[00:00:00] ====>> Creating the reference jail... done [00:00:00] ====>> Mounting system devices for releng_10_1-default [00:00:00] ====>> Mounting ports/packages/distfiles [00:00:00] ====>> Stashing existing package repository [00:00:00] ====>> Mounting packages from: /usr/local/poudriere/data/packages/releng_10_1-default [00:00:00] ====>> Copying /var/db/ports from: /usr/local/etc/poudriere.d/options [00:00:01] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/make.conf [00:00:01] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/releng_10_1-make.conf /etc/resolv.conf -> /usr/local/poudriere/data/.m/releng_10_1-default/ref/etc/resolv.conf [00:00:01] ====>> Starting jail releng_10_1-default [00:00:02] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_10_1-default/2015-04-27_18h11m46s [00:00:02] ====>> Loading MOVED [00:00:02] ====>> Calculating ports order and dependencies [00:00:03] ====>> Sanity checking the repository [00:00:04] ====>> Checking packages for incremental rebuild needed [00:00:05] ====>> Deleting stale symlinks [00:00:05] ====>> Deleting empty directories [00:00:05] ====>> Cleaning the build queue [00:00:05] ====>> Recording filesystem state for prepkg... done [00:00:06] ====>> Building 1 packages using 1 builders [00:00:06] ====>> Starting/Cloning builders [00:00:07] ====>> Hit CTRL+t at any time to see build progress and stats [00:00:07] ====>> [01][00:00:00] Starting build of math/gsl [00:02:39] ====>> [01][00:02:32] Finished build of math/gsl: Success [00:02:40] ====>> Stopping 1 builders [00:02:44] ====>> Creating pkgng repository Creating repository in /tmp/packages... done Packing files for repository... done [00:02:47] ====>> Committing packages to repository [00:02:47] ====>> Removing old packages [00:02:47] ====>> Portlint check WARN: /usr/local/poudriere/data/.m/releng_10_1-default/ref/usr/ports/biology/bcftools/pkg-plist: There are only 4 items in the plist. Consider using PLIST_FILES instead of pkg-plist when installing less than 6 items. WARN: Makefile: "LICENSE" has to appear earlier. 0 fatal errors and 2 warnings found. [00:02:48] ====>> Building with flags: [00:02:48] ====>> Removing existing /usr/local build started at Mon Apr 27 18:14:34 MST 2015 port directory: /usr/ports/biology/bcftools building for: FreeBSD releng_10_1-default 10.1-RELEASE FreeBSD 10.1-RELEASE amd64 maintained by: cartwright@asu.edu ident warning: no id keywords in /usr/local/poudriere/data/.m/releng_10_1-default/ref//usr/ports/biology/bcftools/Makefile Makefile ident: Poudriere version: 3.1.4 Host OSVERSION: 1001000 Jail OSVERSION: 1001000 ---Begin Environment--- PKGREPOSITORY=/tmp/pkgs PACKAGES=/tmp/pkgs OSVERSION=1001000 UNAME_v=FreeBSD 10.1-RELEASE UNAME_r=10.1-RELEASE BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 WARNING_WAIT=0 SAVED_TERM=xterm-color NO_WARNING_PKG_INSTALL_EOL=yes MASTERMNT=/usr/local/poudriere/data/.m/releng_10_1-default/ref FORCE_PACKAGE=yes PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk OLDPWD=/usr/local/poudriere/data/.m/releng_10_1-default/ref/.p/pool PWD=/usr/local/poudriere/data/.m/releng_10_1-default/ref/usr/ports/biology/bcftools MASTERNAME=releng_10_1-default USER=root HOME=/root POUDRIERE_VERSION=3.1.4 TRYBROKEN=yes LOCALBASE=/usr/local PACKAGE_BUILDING=yes DEV_WARNING_WAIT=0 ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for bcftools-1.2: 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 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcftools/work HOME=/wrkdirs/usr/ports/biology/bcftools/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- INSTALL_LIB="install -s -o root -g wheel -m 444" INSTALL_DATA="install -o root -g wheel -m 0644" INSTALL_PROGRAM="install -s -o root -g wheel -m 555" INSTALL_SCRIPT="install -o root -g wheel -m 555" INSTALL_DIR="/bin/mkdir -p" USE_GPL=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcftools/work HOME=/wrkdirs/usr/ports/biology/bcftools/work TMPDIR="/tmp" NO_PIE=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector" CPP="cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 0644" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTVERSION="1.2" OSREL=10.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib 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 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### CFLAGS += -O2 -fno-strict-aliasing -pipe #DEFAULT_VERSIONS=python=2.7 python2=2.7 python3=3.4 #WITH_BDB_VER=6 #WITH_BDB6_PERMITTED=yes TEX_DEFAULT=texlive MAKE_JOBS_NUMBER_LIMIT=8 #### /usr/local/etc/poudriere.d/releng_10_1-make.conf #### CPUTYPE?=bdver1 ---End make.conf--- =================================================== ===> License GPLv3 accepted by the user ===> Found saved configuration for bcftools-1.2 =========================================================================== =================================================== ===> bcftools-1.2 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.5.1.txz [releng_10_1-default] Installing pkg-1.5.1... [releng_10_1-default] Extracting pkg-1.5.1... done Message for pkg-1.5.1: If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of bcftools-1.2 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Found saved configuration for bcftools-1.2 ===> bcftools-1.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bcftools-1.2 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Found saved configuration for bcftools-1.2 ===> bcftools-1.