=> Building biology/bcftools Started : Sunday, 7 JUL 2019 at 04:00:48 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for bcftools-1.9: GPL=on: Enable modules that rely on GPL code ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/construction/biology/bcftools XDG_CONFIG_HOME=/construction/biology/bcftools HOME=/construction/biology/bcftools TMPDIR="/tmp" PATH=/construction/biology/bcftools/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- USE_GPL=1 PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/bcftools XDG_CONFIG_HOME=/construction/biology/bcftools HOME=/construction/biology/bcftools TMPDIR="/tmp" PATH=/construction/biology/bcftools/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/bcftools/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.28 PROFILE="@comment " DOCSDIR="share/doc/bcftools" EXAMPLESDIR="share/examples/bcftools" DATADIR="share/bcftools" WWWDIR="www/bcftools" ETCDIR="etc/bcftools" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bcftools DOCSDIR=/usr/local/share/doc/bcftools EXAMPLESDIR=/usr/local/share/examples/bcftools WWWDIR=/usr/local/www/bcftools ETCDIR=/usr/local/etc/bcftools -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License MIT GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> bcftools-1.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> bcftools-1.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bcftools-1.9 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License MIT GPLv3 accepted by the user ===> Fetching all distfiles required by bcftools-1.9 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License MIT GPLv3 accepted by the user ===> Fetching all distfiles required by bcftools-1.9 for building => SHA256 Checksum OK for samtools-bcftools-1.9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License MIT GPLv3 accepted by the user ===> Fetching all distfiles required by bcftools-1.9 for building ===> Extracting for bcftools-1.9 => SHA256 Checksum OK for samtools-bcftools-1.9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for bcftools-1.9 ===> Applying ports patches for bcftools-1.9 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> bcftools-1.9 depends on package: htslib>=1.6 - not found ===> Installing existing package /packages/All/htslib-1.9.txz Installing htslib-1.9... `-- Installing curl-7.65.1... | `-- Installing ca_root_nss-3.44... | `-- Extracting ca_root_nss-3.44: ........ done | `-- Installing libnghttp2-1.39.1... | `-- Extracting libnghttp2-1.39.1: .......... done | `-- Installing libressl-2.9.2... | `-- Extracting libressl-2.9.2: .......... done `-- Extracting curl-7.65.1: .......... done Extracting htslib-1.9: .......... done Message from ca_root_nss-3.44: ********************************* WARNING ********************************* 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. *********************************** NOTE ********************************** 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 *************************************************************************** ===> bcftools-1.9 depends on package: htslib>=1.6 - found ===> Returning to build of bcftools-1.9 ===> bcftools-1.9 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_2.txz Installing autoconf-2.69_2... `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: .......... done `-- Installing indexinfo-0.3.1... `-- Extracting indexinfo-0.3.1: .... done `-- Installing m4-1.4.18_1,1... `-- Extracting m4-1.4.18_1,1: .......... done `-- Installing perl5-5.28.2... `-- Extracting perl5-5.28.2: .......... done Extracting autoconf-2.69_2: .......... done Message from perl5-5.28.2: 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. ===> bcftools-1.9 depends on package: autoconf>=2.69 - found ===> Returning to build of bcftools-1.9 ===> bcftools-1.9 depends on package: automake>=1.16.1 - not found ===> Installing existing package /packages/All/automake-1.16.1_1.txz Installing automake-1.16.1_1... Extracting automake-1.16.1_1: .......... done ===> bcftools-1.9 depends on package: automake>=1.16.1 - found ===> Returning to build of bcftools-1.9 ===> bcftools-1.9 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> bcftools-1.9 depends on executable: gmake - found ===> Returning to build of bcftools-1.9 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> bcftools-1.9 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.9 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.5_1.txz Installing gsl-2.5_1... Extracting gsl-2.5_1: .......... done ===> bcftools-1.9 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of bcftools-1.9 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for bcftools-1.9 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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for bcftools-1.9 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 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:102:7: 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 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 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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-switch-rate.so version.c plugins/trio-switch-rate.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/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/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/setGT.so filter.c version.c plugins/setGT.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' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for bcftools-1.9 ===> 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 -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for bcftools-1.9 file sizes/checksums [41]: . done packing files [41]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:02:18 UTC Duration: 00:01:30