------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for bcftools-1.12: GPL=on: Enable modules that rely on GPL code ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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/python3.7" 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/bcftools/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 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/5.32 PROFILE="@comment " DOCSDIR="share/doc/bcftools" EXAMPLESDIR="share/examples/bcftools" DATADIR="share/bcftools" WWWDIR="www/bcftools" ETCDIR="etc/bcftools" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.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/perl5-5.32.1_1.txz Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.3.txz Installing /packages/All/libdeflate-1.7.txz Installing /packages/All/libnghttp2-1.43.0.txz Installing /packages/All/ca_root_nss-3.63.txz ===== Message from ca_root_nss-3.63: -- 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-1.1.1k_1,1.txz Installing /packages/All/curl-7.76.0.txz Installing /packages/All/htslib-1.12.txz Installing /packages/All/gsl-2.6.txz Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < bcftools-1.12 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> bcftools-1.12 depends on file: /usr/local/sbin/pkg - found => samtools-bcftools-1.12_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/samtools/bcftools/tar.gz/1.12?dummy=/samtools-bcftools-1.12_GH0.tar.gz fetch: https://codeload.github.com/samtools/bcftools/tar.gz/1.12?dummy=/samtools-bcftools-1.12_GH0.tar.gz: size unknown fetch: https://codeload.github.com/samtools/bcftools/tar.gz/1.12?dummy=/samtools-bcftools-1.12_GH0.tar.gz: size of remote file is not known samtools-bcftools-1.12_GH0.tar.gz 0 B 0 Bps samtools-bcftools-1.12_GH0.tar.gz 2977 kB 5037 kBps 00s ===> Fetching all distfiles required by bcftools-1.12 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> bcftools-1.12 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bcftools-1.12 for building => SHA256 Checksum OK for samtools-bcftools-1.12_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> bcftools-1.12 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bcftools-1.12 for building ===> Extracting for bcftools-1.12 => SHA256 Checksum OK for samtools-bcftools-1.12_GH0.tar.gz. Extracted Memory Use: 17.15M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for bcftools-1.12 ===> Applying ports patches for bcftools-1.12 from /xports/biology/bcftools/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> bcftools-1.12 depends on package: gmake>=4.3 - found ===> bcftools-1.12 depends on package: autoconf>=2.69 - found ===> bcftools-1.12 depends on package: automake>=1.16.1 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> bcftools-1.12 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.12 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> bcftools-1.12 depends on package: gmake>=4.3 - found ===> bcftools-1.12 depends on package: autoconf>=2.69 - found ===> bcftools-1.12 depends on package: automake>=1.16.1 - found ===> bcftools-1.12 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.12 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Configuring for bcftools-1.12 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 checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for bcftools-1.12 gmake[1]: Entering directory '/construction/biology/bcftools/bcftools-1.12' echo '#define BCFTOOLS_VERSION "1.12"' > 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 cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconvert.o vcfconvert.c In function 'init_data', inlined from 'main_vcfcall' at vcfcall.c:1092:5: vcfcall.c:659:39: 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:30, from /usr/local/include/htslib/hts.h:37, from /usr/local/include/htslib/vcf.h:39, from vcfcall.c:33: 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 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 -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 cols.o cols.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o extsort.o extsort.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o dist.o dist.c cc -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o abuf.o abuf.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 -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 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/add-variantkey.so version.c plugins/add-variantkey.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/allele-length.so version.c plugins/allele-length.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/gvcfz.so version.c plugins/gvcfz.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/indel-stats.so version.c plugins/indel-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/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/parental-origin.so version.c plugins/parental-origin.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/remove-overlaps.so version.c plugins/remove-overlaps.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/scatter.so version.c plugins/scatter.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 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-vep.so version.c plugins/split-vep.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-dnm2.so version.c plugins/trio-dnm2.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 -fPIC -shared -Wall -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.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 -lhts -lpthread -lz -L/usr/local/lib cc -rdynamic -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 extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o vcfplugin.o -lhts -lm -lz -L/usr/local/lib -lpthread gmake[1]: Leaving directory '/construction/biology/bcftools/bcftools-1.12' SUCCEEDED 00:00:28 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> bcftools-1.12 depends on executable: bash - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for bcftools-1.12 ===> bcftools-1.12 depends on executable: bash - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/bcftools/bcftools-1.12' mkdir -p /construction/biology/bcftools/stage/usr/local/bin /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/gff2gff.py 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 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-1.12' /bin/mv /construction/biology/bcftools/stage/usr/local/bin/color-chrs.pl /construction/biology/bcftools/stage/usr/local/bin/color-chrs /bin/mv /construction/biology/bcftools/stage/usr/local/bin/guess-ploidy.py /construction/biology/bcftools/stage/usr/local/bin/guess-ploidy /bin/mv //construction/biology/bcftools/stage/usr/local/bin/plot-roh.py /construction/biology/bcftools/stage/usr/local/bin/plot-roh /bin/mv /construction/biology/bcftools/stage/usr/local/bin/run-roh.pl /construction/biology/bcftools/stage/usr/local/bin/run-roh /bin/mv /construction/biology/bcftools/stage/usr/local/bin/vcfutils.pl /construction/biology/bcftools/stage/usr/local/bin/vcfutils /bin/mv /construction/biology/bcftools/stage/usr/local/bin/plot-vcfstats /construction/biology/bcftools/stage/usr/local/bin/ ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for bcftools-1.12 file sizes/checksums [47]: 0% file sizes/checksums [47]: 100% packing files [47]: 0% packing files [47]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:05 TOTAL TIME 00:01:07