Attachment 164521 Details for Bug 205526 – poudriere testport output for releng_9_3

poudriere testport output for releng_9_3

bcftools-1.3_releng_9.txt (text/plain), 29.37 KB, created by cartwright on 2015-12-22 23:27:30 UTC

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Creator: cartwright

Created: 2015-12-22 23:27:30 UTC

Size: 29.37 KB

patch

obsolete

>[00:00:00] ====>> Creating the reference jail... done
>[00:00:01] ====>> Mounting system devices for releng_9_3-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_9_3-default
>[00:00:01] ====>> Copying /var/db/ports from: /usr/local/etc/poudriere.d/options
>[00:00:01] ====>> Appending to make.conf: /usr/local/etc/poudriere.d/make.conf
>/etc/resolv.conf -> /usr/local/poudriere/data/.m/releng_9_3-default/ref/etc/resolv.conf
>[00:00:01] ====>> Starting jail releng_9_3-default
>[00:00:01] ====>> Logs: /usr/local/poudriere/data/logs/bulk/releng_9_3-default/2015-12-22_16h08m55s
>[00:00:01] ====>> Loading MOVED
>[00:00:01] ====>> Calculating ports order and dependencies
>[00:00:04] ====>> Sanity checking the repository
>[00:00:04] ====>> Checking packages for incremental rebuild needed
>[00:00:05] ====>> Deleting gsl-1.16_2.txz: missing dependency: indexinfo-0.2.3
>[00:00:05] ====>> Deleting stale symlinks
>[00:00:05] ====>> Deleting empty directories
>[00:00:05] ====>> Cleaning the build queue
>[00:00:05] ====>> Recording filesystem state for prepkg... done
>[00:00:06] ====>> Building 1 packages using 1 builders
>[00:00:06] ====>> Starting/Cloning builders
>[00:00:07] ====>> Hit CTRL+t at any time to see build progress and stats
>[00:00:07] ====>> [01][00:00:00] Starting build of math/gsl
>[00:02:48] ====>> [01][00:02:41] Finished build of math/gsl: Success
>[00:02:49] ====>> Stopping 1 builders
>[00:02:52] ====>> Creating pkgng repository
>Creating repository in /tmp/packages: . done
>Packing files for repository: .... done
>[00:02:53] ====>> Committing packages to repository
>[00:02:53] ====>> Removing old packages
>[00:02:53] ====>> Portlint check
>WARN: Makefile: "LICENSE" has to appear earlier.
>0 fatal errors and 1 warning found.
>[00:02:54] ====>> Building with flags: 
>[00:02:54] ====>> Removing existing /usr/local
>build started at Tue Dec 22 16:11:48 MST 2015
>port directory: /usr/ports/biology/bcftools
>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/bcftools/Makefile 388638 2015-06-05 21:01:13Z pi $
>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=/usr/local/poudriere/data/.m/releng_9_3-default/ref/.p/pool
>PWD=/usr/local/poudriere/data/.m/releng_9_3-default/ref/usr/ports/biology/bcftools
>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 bcftools-1.3:
>     GPL=on: Enable modules that rely on GPL code
>===> Use 'make config' to modify these settings
>---End OPTIONS List---
>
>--CONFIGURE_ARGS--
>
>--End CONFIGURE_ARGS--
>
>--CONFIGURE_ENV--
>MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcftools/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcftools/work  HOME=/wrkdirs/usr/ports/biology/bcftools/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
>--End CONFIGURE_ENV--
>
>--MAKE_ENV--
>INSTALL_LIB="install  -s -m 444"  INSTALL_DATA="install  -m 0644"  INSTALL_PROGRAM="install  -s -m 555"  INSTALL_SCRIPT="install  -m 555"  INSTALL_DIR="/bin/mkdir -p" USE_GPL=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcftools/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcftools/work  HOME=/wrkdirs/usr/ports/biology/bcftools/work TMPDIR="/tmp" NO_PIE=yes 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/bcftools"
>EXAMPLESDIR="share/examples/bcftools"
>DATADIR="share/bcftools"
>WWWDIR="www/bcftools"
>ETCDIR="etc/bcftools"
>--End PLIST_SUB--
>
>--SUB_LIST--
>PREFIX=/usr/local
>LOCALBASE=/usr/local
>DATADIR=/usr/local/share/bcftools
>DOCSDIR=/usr/local/share/doc/bcftools
>EXAMPLESDIR=/usr/local/share/examples/bcftools
>WWWDIR=/usr/local/www/bcftools
>ETCDIR=/usr/local/etc/bcftools
>--End SUB_LIST--
>
>---Begin make.conf---
>USE_PACKAGE_DEPENDS=yes
>BATCH=yes
>WRKDIRPREFIX=/wrkdirs
>USE_PACKAGE_DEPENDS=yes
>BATCH=yes
>WRKDIRPREFIX=/wrkdirs
>PORTSDIR=/usr/ports
>PACKAGES=/packages
>DISTDIR=/distfiles
>#### /usr/local/etc/poudriere.d/make.conf ####
>CFLAGS += -O2 -fno-strict-aliasing -pipe
>
>#DEFAULT_VERSIONS=python=2.7 python2=2.7 python3=3.4
>#WITH_BDB_VER=6
>#WITH_BDB6_PERMITTED=yes
>TEX_DEFAULT=texlive
>
>MAKE_JOBS_NUMBER_LIMIT=8
>
>---End make.conf---
>=======================<phase: check-sanity   >============================
>===>  License GPLv3 accepted by the user
