=> Building biology/primer3 Started : Thursday, 30 AUG 2018 at 10:55:04 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/primer3 XDG_CONFIG_HOME=/construction/biology/primer3 HOME=/construction/biology/primer3 TMPDIR="/tmp" PATH=/construction/biology/primer3/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/primer3 XDG_CONFIG_HOME=/construction/biology/primer3 HOME=/construction/biology/primer3 TMPDIR="/tmp" PATH=/construction/biology/primer3/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin 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 NOPROFILE=1 CC="cc" CFLAGS="-pipe -fpermissive -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -fpermissive -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- CC="cc" CPP="c++" DESTDIR=/construction/biology/primer3/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/primer3" EXAMPLESDIR="share/examples/primer3" DATADIR="share/primer3" WWWDIR="www/primer3" ETCDIR="etc/primer3" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- 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-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_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 ===> 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: 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_2.txz Installing gmake-4.2.1_2... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_2: .......... 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[2]: Entering directory '/construction/biology/primer3/primer3-2.3.6/src' c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ primer3_boulder_main.c c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o format_output.o format_output.c c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o read_boulder.o read_boulder.c c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o print_boulder.o print_boulder.c c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated -o libprimer3.o libprimer3.c c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o p3_seq_lib.o p3_seq_lib.c c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o dpal_primer.o dpal.c c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -ffloat-store -o thal_primer.o thal.c cc -pipe -fpermissive -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 c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o dpal.o dpal.c cc1: warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for C c++ -c -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o thal_main.o thal_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 -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -ffloat-store -o thal.o thal.c ar rv liboligotm.a oligotm.o c++ -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm /usr/libexec/binutils227/elf/ar: creating liboligotm.a a - oligotm.o ranlib liboligotm.a c++ -pipe -fpermissive -O2 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o oligotm oligotm_main.c liboligotm.a -lm ar rv libdpal.a dpal_primer.o /usr/libexec/binutils227/elf/ar: creating libdpal.a a - dpal_primer.o ranlib libdpal.a c++ -o ntdpal ntdpal_main.o dpal.o 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[2]: Leaving directory '/construction/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 /construction/biology/primer3/primer3-2.3.6/src/primer3_core /construction/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 -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 10:55:15 UTC Duration: 00:00:10