Attachment 153847 Details for Bug 198292 – Poudriere Log for 10.1

Poudriere Log for 10.1

samtools-1.2-10_1.log (text/x-log), 29.99 KB, created by cartwright on 2015-03-05 17:39:30 UTC

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Creator: cartwright

Created: 2015-03-05 17:39:30 UTC

Size: 29.99 KB

patch

obsolete

>[00:00:00] ====>> Creating the reference jail... done
>[00:00:01] ====>> Mounting system devices for releng_10_1-default
>[00:00:01] ====>> Mounting ports/packages/distfiles
>[00:00:01] ====>> Stashing existing package repository
>[00:00:01] ====>> Mounting packages from: /usr/local/poudriere/data/packages/releng_10_1-default
>[00:00:01] ====>> Mounting /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
>[00:00:01] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_10_1-default/2015-03-05_10h34m27s
>[00:00:01] ====>> Loading MOVED
>[00:00:01] ====>> 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 stale symlinks
>[00:00:04] ====>> Deleting empty directories
>[00:00:04] ====>> Cleaning the build queue
>[00:00:04] ====>> Recording filesystem state for prepkg... done
>[00:00:05] ====>> Committing packages to repository
>[00:00:05] ====>> Removing old packages
>[00:00:05] ====>> Portlint check
>looks fine.
>[00:00:06] ====>> Building with flags: 
>[00:00:06] ====>> Removing existing /usr/local
>build started at Thu Mar  5 10:34:33 MST 2015
>port directory: /usr/ports/biology/samtools
>building for: FreeBSD releng_10_1-default 10.1-RELEASE FreeBSD 10.1-RELEASE amd64
>maintained by: cartwright@asu.edu
>Makefile ident:      $FreeBSD: head/biology/samtools/Makefile 374767 2014-12-15 21:59:19Z pawel $
>Poudriere version: 3.1.1
>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=/
>PWD=/usr/local/poudriere/data/.m/releng_10_1-default/ref/usr/ports/biology/samtools
>MASTERNAME=releng_10_1-default
>USER=root
>HOME=/root
>POUDRIERE_VERSION=3.1.1
>TRYBROKEN=yes
>LOCALBASE=/usr/local
>PACKAGE_BUILDING=yes
>DEV_WARNING_WAIT=0
>---End Environment---
>
>---Begin OPTIONS List---
>---End OPTIONS List---
>
>--CONFIGURE_ARGS--
>
>--End CONFIGURE_ARGS--
>
>--CONFIGURE_ENV--
>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" MAKE=gmake 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" 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 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/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---
>=======================<phase: check-sanity   >============================
>===>  License MIT accepted by the user
>===========================================================================
>=======================<phase: pkg-depends    >============================
>===>   samtools-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-1.4.12.txz
>[releng_10_1-default] Installing pkg-1.4.12...
>[releng_10_1-default] Extracting pkg-1.4.12... done
>Message for pkg-1.4.12:
> If you are upgrading from the old package format, first run:
>
>  # pkg2ng
>===>   Returning to build of samtools-1.2
>===========================================================================
>=======================<phase: fetch-depends  >============================
>===========================================================================
>=======================<phase: fetch          >============================
>===>  License MIT accepted by the user
>===>   samtools-1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by samtools-1.2 for building
>===========================================================================
>=======================<phase: checksum       >============================
>===>  License MIT accepted by the user
>===>   samtools-1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by samtools-1.2 for building
>=> SHA256 Checksum OK for samtools-1.2.tar.gz.
>===========================================================================
>=======================<phase: extract-depends>============================
>===========================================================================
>=======================<phase: extract        >============================
>===>  License MIT accepted by the user
>===>   samtools-1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by samtools-1.2 for building
>===>  Extracting for samtools-1.2
>=> SHA256 Checksum OK for samtools-1.2.tar.gz.
>===========================================================================
>=======================<phase: patch-depends  >============================
>===========================================================================
>=======================<phase: patch          >============================
>===>  Patching for samtools-1.2
>===>  Applying FreeBSD patches for samtools-1.2
>===========================================================================
>=======================<phase: build-depends  >============================
>===>   samtools-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 samtools-1.2
>===>   samtools-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-0.2.2...
>[releng_10_1-default] |   `-- Extracting indexinfo-0.2.2... 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 samtools-1.2
>===========================================================================
>=======================<phase: lib-depends    >============================
>===>   samtools-1.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so.1.2.1)
>===========================================================================
>====>> Recording filesystem state for prebuild... done
>=======================<phase: configure      >============================
>===>   samtools-1.2 depends on package: htslib>=1.2 - found
>===>   samtools-1.2 depends on executable: gmake - found
>===>   samtools-1.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so.1.2.1)
>===>  Configuring for samtools-1.2
>===========================================================================
>=======================<phase: build          >============================
>===>  Building for samtools-1.2
>gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/samtools/work/samtools-samtools-6af451d'
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o bedidx.o bedidx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o kprobaln.o kprobaln.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o bam_color.o bam_color.c