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bcftools-1.2 for building => SHA256 Checksum OK for bcftools-1.2_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Found saved configuration for bcftools-1.2 ===> bcftools-1.2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bcftools-1.2 for building ===> Extracting for bcftools-1.2 => SHA256 Checksum OK for bcftools-1.2_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bcftools-1.2 ===> Applying FreeBSD patches for bcftools-1.2 =========================================================================== =================================================== ===> bcftools-1.2 depends on package: htslib>=1.2 - not found ===> Verifying install for htslib>=1.2 in /usr/ports/biology/htslib ===> Installing existing package /packages/All/htslib-1.2.1.txz [releng_10_1-default] Installing htslib-1.2.1... [releng_10_1-default] Extracting htslib-1.2.1... done ===> Returning to build of bcftools-1.2 ===> bcftools-1.2 depends on executable: gmake - not found ===> Verifying install for gmake in /usr/ports/devel/gmake ===> Installing existing package /packages/All/gmake-4.1_1.txz [releng_10_1-default] Installing gmake-4.1_1... [releng_10_1-default] `-- Installing gettext-runtime-0.19.4... [releng_10_1-default] | `-- Installing indexinfo-0.2.3... [releng_10_1-default] | `-- Extracting indexinfo-0.2.3... done [releng_10_1-default] `-- Extracting gettext-runtime-0.19.4... done [releng_10_1-default] Extracting gmake-4.1_1... done ===> Returning to build of bcftools-1.2 =========================================================================== =================================================== ===> bcftools-1.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.2 depends on shared library: libgsl.so - not found ===> Verifying for libgsl.so in /usr/ports/math/gsl ===> Installing existing package /packages/All/gsl-1.16_2.txz [releng_10_1-default] Installing gsl-1.16_2... [releng_10_1-default] Extracting gsl-1.16_2... done ===> Returning to build of bcftools-1.2 =========================================================================== ====>> Recording filesystem state for prebuild... done =================================================== ===> bcftools-1.2 depends on package: htslib>=1.2 - found ===> bcftools-1.2 depends on executable: gmake - found ===> bcftools-1.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.2 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Configuring for bcftools-1.2 =========================================================================== =================================================== ===> Building for bcftools-1.2 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bcftools/work/bcftools-1.2' echo '#define BCFTOOLS_VERSION "1.2"' > version.h cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfindex.c -o vcfindex.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include tabix.c -o tabix.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfstats.c -o vcfstats.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfisec.c -o vcfisec.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfmerge.c -o vcfmerge.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfquery.c -o vcfquery.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcffilter.c -o vcffilter.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include filter.c -o filter.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfsom.c -o vcfsom.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfnorm.c -o vcfnorm.o vcfmerge.c:39:1: warning: unused function 'kh_del_strdict' [-Wunused-function] KHASH_MAP_INIT_STR(strdict, int) ^ /usr/local/include/htslib/khash.h:617:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ /usr/local/include/htslib/khash.h:358:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static kh_inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ /usr/local/include/htslib/khash.h:355:2: note: expanded from macro 'KHASH_INIT2' __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ /usr/local/include/htslib/khash.h:341:13: note: expanded from macro '__KHASH_IMPL' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :108:1: note: expanded from here kh_del_strdict ^ cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfgtcheck.c -o vcfgtcheck.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfview.c -o vcfview.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfannotate.c -o vcfannotate.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfroh.c -o vcfroh.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfconcat.c -o vcfconcat.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfcall.c -o vcfcall.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include mcall.c -o mcall.o mcall.c:541:22: warning: unused function 'logsumexp' [-Wunused-function] static inline double logsumexp(double *vals, int nvals) ^ cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcmp.c -o vcmp.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include gvcf.c -o gvcf.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include reheader.c -o reheader.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include convert.c -o convert.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfconvert.c -o vcfconvert.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include tsv2vcf.c -o tsv2vcf.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfcnv.c -o vcfcnv.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include HMM.c -o HMM.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include vcfplugin.c -o vcfplugin.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include consensus.c -o consensus.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include ploidy.c -o ploidy.o 1 warning generated. cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include version.c -o version.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include ccall.c -o ccall.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include em.c -o em.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include prob1.c -o prob1.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include kmin.c -o kmin.