[00:00:00] ====>> Creating the reference jail... done [00:00:01] ====>> Mounting system devices for releng_10_1-default [00:00:02] ====>> Mounting ports/packages/distfiles [00:00:02] ====>> Stashing existing package repository [00:00:02] ====>> Mounting packages from: /usr/local/poudriere/data/packages/releng_10_1-default [00:00:02] ====>> Copying /var/db/ports from: /usr/local/etc/poudriere.d/options [00:00:02] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/make.conf [00:00:02] ====>> 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 [00:00:02] ====>> Starting jail releng_10_1-default [00:00:02] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_10_1-default/2015-12-22_16h05m03s [00:00:02] ====>> Loading MOVED [00:00:02] ====>> Calculating ports order and dependencies [00:00:03] ====>> Sanity checking the repository [00:00:03] ====>> Checking packages for incremental rebuild needed [00:00:04] ====>> Deleting htslib-1.2.1.txz: new version: 1.3 [00:00:04] ====>> Deleting stale symlinks [00:00:04] ====>> Deleting empty directories [00:00:04] ====>> Cleaning the build queue [00:00:05] ====>> Recording filesystem state for prepkg... done [00:00:05] ====>> Building 1 packages using 1 builders [00:00:05] ====>> Starting/Cloning builders [00:00:06] ====>> Hit CTRL+t at any time to see build progress and stats [00:00:06] ====>> [01][00:00:00] Starting build of biology/htslib [00:00:40] ====>> [01][00:00:34] Finished build of biology/htslib: Success [00:00:40] ====>> Stopping 1 builders [00:00:44] ====>> Creating pkgng repository Creating repository in /tmp/packages: . done Packing files for repository: .... done [00:00:45] ====>> Committing packages to repository [00:00:45] ====>> Removing old packages [00:00:45] ====>> Portlint check WARN: /usr/local/poudriere/data/.m/releng_10_1-default/ref/usr/ports/biology/samtools/work/pkg-message: possible use of absolute pathname "/usr/local/bin/samto...". WARN: /usr/local/poudriere/data/.m/releng_10_1-default/ref/usr/ports/biology/samtools/work/pkg-message: possible direct use of "Add /usr/local" found. if so, use ${PREFIX} or ${LOCALBASE}, as appropriate. FATAL: work: be sure to cleanup the working directory before committing the port. 1 fatal error and 2 warnings found. [00:00:46] ====>> Building with flags: [00:00:46] ====>> Removing existing /usr/local build started at Tue Dec 22 16:05:49 MST 2015 port directory: /usr/ports/biology/samtools building for: FreeBSD releng_10_1-default 10.2-RELEASE-p8 FreeBSD 10.2-RELEASE-p8 amd64 maintained by: cartwright@asu.edu Makefile ident: $FreeBSD: head/biology/samtools/Makefile 385521 2015-05-06 15:16:53Z mat $ Poudriere version: 3.1.8 Host OSVERSION: 1002000 Jail OSVERSION: 1002000 ---Begin Environment--- PKGREPOSITORY=/tmp/pkgs PACKAGES=/tmp/pkgs OSVERSION=1002000 UNAME_v=FreeBSD 10.2-RELEASE-p8 UNAME_r=10.2-RELEASE-p8 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_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/samtools MASTERNAME=releng_10_1-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--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --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/samtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/samtools/work HOME=/wrkdirs/usr/ports/biology/samtools/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_SCRIPT="install -m 555" INSTALL_DIR="/bin/mkdir -p" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/samtools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/samtools/work HOME=/wrkdirs/usr/ports/biology/samtools/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 -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 -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=10.2 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/samtools" EXAMPLESDIR="share/examples/samtools" DATADIR="share/samtools" WWWDIR="www/samtools" ETCDIR="etc/samtools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/samtools DOCSDIR=/usr/local/share/doc/samtools EXAMPLESDIR=/usr/local/share/examples/samtools WWWDIR=/usr/local/www/samtools ETCDIR=/usr/local/etc/samtools --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 MIT accepted by the user =========================================================================== =================================================== ===> samtools-1.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.6.2.txz [releng_10_1-default] Installing pkg-1.6.2... [releng_10_1-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 ===> samtools-1.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of samtools-1.3 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> samtools-1.3 depends on file: /usr/local/sbin/pkg - found => samtools-samtools-1.3_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/samtools/samtools/tar.gz/1.3?dummy=/samtools-samtools-1.3_GH0.tar.gz fetch: https://codeload.github.com/samtools/samtools/tar.gz/1.3?dummy=/samtools-samtools-1.3_GH0.tar.gz: size unknown fetch: https://codeload.github.com/samtools/samtools/tar.gz/1.3?dummy=/samtools-samtools-1.3_GH0.tar.gz: size of remote file is not known samtools-samtools-1.3_GH0.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by samtools-1.3 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> samtools-1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by samtools-1.3 for building => SHA256 Checksum OK for samtools-samtools-1.3_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> samtools-1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by samtools-1.3 for building ===> Extracting for samtools-1.3 => SHA256 Checksum OK for samtools-samtools-1.3_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for samtools-1.3 ===> Applying FreeBSD patches for samtools-1.3 /bin/cp /usr/ports/biology/samtools/files/ax_with_htslib.m4 /wrkdirs/usr/ports/biology/samtools/work/samtools-1.3/ /bin/cp /usr/ports/biology/samtools/files/ax_with_curses.m4 /wrkdirs/usr/ports/biology/samtools/work/samtools-1.3/ =========================================================================== =================================================== ===> samtools-1.3 depends on package: htslib>=1.3 - not found ===> Installing existing package /packages/All/htslib-1.3.txz [releng_10_1-default] Installing htslib-1.3... [releng_10_1-default] `-- Installing curl-7.46.0_1... [releng_10_1-default] | `-- Installing ca_root_nss-3.20.1... [releng_10_1-default] | `-- Extracting ca_root_nss-3.20.1: ....... done [releng_10_1-default] `-- Extracting curl-7.46.0_1: .......... done [releng_10_1-default] Extracting htslib-1.3: .......... 