>echo '#define SAMTOOLS_VERSION "1.2"' > version.h
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o bam2bcf.o bam2bcf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o errmod.o errmod.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o sample.o sample.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o phase.o phase.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o bam2depth.o bam2depth.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o padding.o padding.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o bedcov.o bedcov.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o bamshuf.o bamshuf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o faidx.o faidx.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o stats.o stats.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o bam.o bam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o sam.o sam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o misc/md5.o misc/md5.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -I. -I/usr/local/include -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -march=bdver1  -fstack-protector -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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 -Wall -Wno-unused-function -Wno-implicit-function-declaration -I/usr/local/include -D_CURSES_LIB=1 -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  -L/usr/local/lib -fstack-protector  -o misc/md5fa misc/md5fa.o misc/md5.o  -lz
>cc  -L/usr/local/lib -fstack-protector  -o misc/md5sum-lite misc/md5sum-lite.o 
>cc  -L/usr/local/lib -fstack-protector  -o misc/wgsim misc/wgsim.o  -lm -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/split/test_count_rg test/split/test_count_rg.o test/test.o -lhts  -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o -lhts  -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o -lhts  -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/vcf-miniview test/vcf-miniview.o -lhts  -lz
>cc -pthread  -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 cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.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 libbam.a -lhts  -lcurses  -lm -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/split/test_parse_args test/split/test_parse_args.o test/test.o -lhts  -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o -lhts  -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o -lhts  -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/merge/test_pretty_header test/merge/test_pretty_header.o -lhts  -lz
>cc -pthread  -L/usr/local/lib -fstack-protector  -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o -lhts  -lz
>gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/samtools/work/samtools-samtools-6af451d'
>===========================================================================
>====>> Checking for filesystem violations... done
>=======================<phase: run-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prestage... done
>=======================<phase: stage          >============================
>===>  Staging for samtools-1.2
>===>   samtools-1.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so.1.2.1)
>===>   Generating temporary packing list
>gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/samtools/work/samtools-samtools-6af451d'
>/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 -o root -g wheel -m 555 samtools /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/bin
>install  -s -o root -g wheel -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  -o root -g wheel -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  -o root -g wheel -m 0644 samtools.1 /wrkdirs/usr/ports/biology/samtools/work/stage/usr/local/man/man1
>gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/samtools/work/samtools-samtools-6af451d'
>====> 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
>=======================<phase: package        >============================
>===>  Building package for samtools-1.2
>/usr/local/lib/libhts.so.1.2.1
>===========================================================================
>=======================<phase: install-mtree  >============================
>===========================================================================
>====>> Recording filesystem state for preinst... done
>=======================<phase: install        >============================
>===>  Installing for samtools-1.2
>===>   samtools-1.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so.1.2.1)
>===>  Checking if samtools already installed
>/usr/local/lib/libhts.so.1.2.1
>===>   Registering installation for samtools-1.2
>[releng_10_1-default] Installing samtools-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: [libhts.so.1]
> 0x0000000000000001 (NEEDED)             Shared library: [libm.so.5]
> 0x0000000000000001 (NEEDED)             Shared library: [libncurses.so.8]
> 0x0000000000000001 (NEEDED)             Shared library: [libthr.so.3]
> 0x0000000000000001 (NEEDED)             Shared library: [libz.so.6]
>=======================<phase: deinstall      >============================
>===>  Deinstalling for samtools
>===>   Deinstalling samtools-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:
>	samtools-1.2
>
>The operation will free 549 KiB.
>[releng_10_1-default] [1/1] Deinstalling samtools-1.2...
>[releng_10_1-default] [1/1] Deleting files for samtools-1.2... done
>===========================================================================
>====>> Checking for extra files and directories
>[00:00:17] ====>> Installing from package
>[releng_10_1-default] Installing samtools-1.2...
>[releng_10_1-default] Extracting samtools-1.2... done
>Message for samtools-1.2:
> Add /usr/local/bin/samtools_misc to your path to use miscellaneous tools.
>[00:00:17] ====>> Cleaning up
>===>  Cleaning for samtools-1.2
>[00:00:17] ====>> 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-1.2
>
>The operation will free 549 KiB.
>[releng_10_1-default] [1/1] Deinstalling samtools-1.2...
>[releng_10_1-default] [1/1] Deleting files for samtools-1.2... done
>build of biology/samtools ended at Thu Mar  5 10:34:44 MST 2015
>build time: 00:00:11
>[00:00:17] ====>> Cleaning up
>[00:00:18] ====>> Umounting file systems

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Attachments on bug 198292: 153798 | 153846 | 153847