build started at Thu Feb 4 09:48:34 CST 2016
port directory: /usr/ports/biology/vcftools
building for: FreeBSD 9-3-i386-default 9.3-RELEASE-p36 FreeBSD 9.3-RELEASE-p36 i386
maintained by: bacon4000@gmail.com
ident warning: no id keywords in /usr/local/poudriere/data/.m/9-3-i386-default/ref//usr/ports/biology/vcftools/Makefile
Makefile ident:
Poudriere version: 3.1.10
Host OSVERSION: 1001000
Jail OSVERSION: 903000
---Begin Environment---
PKGREPOSITORY=/tmp/pkgs
PACKAGES=/tmp/pkgs
UNAME_p=i386
UNAME_m=i386
OSVERSION=903000
UNAME_v=FreeBSD 9.3-RELEASE-p36
UNAME_r=9.3-RELEASE-p36
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
WARNING_WAIT=0
SAVED_TERM=xterm
NO_WARNING_PKG_INSTALL_EOL=yes
MASTERMNT=/usr/local/poudriere/data/.m/9-3-i386-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/home/bacon
PWD=/
MASTERNAME=9-3-i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.10
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 ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
ZLIB_CFLAGS=" " ZLIB_LIBS="-lz" MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work HOME=/wrkdirs/usr/ports/biology/vcftools/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/vcftools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/vcftools/work HOME=/wrkdirs/usr/ports/biology/vcftools/work TMPDIR="/tmp" NO_PIE=yes NO_DEBUG_FILES=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
OSREL=9.3
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
PERL_VERSION=5.20.3
PERL_VER=5.20
PERL5_MAN1=lib/perl5/site_perl/man/man1
PERL5_MAN3=lib/perl5/site_perl/man/man3
SITE_PERL=lib/perl5/site_perl
SITE_ARCH=lib/perl5/site_perl/mach/5.20
DOCSDIR="share/doc/vcftools"
EXAMPLESDIR="share/examples/vcftools"
DATADIR="share/vcftools"
WWWDIR="www/vcftools"
ETCDIR="etc/vcftools"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/vcftools
DOCSDIR=/usr/local/share/doc/vcftools
EXAMPLESDIR=/usr/local/share/examples/vcftools
WWWDIR=/usr/local/www/vcftools
ETCDIR=/usr/local/etc/vcftools
--End SUB_LIST--
---Begin make.conf---
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
---End make.conf---
=======================<phase: check-sanity >============================
===> License LGPL3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> vcftools-0.1.14 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.6.3.txz
[9-3-i386-default] Installing pkg-1.6.3...
[9-3-i386-default] Extracting pkg-1.6.3: .......... done
Message from pkg-1.6.3:
If you are upgrading from the old package format, first run:
# pkg2ng
===> vcftools-0.1.14 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of vcftools-0.1.14
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL3 accepted by the user
===> vcftools-0.1.14 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by vcftools-0.1.14 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL3 accepted by the user
===> vcftools-0.1.14 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by vcftools-0.1.14 for building
=> SHA256 Checksum OK for vcftools_0.1.14_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License LGPL3 accepted by the user
===> vcftools-0.1.14 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by vcftools-0.1.14 for building
===> Extracting for vcftools-0.1.14
=> SHA256 Checksum OK for vcftools_0.1.14_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for vcftools-0.1.14
===========================================================================
=======================<phase: build-depends >============================
===> vcftools-0.1.14 depends on executable: pkg-config - not found
===> Installing existing package /packages/All/pkgconf-0.9.12_1.txz
[9-3-i386-default] Installing pkgconf-0.9.12_1...
[9-3-i386-default] Extracting pkgconf-0.9.12_1: ....... done
===> vcftools-0.1.14 depends on executable: pkg-config - found
===> Returning to build of vcftools-0.1.14
===> vcftools-0.1.14 depends on executable: autoconf-2.69 - not found
===> Installing existing package /packages/All/autoconf-2.69.txz
[9-3-i386-default] Installing autoconf-2.69...
[9-3-i386-default] `-- Installing indexinfo-0.2.4...
[9-3-i386-default] `-- Extracting indexinfo-0.2.4: .... done
[9-3-i386-default] `-- Installing autoconf-wrapper-20131203...
[9-3-i386-default] `-- Extracting autoconf-wrapper-20131203: ........ done
[9-3-i386-default] `-- Installing perl5-5.20.3_8...
