[00:00:00] ====>> Creating the reference jail... done [00:00:00] ====>> Mounting system devices for releng_9_3-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_9_3-default [00:00:00] ====>> Copying /var/db/ports from: /usr/local/etc/poudriere.d/options [00:00:00] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/make.conf /etc/resolv.conf -> /usr/local/poudriere/data/.m/releng_9_3-default/ref/etc/resolv.conf [00:00:00] ====>> Starting jail releng_9_3-default [00:00:00] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_9_3-default/2015-12-22_16h02m54s [00:00:00] ====>> Loading MOVED [00:00:01] ====>> Calculating ports order and dependencies [00:00:02] ====>> Sanity checking the repository [00:00:02] ====>> Checking packages for incremental rebuild needed [00:00:03] ====>> Deleting stale symlinks [00:00:03] ====>> Deleting empty directories [00:00:03] ====>> Cleaning the build queue [00:00:03] ====>> Recording filesystem state for prepkg... done [00:00:04] ====>> Committing packages to repository [00:00:04] ====>> Removing old packages [00:00:04] ====>> Portlint check WARN: Makefile: [26]: possible direct use of command "file" found. use ${FILE} instead. 0 fatal errors and 1 warning found. [00:00:05] ====>> Building with flags: [00:00:05] ====>> Removing existing /usr/local build started at Tue Dec 22 16:02:59 MST 2015 port directory: /usr/ports/biology/htslib building for: FreeBSD releng_9_3-default 9.3-RELEASE FreeBSD 9.3-RELEASE amd64 maintained by: cartwright@asu.edu Makefile ident: $FreeBSD: head/biology/htslib/Makefile 385521 2015-05-06 15:16:53Z mat $ Poudriere version: 3.1.8 Host OSVERSION: 1002000 Jail OSVERSION: 903000 ---Begin Environment--- PKGREPOSITORY=/tmp/pkgs PACKAGES=/tmp/pkgs OSVERSION=903000 UNAME_v=FreeBSD 9.3-RELEASE UNAME_r=9.3-RELEASE BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 WARNING_WAIT=0 SAVED_TERM=xterm-256color NO_WARNING_PKG_INSTALL_EOL=yes MASTERMNT=/usr/local/poudriere/data/.m/releng_9_3-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=/ PWD=/usr/local/poudriere/data/.m/releng_9_3-default/ref/usr/ports/biology/htslib MASTERNAME=releng_9_3-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.8 SCRIPTPATH=/usr/local/share/poudriere/testport.sh TRYBROKEN=yes LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes DEV_WARNING_WAIT=0 ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for htslib-1.3: libcurl=on: Use libcurl for network file access (HTTPS and S3 support). ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --enable-libcurl --prefix=/usr/local ${_LATE_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/usr/ports/biology/htslib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/htslib/work HOME=/wrkdirs/usr/ports/biology/htslib/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- INSTALL_LIB="install -s -m 444" INSTALL_DATA="install -m 0644" INSTALL_PROGRAM="install -s -m 555" INSTALL_DIR="/bin/mkdir -p" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/htslib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/htslib/work HOME=/wrkdirs/usr/ports/biology/htslib/work TMPDIR="/tmp" NO_PIE=yes NO_DEBUG_FILES=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 -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 -fstack-protector" 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" OSREL=9.3 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 DOCSDIR="share/doc/htslib" EXAMPLESDIR="share/examples/htslib" DATADIR="share/htslib" WWWDIR="www/htslib" ETCDIR="etc/htslib" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/htslib DOCSDIR=/usr/local/share/doc/htslib EXAMPLESDIR=/usr/local/share/examples/htslib WWWDIR=/usr/local/www/htslib ETCDIR=/usr/local/etc/htslib --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 ---End make.conf--- =================================================== ===> License BSD3CLAUSE MIT accepted by the user =========================================================================== =================================================== ===> htslib-1.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.6.2.txz [releng_9_3-default] Installing pkg-1.6.2... [releng_9_3-default] Extracting pkg-1.6.2: .......... done Message from pkg-1.6.2: If you are upgrading from the old package format, first run: # pkg2ng ===> htslib-1.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of htslib-1.3 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE MIT accepted by the user ===> htslib-1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by htslib-1.3 for building =========================================================================== =================================================== ===> License BSD3CLAUSE MIT accepted by the user ===> htslib-1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by htslib-1.3 for building => SHA256 Checksum OK for samtools-htslib-1.3_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE MIT accepted by the user ===> htslib-1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by htslib-1.3 for building ===> Extracting for htslib-1.3 => SHA256 Checksum OK for samtools-htslib-1.3_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for htslib-1.3 ===> Applying FreeBSD patches for htslib-1.3 =========================================================================== =================================================== ===> htslib-1.3 depends on executable: autoconf-2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69.txz [releng_9_3-default] Installing autoconf-2.69... [releng_9_3-default] `-- Installing indexinfo-0.2.4... [releng_9_3-default] `-- Extracting indexinfo-0.2.4: .... done [releng_9_3-default] `-- Installing autoconf-wrapper-20131203... [releng_9_3-default] `-- Extracting autoconf-wrapper-20131203: ........ done [releng_9_3-default] `-- Installing perl5-5.20.3_8... [releng_9_3-default] `-- Extracting perl5-5.20.3_8: .......... done [releng_9_3-default] `-- Installing m4-1.4.17_1,1... [releng_9_3-default] `-- Extracting m4-1.4.17_1,1: .......... done [releng_9_3-default] Extracting autoconf-2.69: .......... done Message from perl5-5.20.3_8: 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. ===> htslib-1.3 depends on executable: autoconf-2.69 - found ===> Returning to build of htslib-1.3 ===> htslib-1.3 depends on executable: autoheader-2.69 - found ===> htslib-1.3 depends on executable: autoreconf-2.69 - found ===> htslib-1.3 depends on executable: aclocal-1.15 - not found ===> Installing existing package /packages/All/automake-1.15_1.txz [releng_9_3-default] Installing automake-1.15_1... [releng_9_3-default] `-- Installing automake-wrapper-20131203... [releng_9_3-default] `-- Extracting automake-wrapper-20131203: ... done [releng_9_3-default] Extracting automake-1.15_1: .......... done ===> htslib-1.3 depends on executable: aclocal-1.15 - found ===> Returning to build of htslib-1.3 ===> htslib-1.3 depends on executable: automake-1.15 - found ===> htslib-1.3 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.1_2.txz [releng_9_3-default] Installing gmake-4.1_2... [releng_9_3-default] `-- Installing libiconv-1.14_9... [releng_9_3-default] `-- Extracting libiconv-1.14_9: .......... done [releng_9_3-default] `-- Installing gettext-runtime-0.19.6... [releng_9_3-default] `-- Extracting gettext-runtime-0.19.6: .......... done [releng_9_3-default] Extracting gmake-4.1_2: .......... done ===> htslib-1.3 depends on executable: gmake - found ===> Returning to build of htslib-1.3 =========================================================================== =================================================== ===> htslib-1.3 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-7.46.0_1.txz [releng_9_3-default] Installing curl-7.46.0_1... [releng_9_3-default] `-- Installing ca_root_nss-3.20.1... [releng_9_3-default] `-- Extracting ca_root_nss-3.20.1: ....... done [releng_9_3-default] Extracting curl-7.46.0_1: .......... done Message from ca_root_nss-3.20.1: ********************************* 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 *************************************************************************** ===> htslib-1.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of htslib-1.3 =========================================================================== ====>> Recording filesystem state for prebuild... done =================================================== ===> htslib-1.3 depends on executable: autoconf-2.69 - found ===> htslib-1.3 depends on executable: autoheader-2.69 - found ===> htslib-1.3 depends on executable: autoreconf-2.69 - found ===> htslib-1.3 depends on executable: aclocal-1.15 - found ===> htslib-1.3 depends on executable: automake-1.15 - found ===> htslib-1.3 depends on executable: gmake - found ===> htslib-1.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Configuring for htslib-1.3 configure: loading site script /usr/ports/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 ranlib... ranlib checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getpagesize... (cached) yes checking for working mmap... (cached) yes checking for gmtime_r... yes checking for zlib.h... (cached) yes checking for inflate in -lz... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto configure: creating ./config.status config.status: creating config.mk config.status: creating config.h =========================================================================== =================================================== ===> Building for htslib-1.3 cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o kfunc.o kfunc.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o knetfile.o knetfile.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o kstring.o kstring.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o bgzf.o bgzf.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o faidx.o faidx.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o hfile.o hfile.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.3"' > version.h cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o md5.o md5.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o regidx.o regidx.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o sam.o sam.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o synced_bcf_reader.o synced_bcf_reader.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o vcf_sweep.o vcf_sweep.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o tbx.o tbx.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o vcf.o vcf.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o vcfutils.o vcfutils.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/cram_codecs.o cram/cram_codecs.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/cram_decode.o cram/cram_decode.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/cram_encode.o cram/cram_encode.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/cram_external.o cram/cram_external.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/cram_index.o cram/cram_index.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/cram_io.o cram/cram_io.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/cram_samtools.o cram/cram_samtools.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/cram_stats.o cram/cram_stats.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/files.o cram/files.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/mFILE.o cram/mFILE.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/open_trace_file.o cram/open_trace_file.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/rANS_static.o cram/rANS_static.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/sam_header.o cram/sam_header.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/string_alloc.o cram/string_alloc.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/thread_pool.o cram/thread_pool.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/vlen.o cram/vlen.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o cram/zfio.o cram/zfio.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o hfile_libcurl.o hfile_libcurl.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o kfunc.pico kfunc.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o knetfile.pico knetfile.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o kstring.pico kstring.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o bgzf.pico bgzf.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o faidx.pico faidx.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o hfile.pico hfile.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o hfile_net.pico hfile_net.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o hts.pico hts.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o md5.pico md5.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o regidx.pico regidx.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o sam.pico sam.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o vcf_sweep.pico vcf_sweep.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o tbx.pico tbx.