=> Building biology/samtools build started at Tue Oct 4 19:29:05 PDT 2016 port directory: /usr/ports/biology/samtools 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/../02//usr/ports/biology/samtools/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=samtools-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--- ---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/biology/samtools XDG_CONFIG_HOME=/wrkdirs/biology/samtools HOME=/wrkdirs/biology/samtools TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 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/biology/samtools XDG_CONFIG_HOME=/wrkdirs/biology/samtools HOME=/wrkdirs/biology/samtools 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 -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib" LIBS="" CXX="c++" CXXFLAGS=" -pipe -I/usr/local/include -I/usr/local/include/ncurses -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/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 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 MIT accepted by the user =========================================================================== =================================================== ===> samtools-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 ===> samtools-1.3.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of samtools-1.3.1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by samtools-1.3.1 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by samtools-1.3.1 for building => SHA256 Checksum OK for samtools-samtools-1.3.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by samtools-1.3.1 for building ===> Extracting for samtools-1.3.1 => SHA256 Checksum OK for samtools-samtools-1.3.1_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for samtools-1.3.1 ===> Applying ports patches for samtools-1.3.1 /bin/cp /usr/ports/biology/samtools/files/ax_with_htslib.m4 /wrkdirs/biology/samtools/samtools-1.3.1/ /bin/cp /usr/ports/biology/samtools/files/ax_with_curses.m4 /wrkdirs/biology/samtools/samtools-1.3.1/ =========================================================================== =================================================== ===> samtools-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 *************************************************************************** ===> samtools-1.3.1 depends on package: htslib>=1.3 - found ===> Returning to build of samtools-1.3.1 ===> samtools-1.3.1 depends on executable: autoconf-2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_1.txz Installing autoconf-2.69_1... `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: ........ done `-- Installing perl5-5.20.3_15... `-- Extracting perl5-5.20.3_15: .......... done `-- Installing m4-1.4.17_1,1... `-- Extracting m4-1.4.17_1,1: .......... done Extracting autoconf-2.69_1: .......... done Message from perl5-5.20.3_15: 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-1.3.1 depends on executable: autoconf-2.69 - found ===> Returning to build of samtools-1.3.1 ===> samtools-1.3.1 depends on executable: autoheader-2.69 - found ===> samtools-1.3.1 depends on executable: autoreconf-2.69 - found ===> samtools-1.3.1 depends on executable: aclocal-1.15 - not found ===> Installing existing package /packages/All/automake-1.15_1.txz Installing automake-1.15_1... `-- Installing automake-wrapper-20131203... `-- Extracting automake-wrapper-20131203: ... done Extracting automake-1.15_1: .......... done ===> samtools-1.3.1 depends on executable: aclocal-1.15 - found ===> Returning to build of samtools-1.3.1 ===> samtools-1.3.1 depends on executable: automake-1.15 - found ===> samtools-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 ===> samtools-1.3.1 depends on executable: gmake - found ===> Returning to build of samtools-1.3.1 ===> samtools-1.3.1 depends on file: /usr/local/lib/libncurses.so.6 - not found ===> Installing existing package /packages/All/ncurses-6.0_5.txz Installing ncurses-6.0_5... Extracting ncurses-6.0_5: .......... done Message from ncurses-6.0_5: ===> NOTICE: The ncurses 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 ===> samtools-1.3.1 depends on file: /usr/local/lib/libncurses.so.6 - found ===> Returning to build of samtools-1.3.1 =========================================================================== =================================================== ===> samtools-1.3.1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) =========================================================================== =================================================== ===> Configuring for samtools-1.3.1 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 special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking location of HTSlib source tree... none found checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking 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-1.3.1 gmake[1]: Entering directory '/wrkdirs/biology/samtools/samtools-1.3.1' cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_index.o bam_index.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_plcmd.o bam_plcmd.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o sam_view.o sam_view.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_cat.o bam_cat.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_md.o bam_md.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_reheader.o bam_reheader.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_sort.o bam_sort.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bedidx.o bedidx.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o kprobaln.o kprobaln.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_rmdup.o bam_rmdup.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_rmdupse.o bam_rmdupse.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_mate.o bam_mate.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_stat.o bam_stat.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam2bcf.o bam2bcf.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam2bcf_indel.o bam2bcf_indel.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o errmod.o errmod.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o sample.o sample.