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 *************************************************************************** ===> samtools-1.3 depends on package: htslib>=1.3 - found ===> Returning to build of samtools-1.3 ===> samtools-1.3 depends on executable: autoconf-2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69.txz [releng_10_1-default] Installing autoconf-2.69... [releng_10_1-default] `-- Installing indexinfo-0.2.4... [releng_10_1-default] `-- Extracting indexinfo-0.2.4: .... done [releng_10_1-default] `-- Installing autoconf-wrapper-20131203... [releng_10_1-default] `-- Extracting autoconf-wrapper-20131203: ........ done [releng_10_1-default] `-- Installing perl5-5.20.3_8... [releng_10_1-default] `-- Extracting perl5-5.20.3_8: .......... done [releng_10_1-default] `-- Installing m4-1.4.17_1,1... [releng_10_1-default] `-- Extracting m4-1.4.17_1,1: .......... done [releng_10_1-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. ===> samtools-1.3 depends on executable: autoconf-2.69 - found ===> Returning to build of samtools-1.3 ===> samtools-1.3 depends on executable: autoheader-2.69 - found ===> samtools-1.3 depends on executable: autoreconf-2.69 - found ===> samtools-1.3 depends on executable: aclocal-1.15 - not found ===> Installing existing package /packages/All/automake-1.15_1.txz [releng_10_1-default] Installing automake-1.15_1... [releng_10_1-default] `-- Installing automake-wrapper-20131203... [releng_10_1-default] `-- Extracting automake-wrapper-20131203: ... done [releng_10_1-default] Extracting automake-1.15_1: .......... done ===> samtools-1.3 depends on executable: aclocal-1.15 - found ===> Returning to build of samtools-1.3 ===> samtools-1.3 depends on executable: automake-1.15 - found ===> samtools-1.3 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.1_2.txz [releng_10_1-default] Installing gmake-4.1_2... [releng_10_1-default] `-- Installing gettext-runtime-0.19.6... [releng_10_1-default] `-- Extracting gettext-runtime-0.19.6: .......... done [releng_10_1-default] Extracting gmake-4.1_2: .......... done ===> samtools-1.3 depends on executable: gmake - found ===> Returning to build of samtools-1.3 =========================================================================== =================================================== ===> samtools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) =========================================================================== ====>> Recording filesystem state for prebuild... done =================================================== ===> samtools-1.3 depends on package: htslib>=1.3 - found ===> samtools-1.3 depends on executable: autoconf-2.69 - found ===> samtools-1.3 depends on executable: autoheader-2.69 - found ===> samtools-1.3 depends on executable: autoreconf-2.69 - found ===> samtools-1.3 depends on executable: aclocal-1.15 - found ===> samtools-1.3 depends on executable: automake-1.15 - found ===> samtools-1.3 depends on executable: gmake - found ===> samtools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Configuring for samtools-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 location of HTSlib source tree... none found checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for NcursesW wide-character library... yes checking for working ncursesw/curses.h... no checking for working ncursesw.h... no checking for working ncurses.h... yes checking for zlib.h... (cached) yes checking for inflate in -lz... yes configure: creating ./config.status config.status: creating config.mk config.status: creating config.h =========================================================================== =================================================== ===> Building for samtools-1.3 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/samtools/work/samtools-1.3' cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_index.o bam_index.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_plcmd.o bam_plcmd.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o sam_view.o sam_view.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_cat.o bam_cat.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_md.o bam_md.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_reheader.o bam_reheader.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_sort.o bam_sort.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bedidx.o bedidx.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o kprobaln.o kprobaln.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_rmdup.o bam_rmdup.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_rmdupse.o bam_rmdupse.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_mate.o bam_mate.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_stat.o bam_stat.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.3"' > version.h cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam2bcf.o bam2bcf.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam2bcf_indel.o bam2bcf_indel.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o errmod.o errmod.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o sample.o sample.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o sam_opts.o sam_opts.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o cut_target.o cut_target.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o phase.o phase.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam2depth.o bam2depth.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o padding.o padding.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bedcov.o bedcov.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bamshuf.o bamshuf.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o faidx.o faidx.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o dict.o dict.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o stats.o stats.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o stats_isize.o stats_isize.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_flags.o bam_flags.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_split.o bam_split.