[9-3-i386-default] `-- Extracting perl5-5.20.3_8: .......... done
[9-3-i386-default] `-- Installing m4-1.4.17_1,1...
[9-3-i386-default] `-- Extracting m4-1.4.17_1,1: .......... done
[9-3-i386-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.
===> vcftools-0.1.14 depends on executable: autoconf-2.69 - found
===> Returning to build of vcftools-0.1.14
===> vcftools-0.1.14 depends on executable: autoheader-2.69 - found
===> vcftools-0.1.14 depends on executable: autoreconf-2.69 - found
===> vcftools-0.1.14 depends on executable: aclocal-1.15 - not found
===> Installing existing package /packages/All/automake-1.15_1.txz
[9-3-i386-default] Installing automake-1.15_1...
[9-3-i386-default] `-- Installing automake-wrapper-20131203...
[9-3-i386-default] `-- Extracting automake-wrapper-20131203: ... done
[9-3-i386-default] Extracting automake-1.15_1: .......... done
===> vcftools-0.1.14 depends on executable: aclocal-1.15 - found
===> Returning to build of vcftools-0.1.14
===> vcftools-0.1.14 depends on executable: automake-1.15 - found
===> vcftools-0.1.14 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.1_2.txz
[9-3-i386-default] Installing gmake-4.1_2...
[9-3-i386-default] `-- Installing libiconv-1.14_9...
[9-3-i386-default] `-- Extracting libiconv-1.14_9: .......... done
[9-3-i386-default] `-- Installing gettext-runtime-0.19.6...
[9-3-i386-default] `-- Extracting gettext-runtime-0.19.6: .......... done
[9-3-i386-default] Extracting gmake-4.1_2: .......... done
===> vcftools-0.1.14 depends on executable: gmake - found
===> Returning to build of vcftools-0.1.14
===> vcftools-0.1.14 depends on package: perl5>=5.20<5.21 - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
====>> Recording filesystem state for prebuild... done
=======================<phase: configure >============================
===> vcftools-0.1.14 depends on executable: pkg-config - found
===> vcftools-0.1.14 depends on executable: autoconf-2.69 - found
===> vcftools-0.1.14 depends on executable: autoheader-2.69 - found
===> vcftools-0.1.14 depends on executable: autoreconf-2.69 - found
===> vcftools-0.1.14 depends on executable: aclocal-1.15 - found
===> vcftools-0.1.14 depends on executable: automake-1.15 - found
===> vcftools-0.1.14 depends on executable: gmake - found
===> vcftools-0.1.14 depends on package: perl5>=5.20<5.21 - found
===> Configuring for vcftools-0.1.14
configure.ac:16: installing './compile'
configure.ac:12: installing './install-sh'
configure.ac:12: installing './missing'
src/cpp/Makefile.am: installing './depcomp'
configure: loading site script /usr/ports/Templates/config.site
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
checking whether gmake supports nested variables... yes
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 c++ accepts -g... yes
checking for style of include used by gmake... GNU
checking dependency style of c++... gcc3
checking for gcc... cc
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 whether cc understands -c and -o together... yes
checking dependency style of cc... gcc3
checking how to run the C preprocessor... cpp
checking for perl... (cached) /usr/local/bin/perl
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ZLIB... yes
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for ANSI C header files... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for arpa/inet.h... (cached) yes
checking for fcntl.h... (cached) yes
checking for limits.h... (cached) yes
checking for netdb.h... (cached) yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for sys/socket.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... (cached) yes
checking for _Bool... (cached) yes
checking for inline... inline
checking for int16_t... (cached) yes
checking for int32_t... (cached) yes
checking for int64_t... (cached) yes
checking for int8_t... (cached) yes
checking for off_t... (cached) yes
checking for size_t... (cached) yes
checking for ssize_t... (cached) yes
checking for uint16_t... (cached) yes
checking for uint32_t... (cached) yes
checking for uint8_t... (cached) yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for error_at_line... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... (cached) yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for gethostbyaddr... yes
checking for gethostbyname... (cached) yes
checking for memset... (cached) yes
checking for pow... no
checking for select... (cached) yes
checking for socket... yes
checking for sqrt... no
checking for strchr... yes
checking for strdup... (cached) yes
checking for strerror... (cached) yes
checking for strstr... yes
checking for strtol... (cached) yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/cpp/Makefile
config.status: creating src/perl/Makefile
config.status: creating config.h
config.status: executing depfiles commands
===========================================================================
=======================<phase: build >============================
===> Building for vcftools-0.1.14
gmake all-recursive
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14'
Making all in src
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
Making all in cpp
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/cpp'
