannotate.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfroh.o vcfroh.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconcat.o vcfconcat.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfcall.o vcfcall.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mcall.o mcall.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcmp.o vcmp.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o gvcf.o gvcf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o reheader.o reheader.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o convert.o convert.c In function 'init_data', inlined from 'main_vcfcall' at vcfcall.c:808:5: vcfcall.c:421:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] args->aux.ploidy = (uint8_t*) malloc(args->nsamples); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/htslib/kstring.h:29, from /usr/local/include/htslib/vcf.h:40, from vcfcall.c:32: vcfcall.c: In function 'main_vcfcall': /usr/include/stdlib.h:105:7: note: in a call to allocation function 'malloc' declared here void *malloc(size_t) __malloclike __heedresult __alloc_size(1); ^~~~~~ cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconvert.o vcfconvert.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tsv2vcf.o tsv2vcf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfcnv.o vcfcnv.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o HMM.o HMM.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -DPLUGINPATH='"/usr/local/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o consensus.o consensus.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ploidy.o ploidy.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bin.o bin.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hclust.o hclust.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o version.o version.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o regidx.o regidx.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o smpl_ilist.o smpl_ilist.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o csq.o csq.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfbuf.o vcfbuf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mpileup.o mpileup.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf.o bam2bcf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf_indel.o bam2bcf_indel.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam_sample.o bam_sample.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsort.o vcfsort.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ccall.o ccall.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o em.o em.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o prob1.o prob1.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kmin.o kmin.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-rbuf.o test/test-rbuf.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-regidx.o test/test-regidx.c cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/GTisec.so version.c plugins/GTisec.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/GTsubset.so version.c plugins/GTsubset.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/contrast.so version.c plugins/contrast.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/counts.so version.c plugins/counts.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/dosage.so version.c plugins/dosage.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fill-tags.so version.c plugins/fill-tags.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/fixref.so version.c plugins/fixref.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/frameshifts.so version.c plugins/frameshifts.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/impute-info.so version.c plugins/impute-info.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/mendelian.so version.c plugins/mendelian.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/missing2ref.so version.c plugins/missing2ref.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/prune.so version.c plugins/prune.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/setGT.so filter.c version.c plugins/setGT.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/split.so version.c plugins/split.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/tag2tag.so version.c plugins/tag2tag.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/trio-stats.so version.c plugins/trio-stats.c -L/usr/local/lib cc -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -L/usr/local/lib cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o main.o main.c cc -o test/test-rbuf test/test-rbuf.o -lz -L/usr/local/lib cc -o test/test-regidx test/test-regidx.o regidx.o -lpthread -lhts -lz -L/usr/local/lib cc -rdynamic -pthread -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 vcfplugin.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 ccall.o em.o prob1.o kmin.o -lhts -lm -lz -L/usr/local/lib gmake[1]: Leaving directory '/construction/biology/bcftools/bcftools-1.9' SUCCEEDED 00:00:17 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for bcftools-1.9_1 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/bcftools/bcftools-1.9' mkdir -p /construction/biology/bcftools/stage/usr/local/bin /construction/biology/bcftools/stage/usr/local/bin/samtools_misc /construction/biology/bcftools/stage/usr/local/man/man1 /construction/biology/bcftools/stage/usr/local/libexec/bcftools install -s -m 555 bcftools /construction/biology/bcftools/stage/usr/local/bin install -m 555 misc/color-chrs.pl misc/guess-ploidy.py misc/plot-vcfstats misc/plot-roh.py misc/run-roh.pl misc/vcfutils.pl /construction/biology/bcftools/stage/usr/local/bin/samtools_misc install -m 444 doc/bcftools.1 /construction/biology/bcftools/stage/usr/local/man/man1 install -s -m 555 plugins/*.so /construction/biology/bcftools/stage/usr/local/libexec/bcftools gmake[1]: Leaving directory '/construction/biology/bcftools/bcftools-1.9' /bin/mv /construction/biology/bcftools/stage/usr/local/bin/samtools_misc/color-chrs.pl /construction/biology/bcftools/stage/usr/local/bin/color-chrs /bin/mv /construction/biology/bcftools/stage/usr/local/bin/samtools_misc/guess-ploidy.py /construction/biology/bcftools/stage/usr/local/bin/guess-ploidy /bin/mv //construction/biology/bcftools/stage/usr/local/bin/samtools_misc/plot-roh.py /construction/biology/bcftools/stage/usr/local/bin/plot-roh /bin/mv /construction/biology/bcftools/stage/usr/local/bin/samtools_misc/run-roh.pl /construction/biology/bcftools/stage/usr/local/bin/run-roh /bin/mv /construction/biology/bcftools/stage/usr/local/bin/samtools_misc/vcfutils.pl /construction/biology/bcftools/stage/usr/local/bin/vcfutils /bin/mv /construction/biology/bcftools/stage/usr/local/bin/samtools_misc/plot-vcfstats /construction/biology/bcftools/stage/usr/local/bin/ /bin/rmdir /construction/biology/bcftools/stage/usr/local/bin/samtools_misc/ ====> Compressing man pages (compress-man) ===> Installing ldconfig configuration file ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for bcftools-1.9_1 file sizes/checksums [37]: 0% file sizes/checksums [37]: 100% packing files [37]: 0% packing files [37]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:00:40