------------------------------------------------------------------------------- -- 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 ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/gffread XDG_CONFIG_HOME=/construction/biology/gffread XDG_CACHE_HOME=/construction/biology/gffread/.cache HOME=/construction/biology/gffread TMPDIR="/tmp" PATH=/construction/biology/gffread/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/gffread/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/gffread XDG_CONFIG_HOME=/construction/biology/gffread XDG_CACHE_HOME=/construction/biology/gffread/.cache HOME=/construction/biology/gffread TMPDIR="/tmp" PATH=/construction/biology/gffread/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/gffread/.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 -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" SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/gffread/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/gffread" EXAMPLESDIR="share/examples/gffread" DATADIR="share/gffread" WWWDIR="www/gffread" ETCDIR="etc/gffread" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gffread DOCSDIR=/usr/local/share/doc/gffread EXAMPLESDIR=/usr/local/share/examples/gffread WWWDIR=/usr/local/www/gffread ETCDIR=/usr/local/etc/gffread 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/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/gmake-4.3_2.pkg 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. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gffread-0.12.7 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gffread-0.12.7 for building => SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. => SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> gffread-0.12.7 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gffread-0.12.7 for building ===> Extracting for gffread-0.12.7 => SHA256 Checksum OK for gpertea-gffread-v0.12.7_GH0.tar.gz. => SHA256 Checksum OK for gpertea-gclib-v0.12.7_GH0.tar.gz. Extracted Memory Use: 2.36M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for gffread-0.12.7 ===> Applying ports patches for gffread-0.12.7 from /xports/biology/gffread/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> gffread-0.12.7 depends on package: gmake>=4.3 - found ===> gffread-0.12.7 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> gffread-0.12.7 depends on package: gmake>=4.3 - found ===> gffread-0.12.7 depends on file: /usr/local/bin/ccache - found ===> Configuring for gffread-0.12.7 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for gffread-0.12.7 gmake[1]: Entering directory '/construction/biology/gffread/gffread-0.12.7' c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o gclib/GStr.cpp: In static member function 'static GStr::Data* GStr::new_data(const char*, uint)': gclib/GStr.cpp:42:18: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized] data->cap=len+addcap; ~~~~~~~~~^~~~~~~~~~~ c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gff_utils.cpp -o gff_utils.o c++ -Wall -Wextra -std=c++11 -I. -Igclib -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions -fno-rtti -pipe -O2 -fno-strict-aliasing -c gffread.cpp -o gffread.o gclib/gff.cpp: In constructor 'BEDLine::BEDLine(GffReader*, const char*)': gclib/gff.cpp:258:13: warning: 'bstart' may be used uninitialized in this function [-Wmaybe-uninitialized] bstart[0]=t[11]; ~~~~~~~~~^~~~~~ c++ -o gffread gclib/GBase.o gclib/GArgs.o gclib/GFaSeqGet.o gclib/gdna.o gclib/codons.o gclib/gff.o gclib/GStr.o gclib/GFastaIndex.o gff_utils.o gffread.o gmake[1]: Leaving directory '/construction/biology/gffread/gffread-0.12.7' SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for gffread-0.12.7 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/gffread/gffread-0.12.7' install -c gffread /construction/biology/gffread/stage/usr/local/bin strip /construction/biology/gffread/stage/usr/local/bin/gffread gmake[1]: Leaving directory '/construction/biology/gffread/gffread-0.12.7' ====> 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 00:00:00 ------------------------------------------------------------------------------- -- 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 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for gffread-0.12.7 file sizes/checksums [1]: 0% file sizes/checksums [1]: 100% Service unavailablepacking files [1]: 0% packing files [1]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:07