=> Building biology/primer3
build started at Mon Mar 13 04:54:49 PDT 2017
port directory: /usr/ports/biology/primer3
building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.1380.gb4315f-DEVELOPMENT #0: Fri Mar  3 17:20:21 PST 2017     root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC  x86_64
maintained by: ports@FreeBSD.org
ident warning: no id keywords in /build/boomdata/data/.m/Release48-default/ref/../05//usr/ports/biology/primer3/Makefile
Makefile ident: 
Poudriere version: 3.1-pre
Host OSVERSION: 400713
Jail OSVERSION: 400713

---Begin Environment---
STATUS=1
SAVED_TERM=screen
MASTERMNT=/build/boomdata/data/.m/Release48-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=primer3-2.3.6
OLDPWD=/root/boom
PWD=/build/boomdata/data/.m/Release48-default/ref/.p/pool
MASTERNAME=Release48-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--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/biology/primer3  XDG_CONFIG_HOME=/wrkdirs/biology/primer3  HOME=/wrkdirs/biology/primer3 TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/biology/primer3  XDG_CONFIG_HOME=/wrkdirs/biology/primer3  HOME=/wrkdirs/biology/primer3 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 -O2 -fno-strict-aliasing"  CPP="cpp" CPPFLAGS=""  LDFLAGS="" LIBS=""  CXX="c++" CXXFLAGS=" -pipe -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--
OSREL=4.7
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
PROFILE="@comment
"
DOCSDIR="share/doc/primer3"
EXAMPLESDIR="share/examples/primer3"
DATADIR="share/primer3"
WWWDIR="www/primer3"
ETCDIR="etc/primer3"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/primer3
DOCSDIR=/usr/local/share/doc/primer3
EXAMPLESDIR=/usr/local/share/examples/primer3
WWWDIR=/usr/local/www/primer3
ETCDIR=/usr/local/etc/primer3
--End SUB_LIST--

---Begin make.conf---
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---
=======================<phase: check-sanity   >============================
===>   NOTICE:

The primer3 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

===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.9.4_1.txz
Installing pkg-1.9.4_1...
Extracting pkg-1.9.4_1: .......... done
===>   primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of primer3-2.3.6
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>   NOTICE:

The primer3 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

===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
===========================================================================
=======================<phase: checksum       >============================
===>   NOTICE:

The primer3 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

===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
=> SHA256 Checksum OK for primer3-src-2.3.6.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>   NOTICE:

The primer3 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

===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by primer3-2.3.6 for building
===>  Extracting for primer3-2.3.6
=> SHA256 Checksum OK for primer3-src-2.3.6.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for primer3-2.3.6
===========================================================================
=======================<phase: build-depends  >============================
===>   primer3-2.3.6 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_1.txz
Installing gmake-4.2.1_1...
`-- Installing indexinfo-0.2.6...
`-- Extracting indexinfo-0.2.6: .... done
`-- Installing gettext-runtime-0.19.8.1_1...
`-- Extracting gettext-runtime-0.19.8.1_1: .......... done
Extracting gmake-4.2.1_1: .......... done
===>   primer3-2.3.6 depends on executable: gmake - found
===>   Returning to build of primer3-2.3.6
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for primer3-2.3.6
===========================================================================
=======================<phase: build          >============================
===>  Building for primer3-2.3.6
gmake[1]: Entering directory '/wrkdirs/biology/primer3/primer3-2.3.6/src'
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  primer3_boulder_main.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  -o format_output.o format_output.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  -o read_boulder.o read_boulder.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  -o print_boulder.o print_boulder.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated  -o libprimer3.o libprimer3.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o p3_seq_lib.o p3_seq_lib.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__  -o dpal_primer.o dpal.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -ffloat-store  -o thal_primer.o thal.c
cc -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__   -c -o oligotm.o oligotm.c
c++ -c -g -Wall -D__USE_FIXED_PROTOTYPES__ -o ntdpal_main.o ntdpal_main.c
ntdpal_main.c: In function 'int main(int, const char**)':
ntdpal_main.c:49:9: warning: variable 'tmp_ret' set but not used [-Wunused-but-set-variable]
     int tmp_ret;
         ^
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o dpal.o dpal.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o thal_main.o thal_main.c
c++ -c -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -ffloat-store -o thal.o thal.c
c++ -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o  -lm
ar rv libdpal.a dpal_primer.o
/usr/libexec/binutils227/elf/ar: creating libdpal.a
a - dpal_primer.o
ranlib libdpal.a
ar rv liboligotm.a oligotm.o
/usr/libexec/binutils227/elf/ar: creating liboligotm.a
a - oligotm.o
ranlib liboligotm.a
c++   -o ntdpal ntdpal_main.o dpal.o
c++ -pipe -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o oligotm oligotm_main.c liboligotm.a  -lm
ar rv libthal.a thal_primer.o
/usr/libexec/binutils227/elf/ar: creating libthal.a
a - thal_primer.o
ranlib libthal.a
c++   -o ntthal thal_main.o thal.o -lm
ar rv libprimer3.a libprimer3.o p3_seq_lib.o
/usr/libexec/binutils227/elf/ar: creating libprimer3.a
a - libprimer3.o
a - p3_seq_lib.o
ranlib libprimer3.a
c++   -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o  libprimer3.a libdpal.a libthal.a liboligotm.a   -lm
gmake[1]: Leaving directory '/wrkdirs/biology/primer3/primer3-2.3.6/src'
===========================================================================
=======================<phase: run-depends    >============================
===========================================================================
=======================<phase: stage          >============================
===>  Staging for primer3-2.3.6
===>   Generating temporary packing list
install  -s -m 555 /wrkdirs/biology/primer3/primer3-2.3.6/src/primer3_core  /wrkdirs/biology/primer3/stage/usr/local/bin/primer3
====> Compressing man pages (compress-man)
===========================================================================
=======================<phase: package        >============================
===>  Building package for primer3-2.3.6
file sizes/checksums     [4]: . done
packing files            [4]: . done
packing directories      [0]: . done
===========================================================================
=> Cleaning up wrkdir
===>  Cleaning for primer3-2.3.6
build of biology/primer3 ended at Mon Mar 13 04:55:13 PDT 2017
build time: 00:00:24