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o vcf.pico vcf.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o vcfutils.pico vcfutils.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_decode.pico cram/cram_decode.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_encode.pico cram/cram_encode.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_external.pico cram/cram_external.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_index.pico cram/cram_index.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_io.pico cram/cram_io.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/cram_stats.pico cram/cram_stats.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/files.pico cram/files.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/mFILE.pico cram/mFILE.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/rANS_static.pico cram/rANS_static.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/sam_header.pico cram/sam_header.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/string_alloc.pico cram/string_alloc.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/thread_pool.pico cram/thread_pool.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/vlen.pico cram/vlen.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o cram/zfio.pico cram/zfio.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -fpic -c -o hfile_libcurl.pico hfile_libcurl.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o bgzip.o bgzip.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o htsfile.o htsfile.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o tabix.o tabix.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -I. -I/usr/local/include -c -o hts.o hts.c cc -shared -Wl,-soname,libhts.so.1 -pthread -L/usr/local/lib -fstack-protector -o libhts.so kfunc.pico knetfile.pico kstring.pico bgzf.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/thread_pool.pico cram/vlen.pico cram/zfio.pico hfile_libcurl.pico -lz -lm -lcurl -lcrypto ln -sf libhts.so libhts.so.1 ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o hfile_libcurl.o ranlib libhts.a cc -pthread -L/usr/local/lib -fstack-protector -o bgzip bgzip.o libhts.a -lz -lcurl -lcrypto cc -pthread -L/usr/local/lib -fstack-protector -o htsfile htsfile.o libhts.a -lz -lcurl -lcrypto cc -pthread -L/usr/local/lib -fstack-protector -o tabix tabix.o libhts.a -lz -lcurl -lcrypto =========================================================================== ====>> Checking for filesystem violations... done =================================================== =========================================================================== ====>> Recording filesystem state for prestage... done =================================================== ===> Staging for htslib-1.3 ===> htslib-1.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Generating temporary packing list /bin/mkdir -p /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include/htslib /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/man/man1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/man/man5 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/libdata/pkgconfig if test -n ""; then /bin/mkdir -p /wrkdirs/usr/ports/biology/htslib/work/stage; fi install -s -m 444 libhts.so /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so.1.3 ln -sf libhts.so.1.3 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so ln -sf libhts.so.1.3 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.so.1 sed -e 's#@includedir@#/usr/local/include#g;s#@libdir@#/usr/local/lib#g;s#@PACKAGE_VERSION@#1.3#g' htslib.pc.in > /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/libdata/pkgconfig/htslib.pc chmod 644 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/libdata/pkgconfig/htslib.pc install -s -m 555 bgzip htsfile tabix /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/bin if test -n ""; then install -s -m 555 /wrkdirs/usr/ports/biology/htslib/work/stage; fi install -m 0644 htslib/*.h /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/include/htslib install -m 0644 libhts.a /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/lib/libhts.a install -m 0644 htsfile.1 tabix.1 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/man/man1 install -m 0644 faidx.5 sam.5 vcf.5 /wrkdirs/usr/ports/biology/htslib/work/stage/usr/local/man/man5 ====> 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 htslib-1.3 =========================================================================== =================================================== =========================================================================== ====>> Recording filesystem state for preinst... done =================================================== ===> Installing for htslib-1.3 ===> htslib-1.3 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Checking if htslib already installed ===> Registering installation for htslib-1.3 [releng_9_3-default] Installing htslib-1.3... =========================================================================== ====>> Checking shared library dependencies 0x0000000000000001 (NEEDED) Shared library: [libc.so.7] 0x0000000000000001 (NEEDED) Shared library: [libcrypto.so.6] 0x0000000000000001 (NEEDED) Shared library: [libcurl.so.4] 0x0000000000000001 (NEEDED) Shared library: [libm.so.5] 0x0000000000000001 (NEEDED) Shared library: [libthr.so.3] 0x0000000000000001 (NEEDED) Shared library: [libz.so.6] =================================================== ===> Deinstalling for htslib ===> Deinstalling htslib-1.3 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: htslib-1.3 The operation will free 3 MiB. [releng_9_3-default] [1/1] Deinstalling htslib-1.3... [releng_9_3-default] [1/1] Deleting files for htslib-1.3: .......... done =========================================================================== ====>> Checking for extra files and directories [00:00:28] ====>> Installing from package [releng_9_3-default] Installing htslib-1.3... [releng_9_3-default] Extracting htslib-1.3: .......... done [00:00:29] ====>> Cleaning up ===> Cleaning for htslib-1.3 [00:00:29] ====>> 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: htslib-1.3 The operation will free 3 MiB. [releng_9_3-default] [1/1] Deinstalling htslib-1.3... [releng_9_3-default] [1/1] Deleting files for htslib-1.3: .......... done build of biology/htslib ended at Tue Dec 22 16:03:23 MST 2015 build time: 00:00:24 [00:00:29] ====>> Cleaning up [00:00:29] ====>> Umounting file systems