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-bcf_entry.o -MD -MP -MF .deps/vcftools-bcf_entry.Tpo -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-bcf_entry_setters.o -MD -MP -MF .deps/vcftools-bcf_entry_setters.Tpo -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-bcf_file.o -MD -MP -MF .deps/vcftools-bcf_file.Tpo -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp
cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-bgzf.o -MD -MP -MF .deps/vcftools-bgzf.Tpo -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c
mv -f .deps/vcftools-bgzf.Tpo .deps/vcftools-bgzf.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-dgeev.o -MD -MP -MF .deps/vcftools-dgeev.Tpo -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp
mv -f .deps/vcftools-dgeev.Tpo .deps/vcftools-dgeev.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-entry.o -MD -MP -MF .deps/vcftools-entry.Tpo -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp
mv -f .deps/vcftools-entry.Tpo .deps/vcftools-entry.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-entry_filters.o -MD -MP -MF .deps/vcftools-entry_filters.Tpo -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp
mv -f .deps/vcftools-bcf_file.Tpo .deps/vcftools-bcf_file.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-entry_getters.o -MD -MP -MF .deps/vcftools-entry_getters.Tpo -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp
mv -f .deps/vcftools-bcf_entry_setters.Tpo .deps/vcftools-bcf_entry_setters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-entry_setters.o -MD -MP -MF .deps/vcftools-entry_setters.Tpo -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp
mv -f .deps/vcftools-entry_setters.Tpo .deps/vcftools-entry_setters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-gamma.o -MD -MP -MF .deps/vcftools-gamma.Tpo -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp
mv -f .deps/vcftools-bcf_entry.Tpo .deps/vcftools-bcf_entry.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-header.o -MD -MP -MF .deps/vcftools-header.Tpo -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp
mv -f .deps/vcftools-gamma.Tpo .deps/vcftools-gamma.Po
cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-knetfile.o -MD -MP -MF .deps/vcftools-knetfile.Tpo -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c
mv -f .deps/vcftools-entry_getters.Tpo .deps/vcftools-entry_getters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-output_log.o -MD -MP -MF .deps/vcftools-output_log.Tpo -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp
mv -f .deps/vcftools-knetfile.Tpo .deps/vcftools-knetfile.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-parameters.o -MD -MP -MF .deps/vcftools-parameters.Tpo -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp
mv -f .deps/vcftools-output_log.Tpo .deps/vcftools-output_log.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-variant_file.o -MD -MP -MF .deps/vcftools-variant_file.Tpo -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp
mv -f .deps/vcftools-entry_filters.Tpo .deps/vcftools-entry_filters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-variant_file_diff.o -MD -MP -MF .deps/vcftools-variant_file_diff.Tpo -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp
mv -f .deps/vcftools-variant_file.Tpo .deps/vcftools-variant_file.Po
mv -f .deps/vcftools-header.Tpo .deps/vcftools-header.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-variant_file_filters.o -MD -MP -MF .deps/vcftools-variant_file_filters.Tpo -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-variant_file_format_convert.o -MD -MP -MF .deps/vcftools-variant_file_format_convert.Tpo -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp
mv -f .deps/vcftools-variant_file_filters.Tpo .deps/vcftools-variant_file_filters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-variant_file_output.o -MD -MP -MF .deps/vcftools-variant_file_output.Tpo -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp
mv -f .deps/vcftools-parameters.Tpo .deps/vcftools-parameters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-vcf_entry.o -MD -MP -MF .deps/vcftools-vcf_entry.Tpo -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp
mv -f .deps/vcftools-variant_file_format_convert.Tpo .deps/vcftools-variant_file_format_convert.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-vcf_entry_setters.o -MD -MP -MF .deps/vcftools-vcf_entry_setters.Tpo -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp
mv -f .deps/vcftools-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-vcf_file.o -MD -MP -MF .deps/vcftools-vcf_file.Tpo -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp
mv -f .deps/vcftools-vcf_entry.Tpo .deps/vcftools-vcf_entry.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fno-strict-aliasing -MT vcftools-vcftools.o -MD -MP -MF .deps/vcftools-vcftools.Tpo -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp
mv -f .deps/vcftools-vcf_file.Tpo .deps/vcftools-vcf_file.Po
mv -f .deps/vcftools-vcf_entry_setters.Tpo .deps/vcftools-vcf_entry_setters.Po
mv -f .deps/vcftools-vcftools.Tpo .deps/vcftools-vcftools.Po
mv -f .deps/vcftools-variant_file_output.Tpo .deps/vcftools-variant_file_output.Po
c++ -O2 -pipe -fno-strict-aliasing -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/cpp'
Making all in perl
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/perl'
gmake[3]: Nothing to be done for 'all'.
