------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 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 ------------------------------------------------------------------------------- ===> The following configuration options are available for gemma-0.98.3: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/gemma XDG_CONFIG_HOME=/construction/biology/gemma HOME=/construction/biology/gemma TMPDIR="/tmp" PATH=/construction/biology/gemma/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin 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 ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/gemma XDG_CONFIG_HOME=/construction/biology/gemma HOME=/construction/biology/gemma TMPDIR="/tmp" PATH=/construction/biology/gemma/.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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lopenblas -pthread -L/usr/local/lib -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -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/gemma/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTEXAMPLES="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/gemma" EXAMPLESDIR="share/examples/gemma" DATADIR="share/gemma" WWWDIR="www/gemma" ETCDIR="etc/gemma" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gemma DOCSDIR=/usr/local/share/doc/gemma EXAMPLESDIR=/usr/local/share/examples/gemma WWWDIR=/usr/local/www/gemma ETCDIR=/usr/local/etc/gemma SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gmp-6.2.1.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/metis-5.1.0_8.txz ===== Message from metis-5.1.0_8: -- ===> NOTICE: The metis 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 Installing /packages/All/mpc-1.2.0.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/binutils-2.33.1_4,1.txz Installing /packages/All/gcc8-8.4.0_1.txz ===== Message from gcc8-8.4.0_1: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.13_1,1.txz Installing /packages/All/suitesparse-5.9.0.txz Installing /packages/All/blas-3.5.0_6.txz Installing /packages/All/lapack-3.5.0_8.txz Installing /packages/All/superlu-5.2.2.txz Installing /packages/All/icu-68.2,1.txz Installing /packages/All/boost-libs-1.72.0_4.txz ===== Message from boost-libs-1.72.0_4: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/adol-c-2.7.2.txz Installing /packages/All/fftw3-3.3.9.txz Installing /packages/All/eigen-3.3.9.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/gsl-2.6.txz SUCCEEDED 00:00:54 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> gemma-0.98.3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> gemma-0.98.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gemma-0.98.3 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> gemma-0.98.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gemma-0.98.3 for building => SHA256 Checksum OK for genetics-statistics-GEMMA-0.98.3_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> gemma-0.98.3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gemma-0.98.3 for building ===> Extracting for gemma-0.98.3 => SHA256 Checksum OK for genetics-statistics-GEMMA-0.98.3_GH0.tar.gz. Extracted Memory Use: 90.56M SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for gemma-0.98.3 ===> Applying ports patches for gemma-0.98.3 from /xports/biology/gemma/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> gemma-0.98.3 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> gemma-0.98.3 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> gemma-0.98.3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> gemma-0.98.3 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> gemma-0.98.3 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> gemma-0.98.3 depends on package: gmake>=4.3 - found ===> gemma-0.98.3 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> gemma-0.98.3 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Configuring for gemma-0.98.3 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for gemma-0.98.3 gmake[1]: Entering directory '/construction/biology/gemma/GEMMA-0.98.3' c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/bslmm.o src/bslmm.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/bslmmdap.o src/bslmmdap.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/debug.o src/debug.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/fastblas.o src/fastblas.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/gemma.o src/gemma.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/gemma_io.o src/gemma_io.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/gzstream.o src/gzstream.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/lapack.o src/lapack.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/ldr.o src/ldr.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/lm.o src/lm.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/lmm.o src/lmm.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/logistic.o src/logistic.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/main.o src/main.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/mathfunc.o src/mathfunc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/mvlmm.o src/mvlmm.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/param.o src/param.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/prdt.o src/prdt.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/varcov.o src/varcov.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/vc.o src/vc.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -o gemma src/bslmm.o src/bslmmdap.o src/debug.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/main.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lopenblas -pthread -L/usr/local/lib -L/usr/local/lib -lgsl -lz gmake[1]: Leaving directory '/construction/biology/gemma/GEMMA-0.98.3' SUCCEEDED 00:00:42 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for gemma-0.98.3 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/gemma/GEMMA-0.98.3' mkdir -p /construction/biology/gemma/stage/usr/local/bin install -s -c gemma /construction/biology/gemma/stage/usr/local/bin gmake[1]: Leaving directory '/construction/biology/gemma/GEMMA-0.98.3' (cd /construction/biology/gemma/GEMMA-0.98.3/example && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/gemma/stage/usr/local/share/examples/gemma) ====> 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 gemma-0.98.3 file sizes/checksums [20]: 0% file sizes/checksums [20]: 100% packing files [20]: 0% packing files [20]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:03:06 TOTAL TIME 00:04:49