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o sam_opts.o sam_opts.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o cut_target.o cut_target.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o phase.o phase.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam2depth.o bam2depth.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o padding.o padding.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bedcov.o bedcov.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bamshuf.o bamshuf.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o faidx.o faidx.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o dict.o dict.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o stats.o stats.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o stats_isize.o stats_isize.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_flags.o bam_flags.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_split.o bam_split.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_tview.o bam_tview.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_tview_curses.o bam_tview_curses.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_tview_html.o bam_tview_html.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_lpileup.o bam_lpileup.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_quickcheck.o bam_quickcheck.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_addrprg.o bam_addrprg.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_aux.o bam_aux.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam.o bam.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_import.o bam_import.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o sam.o sam.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o sam_header.o sam_header.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o bam_plbuf.o bam_plbuf.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o misc/ace2sam.o misc/ace2sam.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DMAQ_LONGREADS -I. -I/usr/local/include -c -o misc/maq2sam-long.o misc/maq2sam.c misc/maq2sam.c:34:0: warning: "PACKAGE_VERSION" redefined #define PACKAGE_VERSION "r439" ^ In file included from misc/maq2sam.c:25:0: ./config.h:56:0: note: this is the location of the previous definition #define PACKAGE_VERSION "1.3" ^ cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o misc/maq2sam-short.o misc/maq2sam.c misc/maq2sam.c:34:0: warning: "PACKAGE_VERSION" redefined #define PACKAGE_VERSION "r439" ^ In file included from misc/maq2sam.c:25:0: ./config.h:56:0: note: this is the location of the previous definition #define PACKAGE_VERSION "1.3" ^ cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o misc/md5fa.o misc/md5fa.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o misc/wgsim.o misc/wgsim.c misc/wgsim.c:45:0: warning: "PACKAGE_VERSION" redefined #define PACKAGE_VERSION "0.3.2" ^ In file included from misc/wgsim.c:30:0: ./config.h:56:0: note: this is the location of the previous definition #define PACKAGE_VERSION "1.3" ^ cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/test.o test/test.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/split/test_parse_args.o test/split/test_parse_args.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -I. -I/usr/local/include -c -o test/vcf-miniview.o test/vcf-miniview.c cc -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -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 -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o misc/ace2sam misc/ace2sam.o -lz cc -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o misc/maq2sam-long misc/maq2sam-long.o -lz cc -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o misc/maq2sam-short misc/maq2sam-short.o -lz cc -rdynamic -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o misc/md5fa misc/md5fa.o -lhts -lz cc -rdynamic -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz cc -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o misc/wgsim misc/wgsim.o -lm -lz cc -pthread -rdynamic -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -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 -L/usr/local/lib -Wl,-rpath=/usr/local/lib -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 -L/usr/local/lib -Wl,-rpath=/usr/local/lib -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 -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o test/vcf-miniview test/vcf-miniview.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -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 -L/usr/local/lib -Wl,-rpath=/usr/local/lib -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 -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz cc -pthread -rdynamic -L/usr/local/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz gmake[1]: Leaving directory '/wrkdirs/biology/samtools/samtools-1.3.1' =========================================================================== =================================================== ===> samtools-1.3.1 depends on file: /usr/local/lib/libncurses.so.6 - found =========================================================================== =================================================== ===> Staging for samtools-1.3.1 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/biology/samtools/samtools-1.3.1' /bin/mkdir -p /wrkdirs/biology/samtools/stage/usr/local/bin /wrkdirs/biology/samtools/stage/usr/local/bin/samtools_misc /wrkdirs/biology/samtools/stage/usr/local/man/man1 install -s -m 555 samtools /wrkdirs/biology/samtools/stage/usr/local/bin install -s -m 555 misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /wrkdirs/biology/samtools/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/biology/samtools/stage/usr/local/bin/samtools_misc install -m 0644 samtools.1 misc/wgsim.1 /wrkdirs/biology/samtools/stage/usr/local/man/man1 gmake[1]: Leaving directory '/wrkdirs/biology/samtools/samtools-1.3.1' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for samtools-1.3.1 file sizes/checksums [26]: . done packing files [26]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for samtools-1.3.1 build of biology/samtools ended at Tue Oct 4 19:29:49 PDT 2016 build time: 00:00:44