>===>  Found saved configuration for bcftools-1.2
>===========================================================================
>=======================<phase: pkg-depends    >============================
>===>   bcftools-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
>===>   bcftools-1.3 depends on file: /usr/local/sbin/pkg - found
>===>   Returning to build of bcftools-1.3
>===========================================================================
>=======================<phase: fetch-depends  >============================
>===========================================================================
>=======================<phase: fetch          >============================
>===>  License GPLv3 accepted by the user
>===>  Found saved configuration for bcftools-1.2
>===>   bcftools-1.3 depends on file: /usr/local/sbin/pkg - found
>=> samtools-bcftools-1.3_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
>=> Attempting to fetch https://codeload.github.com/samtools/bcftools/tar.gz/1.3?dummy=/samtools-bcftools-1.3_GH0.tar.gz
>fetch: https://codeload.github.com/samtools/bcftools/tar.gz/1.3?dummy=/samtools-bcftools-1.3_GH0.tar.gz: size unknown
>fetch: https://codeload.github.com/samtools/bcftools/tar.gz/1.3?dummy=/samtools-bcftools-1.3_GH0.tar.gz: size of remote file is not known
>samtools-bcftools-1.3_GH0.tar.gz                        -1  B    0  Bps
>===> Fetching all distfiles required by bcftools-1.3 for building
>===========================================================================
>=======================<phase: checksum       >============================
>===>  License GPLv3 accepted by the user
>===>  Found saved configuration for bcftools-1.2
>===>   bcftools-1.3 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by bcftools-1.3 for building
>=> SHA256 Checksum OK for samtools-bcftools-1.3_GH0.tar.gz.
>===========================================================================
>=======================<phase: extract-depends>============================
>===========================================================================
>=======================<phase: extract        >============================
>===>  License GPLv3 accepted by the user
>===>  Found saved configuration for bcftools-1.2
>===>   bcftools-1.3 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by bcftools-1.3 for building
>===>  Extracting for bcftools-1.3
>=> SHA256 Checksum OK for samtools-bcftools-1.3_GH0.tar.gz.
>===========================================================================
>=======================<phase: patch-depends  >============================
>===========================================================================
>=======================<phase: patch          >============================
>===>  Patching for bcftools-1.3
>===>  Applying FreeBSD patches for bcftools-1.3
>===========================================================================
>=======================<phase: build-depends  >============================
>===>   bcftools-1.3 depends on package: htslib>=1.3 - not found
>===>   Installing existing package /packages/All/htslib-1.3.txz
>[releng_9_3-default] Installing htslib-1.3...
>[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
>[releng_9_3-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
>
>***************************************************************************
>===>   bcftools-1.3 depends on package: htslib>=1.3 - found
>===>   Returning to build of bcftools-1.3
>===>   bcftools-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 indexinfo-0.2.4...
>[releng_9_3-default] `-- Extracting indexinfo-0.2.4: .... done
>[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
>===>   bcftools-1.3 depends on executable: gmake - found
>===>   Returning to build of bcftools-1.3
>===========================================================================
>=======================<phase: lib-depends    >============================
>===>   bcftools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
>===>   bcftools-1.3 depends on shared library: libgsl.so - not found
>===>   Installing existing package /packages/All/gsl-1.16_2.txz
>[releng_9_3-default] Installing gsl-1.16_2...
>[releng_9_3-default] Extracting gsl-1.16_2: .......... done
>===>   bcftools-1.3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
>===>   Returning to build of bcftools-1.3
>===========================================================================
>====>> Recording filesystem state for prebuild... done