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include polysomy.c -o polysomy.o cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include test/test-rbuf.c -o test/test-rbuf.o cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -I. -I/usr/local/include -fPIC -shared -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -lhts cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -I. -I/usr/local/include -fPIC -shared -o plugins/dosage.so version.c plugins/dosage.c -lhts cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -I. -I/usr/local/include -fPIC -shared -o plugins/missing2ref.so version.c plugins/missing2ref.c -lhts cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -I. -I/usr/local/include -fPIC -shared -o plugins/counts.so version.c plugins/counts.c -lhts cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -I. -I/usr/local/include -fPIC -shared -o plugins/vcf2sex.so ploidy.c version.c plugins/vcf2sex.c -lhts cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -I. -I/usr/local/include -fPIC -shared -o plugins/frameshifts.so version.c plugins/frameshifts.c -lhts cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -I. -I/usr/local/include -fPIC -shared -o plugins/fixploidy.so ploidy.c version.c plugins/fixploidy.c -lhts cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -I. -I/usr/local/include -fPIC -shared -o plugins/tag2tag.so version.c plugins/tag2tag.c -lhts 1 warning generated. cc -c -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -I. -I/usr/local/include main.c -o main.o cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -o test/test-rbuf -lm test/test-rbuf.o cc -pthread -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -Wall -DUSE_GPL -L/usr/local/lib -fstack-protector -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 -lhts -lz -lm -lgsl -lgslcblas gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bcftools/work/bcftools-1.2' =========================================================================== ====>> Checking for filesystem violations... done =================================================== =========================================================================== ====>> Recording filesystem state for prestage... done =================================================== ===> Staging for bcftools-1.2 ===> bcftools-1.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.2 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bcftools/work/bcftools-1.2' /bin/mkdir -p /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/samtools_misc /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/man/man1 install -s -o root -g wheel -m 555 bcftools /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin install -o root -g wheel -m 555 plot-vcfstats vcfutils.pl /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/samtools_misc install -o root -g wheel -m 0644 doc/bcftools.1 /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/man/man1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bcftools/work/bcftools-1.2' ====> Compressing man pages (compress-man) =========================================================================== ====> Running Q/A tests (stage-qa) ====> 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) ====>> Checking for staging violations... done =================================================== ===> Building package for bcftools-1.2 =========================================================================== =================================================== =========================================================================== ====>> Recording filesystem state for preinst... done =================================================== ===> Installing for bcftools-1.2 ===> bcftools-1.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> bcftools-1.2 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Checking if bcftools already installed ===> Registering installation for bcftools-1.2 [releng_10_1-default] Installing bcftools-1.2... Add /usr/local/bin/samtools_misc to your path to use miscellaneous tools. =========================================================================== ====>> Checking shared library dependencies 0x0000000000000001 (NEEDED) Shared library: [libc.so.7] 0x0000000000000001 (NEEDED) Shared library: [libgsl.so.0] 0x0000000000000001 (NEEDED) Shared library: [libgslcblas.so.0] 0x0000000000000001 (NEEDED) Shared library: [libhts.so.1] 0x0000000000000001 (NEEDED) Shared library: [libm.so.5] 0x0000000000000001 (NEEDED) Shared library: [libthr.so.3] 0x0000000000000001 (NEEDED) Shared library: [libz.so.6] =================================================== ===> Deinstalling for bcftools ===> Deinstalling bcftools-1.2 Updating database digests format... done Checking integrity... done (0 conflicting) Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): Installed packages to be REMOVED: bcftools-1.2 The operation will free 662 KiB. [releng_10_1-default] [1/1] Deinstalling bcftools-1.2... [releng_10_1-default] [1/1] Deleting files for bcftools-1.2... done =========================================================================== ====>> Checking for extra files and directories [00:02:58] ====>> Installing from package [releng_10_1-default] Installing bcftools-1.2... [releng_10_1-default] Extracting bcftools-1.2... done Message for bcftools-1.2: Add /usr/local/bin/samtools_misc to your path to use miscellaneous tools. [00:02:58] ====>> Cleaning up ===> Cleaning for bcftools-1.2 [00:02:59] ====>> Deinstalling package Updating database digests format... done Checking integrity... done (0 conflicting) Deinstallation has been requested for the following 1 packages (of 0 packages in the universe): Installed packages to be REMOVED: bcftools-1.2 The operation will free 662 KiB. [releng_10_1-default] [1/1] Deinstalling bcftools-1.2... [releng_10_1-default] [1/1] Deleting files for bcftools-1.2... done build of biology/bcftools ended at Mon Apr 27 18:14:45 MST 2015 build time: 00:00:11 [00:02:59] ====>> Cleaning up [00:02:59] ====>> Umounting file systems