=> Building biology/bcftools build started at Tue Oct 4 15:12:32 PDT 2016 port directory: /usr/ports/biology/bcftools building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: cartwright@asu.edu ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../10//usr/ports/biology/bcftools/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=bcftools-1.3.1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for bcftools-1.3.1: GPL=on: Enable modules that rely on GPL code ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/biology/bcftools XDG_CONFIG_HOME=/wrkdirs/biology/bcftools HOME=/wrkdirs/biology/bcftools TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- INSTALL_LIB="install -s -m 444" INSTALL_DATA="install -m 0644" INSTALL_PROGRAM="install -s -m 555" INSTALL_SCRIPT="install -m 555" INSTALL_DIR="/bin/mkdir -p" USE_GPL=1 XDG_DATA_HOME=/wrkdirs/biology/bcftools XDG_CONFIG_HOME=/wrkdirs/biology/bcftools HOME=/wrkdirs/biology/bcftools TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTVERSION="1.3.1" OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 PERL_VER=5.20 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/5.20 PROFILE="@comment " DOCSDIR="share/doc/bcftools" EXAMPLESDIR="share/examples/bcftools" DATADIR="share/bcftools" WWWDIR="www/bcftools" ETCDIR="etc/bcftools" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> bcftools-1.3.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> bcftools-1.3.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bcftools-1.3.1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bcftools-1.3.1 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bcftools-1.3.1 for building => SHA256 Checksum OK for samtools-bcftools-1.3.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bcftools-1.3.1 for building ===> Extracting for bcftools-1.3.1 => SHA256 Checksum OK for samtools-bcftools-1.3.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bcftools-1.3.1 ===> Applying ports patches for bcftools-1.3.1 =========================================================================== =================================================== ===> bcftools-1.3.1 depends on package: htslib>=1.3 - not found ===> Installing existing package /packages/All/htslib-1.3.1.txz Installing htslib-1.3.1... `-- Installing curl-7.50.3... | `-- Installing libressl-2.4.3... | `-- Extracting libressl-2.4.3: .......... done | `-- Installing ca_root_nss-3.27... | `-- Extracting ca_root_nss-3.27: ....... done | `-- Installing krb5-1.14.4... | | `-- Installing pkgconf-1.0.1... | | `-- Extracting pkgconf-1.0.1: .......... done | | `-- Installing gettext-runtime-0.19.8.1... | | `-- Installing indexinfo-0.2.5... | | `-- Extracting indexinfo-0.2.5: .... done | | `-- Extracting gettext-runtime-0.19.8.1: .......... done | `-- Extracting krb5-1.14.4: .......... done `-- Extracting curl-7.50.3: .......... done Extracting htslib-1.3.1: .......... done Message from ca_root_nss-3.27: ********************************* 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-1.3.1 depends on package: htslib>=1.3 - found ===> Returning to build of bcftools-1.3.1 ===> bcftools-1.3.1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... Extracting gmake-4.2.1_1: .......... done ===> bcftools-1.3.1 depends on executable: gmake - found ===> Returning to build of bcftools-1.3.1 =========================================================================== =================================================== ===> bcftools-1.3.1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.3.1 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-1.16_2.txz Installing gsl-1.16_2... Extracting gsl-1.16_2: .......... done Message from gsl-1.16_2: ===> NOTICE: The gsl port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> bcftools-1.3.1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of bcftools-1.3.1 =========================================================================== =================================================== ===> Configuring for bcftools-1.3.1 =========================================================================== =================================================== ===> Building for bcftools-1.3.1 gmake[1]: Entering directory '/wrkdirs/biology/bcftools/bcftools-1.3.1' echo '#define BCFTOOLS_VERSION "1.3.1"' > version.h cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfindex.o vcfindex.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o tabix.o tabix.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfstats.o vcfstats.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfisec.o vcfisec.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfmerge.o vcfmerge.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfquery.o vcfquery.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcffilter.o vcffilter.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o filter.o filter.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfsom.o vcfsom.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfnorm.o vcfnorm.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfgtcheck.o vcfgtcheck.