=> Building biology/prodigal Started : Thursday, 7 MAR 2019 at 18:28:20 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-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/prodigal XDG_CONFIG_HOME=/construction/biology/prodigal HOME=/construction/biology/prodigal TMPDIR="/tmp" PATH=/construction/biology/prodigal/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/prodigal XDG_CONFIG_HOME=/construction/biology/prodigal HOME=/construction/biology/prodigal TMPDIR="/tmp" PATH=/construction/biology/prodigal/.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=gcc80 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 -------------------------------------------------- INSTALLDIR=/construction/biology/prodigal/stage/usr/local/bin DESTDIR=/construction/biology/prodigal/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/prodigal" EXAMPLESDIR="share/examples/prodigal" DATADIR="share/prodigal" WWWDIR="www/prodigal" ETCDIR="etc/prodigal" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/prodigal DOCSDIR=/usr/local/share/doc/prodigal EXAMPLESDIR=/usr/local/share/examples/prodigal WWWDIR=/usr/local/www/prodigal ETCDIR=/usr/local/etc/prodigal -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE 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=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> prodigal-2.6.3.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> prodigal-2.6.3.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of prodigal-2.6.3.2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user => hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/hyattpd/Prodigal/tar.gz/v2.6.3-2-gfe80417?dummy=/hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz fetch: https://codeload.github.com/hyattpd/Prodigal/tar.gz/v2.6.3-2-gfe80417?dummy=/hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz: size unknown fetch: https://codeload.github.com/hyattpd/Prodigal/tar.gz/v2.6.3-2-gfe80417?dummy=/hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz: size of remote file is not known hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz -1 B 0 Bps ===> Fetching all distfiles required by prodigal-2.6.3.2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by prodigal-2.6.3.2 for building => SHA256 Checksum OK for hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by prodigal-2.6.3.2 for building ===> Extracting for prodigal-2.6.3.2 => SHA256 Checksum OK for hyattpd-Prodigal-v2.6.3-2-gfe80417_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for prodigal-2.6.3.2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> prodigal-2.6.3.2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.19.8.1_2... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_2: .......... done Extracting gmake-4.2.1_3: .......... done ===> prodigal-2.6.3.2 depends on executable: gmake - found ===> Returning to build of prodigal-2.6.3.2 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for prodigal-2.6.3.2 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for prodigal-2.6.3.2 gmake[1]: Entering directory '/construction/biology/prodigal/Prodigal-2.6.3-2-gfe80417' gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -c -o bitmap.o bitmap.c gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -c -o dprog.o dprog.c gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -c -o gene.o gene.c gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -c -o main.o main.c gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -c -o metagenomic.o metagenomic.c gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -c -o node.o node.c gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -c -o sequence.o sequence.c gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -c -o training.o training.c gcc -pipe -O2 -fno-strict-aliasing -pedantic -Wall -O3 -o prodigal bitmap.o dprog.o gene.o main.o metagenomic.o node.o sequence.o training.o -lm gmake[1]: Leaving directory '/construction/biology/prodigal/Prodigal-2.6.3-2-gfe80417' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for prodigal-2.6.3.2 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/prodigal/Prodigal-2.6.3-2-gfe80417' install -d -m 0755 /construction/biology/prodigal/stage/usr/local/bin install -m 0755 prodigal /construction/biology/prodigal/stage/usr/local/bin gmake[1]: Leaving directory '/construction/biology/prodigal/Prodigal-2.6.3-2-gfe80417' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for prodigal-2.6.3.2 file sizes/checksums [4]: . done packing files [4]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:36:42 UTC Duration: 00:08:21