=> Building biology/recombine Started : Thursday, 30 AUG 2018 at 13:00:21 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 -------------------------------------------------- ===> The following configuration options are available for recombine-1.41: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/recombine XDG_CONFIG_HOME=/construction/biology/recombine HOME=/construction/biology/recombine TMPDIR="/tmp" PATH=/construction/biology/recombine/.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/recombine XDG_CONFIG_HOME=/construction/biology/recombine HOME=/construction/biology/recombine TMPDIR="/tmp" PATH=/construction/biology/recombine/.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 -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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/recombine/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/recombine" EXAMPLESDIR="share/examples/recombine" DATADIR="share/recombine" WWWDIR="www/recombine" ETCDIR="etc/recombine" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/recombine DOCSDIR=/usr/local/share/doc/recombine EXAMPLESDIR=/usr/local/share/examples/recombine WWWDIR=/usr/local/www/recombine ETCDIR=/usr/local/etc/recombine -------------------------------------------------- -- /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 recombine 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 -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> recombine-1.41 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 ===> recombine-1.41 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of recombine-1.41 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The recombine 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 ===> Fetching all distfiles required by recombine-1.41 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The recombine 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 ===> Fetching all distfiles required by recombine-1.41 for building => SHA256 Checksum OK for recombine1.41.src.doc.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The recombine 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 ===> Fetching all distfiles required by recombine-1.41 for building ===> Extracting for recombine-1.41 => SHA256 Checksum OK for recombine1.41.src.doc.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for recombine-1.41 ===> Applying ports patches for recombine-1.41 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for recombine-1.41 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for recombine-1.41 --- recombine.o --- --- jdrop.o --- --- rec_modellike.o --- --- jworld.o --- --- getdata.o --- --- traitlike.o --- --- getmsatdata.o --- --- recombine.o --- cc -pipe -O2 -fno-strict-aliasing -g -c recombine.c --- jdrop.o --- cc -pipe -O2 -fno-strict-aliasing -g -c jdrop.c --- rec_modellike.o --- cc -pipe -O2 -fno-strict-aliasing -g -c rec_modellike.c --- jworld.o --- cc -pipe -O2 -fno-strict-aliasing -g -c jworld.c --- getdata.o --- cc -pipe -O2 -fno-strict-aliasing -g -c getdata.c --- traitlike.o --- cc -pipe -O2 -fno-strict-aliasing -g -c traitlike.c --- getmsatdata.o --- cc -pipe -O2 -fno-strict-aliasing -g -c getmsatdata.c --- recombine --- cc -pipe -O2 -fno-strict-aliasing -g -o recombine recombine.o jdrop.o rec_modellike.o jworld.o getdata.o traitlike.o getmsatdata.o -lm -L/usr/local/lib recombine.c:180: warning: warning: this program uses gets(), which is unsafe. recombine.c:172: warning: warning: this program uses gets(), which is unsafe. recombine.c:1888: warning: warning: this program uses gets(), which is unsafe. recombine.c:1881: warning: warning: this program uses gets(), which is unsafe. recombine.c:1867: warning: warning: this program uses gets(), which is unsafe. recombine.c:1874: warning: warning: this program uses gets(), which is unsafe. recombine.c:2102: warning: warning: this program uses gets(), which is unsafe. recombine.c:2094: warning: warning: this program uses gets(), which is unsafe. recombine.c:1975: warning: warning: this program uses gets(), which is unsafe. recombine.c:2111: warning: warning: this program uses gets(), which is unsafe. recombine.c:2015: warning: warning: this program uses gets(), which is unsafe. recombine.c:2160: warning: warning: this program uses gets(), which is unsafe. recombine.c:2140: warning: warning: this program uses gets(), which is unsafe. recombine.c:2150: warning: warning: this program uses gets(), which is unsafe. recombine.c:2131: warning: warning: this program uses gets(), which is unsafe. recombine.c:2121: warning: warning: this program uses gets(), which is unsafe. recombine.c:1994: warning: warning: this program uses gets(), which is unsafe. recombine.c:2000: warning: warning: this program uses gets(), which is unsafe. recombine.c:2242: warning: warning: this program uses gets(), which is unsafe. -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for recombine-1.41 ===> Generating temporary packing list install -s -m 555 /construction/biology/recombine/recombine1.41/recombine /construction/biology/recombine/stage/usr/local/bin install -m 555 /construction/biology/recombine/recombine1.41/filetran /construction/biology/recombine/stage/usr/local/bin install -m 0644 /construction/biology/recombine/recombine1.41/recombine.txt /construction/biology/recombine/stage/usr/local/share/doc/recombine ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for recombine-1.41 file sizes/checksums [3]: . done packing files [3]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:00:35 UTC Duration: 00:00:13