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_tview.o bam_tview.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_tview_curses.o bam_tview_curses.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_tview_html.o bam_tview_html.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_lpileup.o bam_lpileup.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_quickcheck.o bam_quickcheck.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_addrprg.o bam_addrprg.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_aux.o bam_aux.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam.o bam.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_import.o bam_import.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o sam.o sam.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o sam_header.o sam_header.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bam_plbuf.o bam_plbuf.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o misc/ace2sam.o misc/ace2sam.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -DMAQ_LONGREADS -I. -I/usr/local/include -c -o misc/maq2sam-long.o misc/maq2sam.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o misc/maq2sam-short.o misc/maq2sam.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o misc/md5fa.o misc/md5fa.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o misc/wgsim.o misc/wgsim.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/test.o test/test.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o test/vcf-miniview.o test/vcf-miniview.c cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1 -fstack-protector -I. -I/usr/local/include -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o cc -L/usr/local/lib -fstack-protector -o misc/ace2sam misc/ace2sam.o -lz cc -L/usr/local/lib -fstack-protector -o misc/maq2sam-long misc/maq2sam-long.o -lz cc -L/usr/local/lib -fstack-protector -o misc/maq2sam-short misc/maq2sam-short.o -lz cc -rdynamic -L/usr/local/lib -fstack-protector -o misc/md5fa misc/md5fa.o -lhts -lz cc -rdynamic -L/usr/local/lib -fstack-protector -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz cc -L/usr/local/lib -fstack-protector -o misc/wgsim misc/wgsim.o -lm -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o test/vcf-miniview test/vcf-miniview.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a -lhts -lncursesw -lm -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -fstack-protector -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/samtools/work/samtools-1.3' =========================================================================== ====>> Checking for filesystem violations... done =================================================== =========================================================================== ====>> Recording filesystem state for prestage... done =================================================== ===> Staging for samtools-1.3 ===> samtools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/samtools/work/samtools-1.3' /bin/mkdir -p /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin/samtools_misc /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/man/man1 install -s -m 555 samtools /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin install -s -m 555 misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin/samtools_misc install -m 555 misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin/samtools_misc install -m 0644 samtools.1 misc/wgsim.1 /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/man/man1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/samtools/work/samtools-1.3' ====> 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 samtools-1.3 =========================================================================== =================================================== =========================================================================== ====>> Recording filesystem state for preinst... done =================================================== ===> Installing for samtools-1.3 ===> samtools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Checking if samtools already installed ===> Registering installation for samtools-1.3 [releng_10_1-default] Installing samtools-1.3... The miscellaneous tools included with Samtools have been installed to /usr/local/bin/samtools_misc. Add that directory to your path if you want to use these tools. Some of these tools depend on Perl5, and it will need to be installed to use them. =========================================================================== ====>> Checking shared library dependencies 0x0000000000000001 (NEEDED) Shared library: [libc.so.7] 0x0000000000000001 (NEEDED) Shared library: [libhts.so.1] 0x0000000000000001 (NEEDED) Shared library: [libm.so.5] 0x0000000000000001 (NEEDED) Shared library: [libncursesw.so.8] 0x0000000000000001 (NEEDED) Shared library: [libthr.so.3] 0x0000000000000001 (NEEDED) Shared library: [libz.so.6] =================================================== ===> Deinstalling for samtools ===> Deinstalling samtools-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: samtools-1.3 The operation will free 627 KiB. [releng_10_1-default] [1/1] Deinstalling samtools-1.3... [releng_10_1-default] [1/1] Deleting files for samtools-1.3: .......... done =========================================================================== ====>> Checking for extra files and directories [00:01:05] ====>> Installing from package [releng_10_1-default] Installing samtools-1.3... [releng_10_1-default] Extracting samtools-1.3: .......... done Message from samtools-1.3: The miscellaneous tools included with Samtools have been installed to /usr/local/bin/samtools_misc. Add that directory to your path if you want to use these tools. Some of these tools depend on Perl5, and it will need to be installed to use them. [00:01:05] ====>> Cleaning up ===> Cleaning for samtools-1.3 [00:01:06] ====>> 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: samtools-1.3 The operation will free 627 KiB. [releng_10_1-default] [1/1] Deinstalling samtools-1.3... [releng_10_1-default] [1/1] Deleting files for samtools-1.3: .......... done build of biology/samtools ended at Tue Dec 22 16:06:08 MST 2015 build time: 00:00:19 [00:01:06] ====>> Cleaning up [00:01:06] ====>> Umounting file systems