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfview.o vcfview.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfannotate.o vcfannotate.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfroh.o vcfroh.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfconcat.o vcfconcat.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfcall.o vcfcall.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o mcall.o mcall.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcmp.o vcmp.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o gvcf.o gvcf.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o reheader.o reheader.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o convert.o convert.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfconvert.o vcfconvert.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o tsv2vcf.o tsv2vcf.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfcnv.o vcfcnv.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o HMM.o HMM.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o vcfplugin.o vcfplugin.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o consensus.o consensus.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o ploidy.o ploidy.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o version.o version.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o ccall.o ccall.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o em.o em.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o prob1.o prob1.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o kmin.o kmin.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o polysomy.o polysomy.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o peakfit.o peakfit.c cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o test/test-rbuf.o test/test-rbuf.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/impute-info.so version.c plugins/impute-info.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/dosage.so version.c plugins/dosage.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/GTisec.so version.c plugins/GTisec.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/missing2ref.so version.c plugins/missing2ref.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/mendelian.so version.c plugins/mendelian.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/counts.so version.c plugins/counts.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/fill-tags.so version.c plugins/fill-tags.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/vcf2sex.so ploidy.c version.c plugins/vcf2sex.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/frameshifts.so version.c plugins/frameshifts.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/fixploidy.so ploidy.c version.c plugins/fixploidy.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/tag2tag.so version.c plugins/tag2tag.c cc -fPIC -shared -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -L/usr/local/lib -o plugins/setGT.so version.c plugins/setGT.c plugins/color-chrs.c: In function 'flush_viterbi': plugins/color-chrs.c:468:9: warning: 's2' may be used uninitialized in this function [-Wmaybe-uninitialized] fprintf(args->fp,"# SG, shared segment\t[2]Chromosome\t[3]Start\t[4]End\t[5]%s:1\t[6]%s:2\n",s2,s2); ^ plugins/color-chrs.c:531:5: warning: 's1' may be used uninitialized in this function [-Wmaybe-uninitialized] fprintf(args->fp,"SW\t%s\t%s\t%d\t%d\t%f\n", s1,bcf_hdr_id2name(args->hdr,args->prev_rid),args->nhet_mother,nswitch_mother,mrate); ^ cc -pipe -O2 -fno-strict-aliasing -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include -c -o main.o main.c cc -L/usr/local/lib -o test/test-rbuf test/test-rbuf.o -lm cc -rdynamic -L/usr/local/lib -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 version.o ccall.o em.o prob1.o kmin.o polysomy.o peakfit.o -lhts -pthread -lz -lm -lgsl -lgslcblas gmake[1]: Leaving directory '/wrkdirs/biology/bcftools/bcftools-1.3.1' =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for bcftools-1.3.1 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/biology/bcftools/bcftools-1.3.1' /bin/mkdir -p /wrkdirs/biology/bcftools/stage/usr/local/bin /wrkdirs/biology/bcftools/stage/usr/local/bin/samtools_misc /wrkdirs/biology/bcftools/stage/usr/local/man/man1 /wrkdirs/biology/bcftools/stage/usr/local/libexec/bcftools install -s -m 555 bcftools /wrkdirs/biology/bcftools/stage/usr/local/bin install -m 555 plot-vcfstats vcfutils.pl plugins/color-chrs.pl /wrkdirs/biology/bcftools/stage/usr/local/bin/samtools_misc install -m 0644 doc/bcftools.1 /wrkdirs/biology/bcftools/stage/usr/local/man/man1 install -s -m 555 plugins/*.so /wrkdirs/biology/bcftools/stage/usr/local/libexec/bcftools gmake[1]: Leaving directory '/wrkdirs/biology/bcftools/bcftools-1.3.1' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for bcftools-1.3.1 file sizes/checksums [22]: . done packing files [22]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for bcftools-1.3.1 build of biology/bcftools ended at Tue Oct 4 15:13:06 PDT 2016 build time: 00:00:34