>=======================<phase: configure      >============================
>===>   bcftools-1.3 depends on package: htslib>=1.3 - found
>===>   bcftools-1.3 depends on executable: gmake - found
>===>   bcftools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
>===>   bcftools-1.3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
>===>  Configuring for bcftools-1.3
>===========================================================================
>=======================<phase: build          >============================
>===>  Building for bcftools-1.3
>echo '#define BCFTOOLS_VERSION "1.3"' > version.h
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfindex.o vcfindex.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o tabix.o tabix.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfstats.o vcfstats.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfisec.o vcfisec.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfmerge.o vcfmerge.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfquery.o vcfquery.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcffilter.o vcffilter.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o filter.o filter.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfsom.o vcfsom.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfnorm.o vcfnorm.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfgtcheck.o vcfgtcheck.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfview.o vcfview.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfannotate.o vcfannotate.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfroh.o vcfroh.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfconcat.o vcfconcat.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfcall.o vcfcall.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o mcall.o mcall.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcmp.o vcmp.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o gvcf.o gvcf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o reheader.o reheader.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o convert.o convert.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfconvert.o vcfconvert.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o tsv2vcf.o tsv2vcf.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfcnv.o vcfcnv.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o HMM.o HMM.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o vcfplugin.o vcfplugin.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o consensus.o consensus.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o ploidy.o ploidy.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o version.o version.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o ccall.o ccall.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o em.o em.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o prob1.o prob1.c
>consensus.c: In function 'main_consensus':
>consensus.c:241: warning: 'tmp' may be used uninitialized in this function
>consensus.c:241: note: 'tmp' was declared here
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o kmin.o kmin.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o polysomy.o polysomy.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o peakfit.o peakfit.c
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o test/test-rbuf.o test/test-rbuf.c
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/impute-info.so version.c plugins/impute-info.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/dosage.so version.c plugins/dosage.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/missing2ref.so version.c plugins/missing2ref.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/mendelian.so version.c plugins/mendelian.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/counts.so version.c plugins/counts.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/fill-tags.so version.c plugins/fill-tags.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/vcf2sex.so ploidy.c version.c plugins/vcf2sex.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/frameshifts.so version.c plugins/frameshifts.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/fixploidy.so ploidy.c version.c plugins/fixploidy.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/tag2tag.so version.c plugins/tag2tag.c 
>cc -fPIC -shared -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include   -L/usr/local/lib -fstack-protector  -o plugins/setGT.so version.c plugins/setGT.c 
