------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/fasda XDG_CONFIG_HOME=/construction/biology/fasda XDG_CACHE_HOME=/construction/biology/fasda/.cache HOME=/construction/biology/fasda TMPDIR="/tmp" PATH=/construction/biology/fasda/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/fasda/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- VERSION=0.1.3 XDG_DATA_HOME=/construction/biology/fasda XDG_CONFIG_HOME=/construction/biology/fasda XDG_CACHE_HOME=/construction/biology/fasda/.cache HOME=/construction/biology/fasda TMPDIR="/tmp" PATH=/construction/biology/fasda/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/fasda/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/fasda/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/fasda" EXAMPLESDIR="share/examples/fasda" DATADIR="share/fasda" WWWDIR="www/fasda" ETCDIR="etc/fasda" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fasda DOCSDIR=/usr/local/share/doc/fasda EXAMPLESDIR=/usr/local/share/examples/fasda WWWDIR=/usr/local/www/fasda ETCDIR=/usr/local/etc/fasda SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/ccache-3.7.12_4.pkg Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. Installing /packages/All/libxtend-0.1.8.2.pkg Installing /packages/All/biolibc-0.2.4.3.pkg SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> fasda-0.1.3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> fasda-0.1.3 depends on file: /usr/local/sbin/pkg - found => auerlab-fasda-0.1.3_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/auerlab/fasda/tar.gz/0.1.3?dummy=/auerlab-fasda-0.1.3_GH0.tar.gz fetch: https://codeload.github.com/auerlab/fasda/tar.gz/0.1.3?dummy=/auerlab-fasda-0.1.3_GH0.tar.gz: size unknown fetch: https://codeload.github.com/auerlab/fasda/tar.gz/0.1.3?dummy=/auerlab-fasda-0.1.3_GH0.tar.gz: size of remote file is not known auerlab-fasda-0.1.3_GH0.tar.gz 0 B 0 Bps auerlab-fasda-0.1.3_GH0.tar.gz 58 kB 489 kBps 00s ===> Fetching all distfiles required by fasda-0.1.3 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> fasda-0.1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fasda-0.1.3 for building => SHA256 Checksum OK for auerlab-fasda-0.1.3_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> fasda-0.1.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fasda-0.1.3 for building ===> Extracting for fasda-0.1.3 => SHA256 Checksum OK for auerlab-fasda-0.1.3_GH0.tar.gz. Extracted Memory Use: 0.49M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for fasda-0.1.3 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> fasda-0.1.3 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> fasda-0.1.3 depends on shared library: libxtend.so - found (/usr/local/lib/libxtend.so) ===> fasda-0.1.3 depends on shared library: libbiolibc.so - found (/usr/local/lib/libbiolibc.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> fasda-0.1.3 depends on file: /usr/local/bin/ccache - found ===> fasda-0.1.3 depends on shared library: libxtend.so - found (/usr/local/lib/libxtend.so) ===> fasda-0.1.3 depends on shared library: libbiolibc.so - found (/usr/local/lib/libbiolibc.so) ===> Configuring for fasda-0.1.3 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for fasda-0.1.3 cd /construction/biology/fasda/fasda-0.1.3 && make depend LOCALBASE=/usr/local rm -f Makefile.depend for file in *.c; do cc -isystem ../local/include -isystem /usr/local/include -MM ${file} >> Makefile.depend; printf "\t\${CC} -c \${CFLAGS} ${file}\n\n" >> Makefile.depend; done --- fasda.o --- --- alignment-stats-mutators.o --- --- abundance.o --- --- normalize.o --- --- fold-change.o --- --- mann-whitney.o --- --- exact-p-val.o --- --- pval-sim.o --- --- fc-ge.o --- --- fasda.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fasda.c --- alignment-stats-mutators.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include alignment-stats-mutators.c --- abundance.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include abundance.c --- normalize.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include normalize.c --- fold-change.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fold-change.c --- mann-whitney.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include mann-whitney.c --- exact-p-val.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include exact-p-val.c --- pval-sim.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include pval-sim.c --- fc-ge.o --- cc -c -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/fasda\" -DVERSION=\"`./version.sh`\" -isystem /usr/local/include -isystem /usr/local/include fc-ge.c --- fasda --- cc -o fasda fasda.o alignment-stats-mutators.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm --- pval-sim --- cc -o pval-sim pval-sim.o fc-ge.o mann-whitney.o exact-p-val.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm --- normalize --- cc -o normalize normalize.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm --- abundance --- --- fold-change --- --- abundance --- cc -o abundance abundance.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm --- fold-change --- cc -o fold-change fold-change.o mann-whitney.o exact-p-val.o fc-ge.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/lib -Wl,-rpath,/usr/local/lib -lbiolibc -lxtend -lm SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for fasda-0.1.3 ===> Generating temporary packing list mkdir -p /construction/biology/fasda/stage/usr/local/bin /construction/biology/fasda/stage/usr/local/libexec/fasda /construction/biology/fasda/stage/usr/local/man/man1 install -m 0755 fasda /construction/biology/fasda/stage/usr/local/bin install -m 0755 abundance normalize fold-change pval-sim /construction/biology/fasda/stage/usr/local/libexec/fasda install -m 0644 Man/*.1 /construction/biology/fasda/stage/usr/local/man/man1 strip /construction/biology/fasda/stage/usr/local/bin/fasda for f in abundance normalize fold-change pval-sim; do strip /construction/biology/fasda/stage/usr/local/libexec/fasda/${f}; done ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> 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) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for fasda-0.1.3 file sizes/checksums [10]: 0% file sizes/checksums [10]: 100% Service unavailablepacking files [10]: 0% packing files [10]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:00 TOTAL TIME 00:00:03