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/perl'
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
gmake[3]: Nothing to be done for 'all-am'.
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14'
gmake[2]: Nothing to be done for 'all-am'.
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14'
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14'
===========================================================================
====>> Checking for filesystem violations... done
=======================<phase: run-depends >============================
===> vcftools-0.1.14 depends on package: perl5>=5.20<5.21 - found
===========================================================================
====>> Recording filesystem state for prestage... done
=======================<phase: stage >============================
===> Staging for vcftools-0.1.14
===> vcftools-0.1.14 depends on package: perl5>=5.20<5.21 - found
===> Generating temporary packing list
Making install in src
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
Making install in cpp
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/cpp'
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/cpp'
/bin/mkdir -p '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/bin'
install -s -m 555 vcftools '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/bin'
/bin/mkdir -p '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/man/man1'
install -m 0644 vcftools.1 '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/man/man1'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/cpp'
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/cpp'
Making install in perl
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/perl'
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/perl'
/bin/mkdir -p '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/bin'
install -m 555 fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/bin'
/bin/mkdir -p '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/lib/perl5/site_perl'
install -m 0644 FaSlice.pm Vcf.pm VcfStats.pm '/wrkdirs/usr/ports/biology/vcftools/work/stage/usr/local/lib/perl5/site_perl'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/perl'
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src/perl'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
gmake[3]: Nothing to be done for 'install-exec-am'.
gmake[3]: Nothing to be done for 'install-data-am'.
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14/src'
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14'
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14'
gmake[2]: Nothing to be done for 'install-exec-am'.
gmake[2]: Nothing to be done for 'install-data-am'.
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14'
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.14'
====> 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 vcftools-0.1.14
===========================================================================
=======================<phase: install-mtree >============================
===========================================================================
====>> Recording filesystem state for preinst... done
=======================<phase: install >============================
===> Installing for vcftools-0.1.14
===> vcftools-0.1.14 depends on package: perl5>=5.20<5.21 - found
===> Checking if vcftools already installed
===> Registering installation for vcftools-0.1.14
[9-3-i386-default] Installing vcftools-0.1.14...
===========================================================================
====>> Checking shared library dependencies
0x00000001 (NEEDED) Shared library: [libc.so.7]
0x00000001 (NEEDED) Shared library: [libgcc_s.so.1]
0x00000001 (NEEDED) Shared library: [libm.so.5]
0x00000001 (NEEDED) Shared library: [libstdc++.so.6]
0x00000001 (NEEDED) Shared library: [libz.so.6]
=======================<phase: deinstall >============================
===> Deinstalling for vcftools
===> Deinstalling vcftools-0.1.14
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:
vcftools-0.1.14
The operation will free 1 MiB.
[9-3-i386-default] [1/1] Deinstalling vcftools-0.1.14...
[9-3-i386-default] [1/1] Deleting files for vcftools-0.1.14: .......... done
===========================================================================
====>> Checking for extra files and directories
[00:00:42] ====>> Installing from package
[9-3-i386-default] Installing vcftools-0.1.14...
[9-3-i386-default] Extracting vcftools-0.1.14: .......... done
[00:00:42] ====>> Cleaning up
===> Cleaning for vcftools-0.1.14
[00:00:43] ====>> 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:
vcftools-0.1.14
The operation will free 1 MiB.
[9-3-i386-default] [1/1] Deinstalling vcftools-0.1.14...
[9-3-i386-default] [1/1] Deleting files for vcftools-0.1.14: .......... done
build of biology/vcftools ended at Thu Feb 4 09:49:11 CST 2016
build time: 00:00:37