>cc -O2 -pipe -O2 -fno-strict-aliasing -pipe -fstack-protector -Wall -I. -I/usr/local/include -DPLUGINPATH=\"/usr/local/libexec/bcftools\" -DUSE_GPL -I/usr/local/include  -c -o main.o main.c
>cc  -L/usr/local/lib -fstack-protector  -o test/test-rbuf test/test-rbuf.o -lm 
>cc -rdynamic  -L/usr/local/lib -fstack-protector  -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o ccall.o em.o prob1.o kmin.o  polysomy.o peakfit.o -lhts -pthread -lz -lm -lgsl -lgslcblas 
>plugins/color-chrs.c: In function 'flush_viterbi':
>plugins/color-chrs.c:447: warning: 's2' may be used uninitialized in this function
>plugins/color-chrs.c:447: warning: 's1' may be used uninitialized in this function
>===========================================================================
>====>> Checking for filesystem violations... done
>=======================<phase: run-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prestage... done
>=======================<phase: stage          >============================
>===>  Staging for bcftools-1.3
>===>   bcftools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
>===>   bcftools-1.3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
>===>   Generating temporary packing list
>/bin/mkdir -p /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/samtools_misc /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/man/man1 /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/libexec/bcftools
>install  -s -m 555 bcftools /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin
>install  -m 555 plot-vcfstats vcfutils.pl plugins/color-chrs.pl /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/bin/samtools_misc
>install  -m 0644 doc/bcftools.1 /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/man/man1
>install  -s -m 555 plugins/*.so /wrkdirs/usr/ports/biology/bcftools/work/stage/usr/local/libexec/bcftools
>====> 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 bcftools-1.3
>===========================================================================
>=======================<phase: install-mtree  >============================
>===========================================================================
>====>> Recording filesystem state for preinst... done
>=======================<phase: install        >============================
>===>  Installing for bcftools-1.3
>===>   bcftools-1.3 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
>===>   bcftools-1.3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
>===>  Checking if bcftools already installed
>===>   Registering installation for bcftools-1.3
>[releng_9_3-default] Installing bcftools-1.3...
>The miscellaneous tools included with Bcftools 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: [libgsl.so.0]
> 0x0000000000000001 (NEEDED)             Shared library: [libgslcblas.so.0]
> 0x0000000000000001 (NEEDED)             Shared library: [libhts.so.1]
> 0x0000000000000001 (NEEDED)             Shared library: [libm.so.5]
> 0x0000000000000001 (NEEDED)             Shared library: [libthr.so.3]
> 0x0000000000000001 (NEEDED)             Shared library: [libz.so.6]
>=======================<phase: deinstall      >============================
>===>  Deinstalling for bcftools
>===>   Deinstalling bcftools-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:
>	bcftools-1.3
>
>The operation will free 918 KiB.
>[releng_9_3-default] [1/1] Deinstalling bcftools-1.3...
>[releng_9_3-default] [1/1] Deleting files for bcftools-1.3: .......... done
>===========================================================================
>====>> Checking for extra files and directories
>[00:03:07] ====>> Installing from package
>[releng_9_3-default] Installing bcftools-1.3...
>[releng_9_3-default] Extracting bcftools-1.3: .......... done
>Message from bcftools-1.3:
>The miscellaneous tools included with Bcftools 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.
>[00:03:07] ====>> Cleaning up
>===>  Cleaning for bcftools-1.3
>[00:03:07] ====>> Deinstalling package
>Updating database digests format: . done
>Checking integrity... done (0 conflicting)
>Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
>
>Installed packages to be REMOVED:
>	bcftools-1.3
>
>The operation will free 918 KiB.
>[releng_9_3-default] [1/1] Deinstalling bcftools-1.3...
>[releng_9_3-default] [1/1] Deleting files for bcftools-1.3: .......... done
>build of biology/bcftools ended at Tue Dec 22 16:12:02 MST 2015
>build time: 00:00:14
>[00:03:07] ====>> Cleaning up
>[00:03:07] ====>> Umounting file systems

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Attachments on bug 205526: 164519 | 164520 | 164521