=> Building biology/gemma Started : Friday, 14 FEB 2020 at 03:07:36 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.1432.g9cd86-DEVELOPMENT #23: Thu Feb 13 14:43:04 PST 2020 root@sting.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.7-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.7-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 gemma-0.98.1_4: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- 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" -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/gemma/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTEXAMPLES="" OSREL=5.7 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" -------------------------------------------------- -- 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 -------------------------------------------------- -- /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=15 DPORTS_BUILDER= yes DISABLE_LICENSES= yes DEFAULT_VERSIONS= ssl=openssl FORCE_PACKAGE= yes DEVELOPER= yes HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.30.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500709 OSVERSION=9999999 OSREL=5.7 _OSRELEASE=5.7-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> gemma-0.98.1_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0_1.txz Installing pkg-1.12.0_1... Extracting pkg-1.12.0_1: .......... done ===> gemma-0.98.1_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gemma-0.98.1_4 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by gemma-0.98.1_4 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by gemma-0.98.1_4 for building => SHA256 Checksum OK for genetics-statistics-GEMMA-0.98.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by gemma-0.98.1_4 for building ===> Extracting for gemma-0.98.1_4 => SHA256 Checksum OK for genetics-statistics-GEMMA-0.98.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for gemma-0.98.1_4 ===> Applying ports patches for gemma-0.98.1_4 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> gemma-0.98.1_4 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.7.txz Installing eigen-3.3.7... Extracting eigen-3.3.7: .......... done ===> gemma-0.98.1_4 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of gemma-0.98.1_4 ===> gemma-0.98.1_4 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-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: . done `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> gemma-0.98.1_4 depends on executable: gmake - found ===> Returning to build of gemma-0.98.1_4 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> gemma-0.98.1_4 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.6.txz Installing gsl-2.6... Extracting gsl-2.6: .......... done ===> gemma-0.98.1_4 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of gemma-0.98.1_4 ===> gemma-0.98.1_4 depends on shared library: libopenblas.so - not found ===> Installing existing package /packages/All/openblas-0.3.7_2,1.txz Installing openblas-0.3.7_2,1... `-- Installing gcc8-8.3.0_3... | `-- Installing binutils-2.33.1_2,1... | `-- Extracting binutils-2.33.1_2,1: .......... done | `-- Installing gmp-6.1.2_1... | `-- Extracting gmp-6.1.2_1: .......... done | `-- Installing mpc-1.1.0_2... | | `-- Installing mpfr-4.0.2... | | `-- Extracting mpfr-4.0.2: .......... done | `-- Extracting mpc-1.1.0_2: ...... done `-- Extracting gcc8-8.3.0_3: .......... done Extracting openblas-0.3.7_2,1: .......... done ===== Message from gcc8-8.3.0_3: -- 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. ===> gemma-0.98.1_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Returning to build of gemma-0.98.1_4 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for gemma-0.98.1_4 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for gemma-0.98.1_4 gmake[1]: Entering directory '/construction/biology/gemma/GEMMA-0.98.1' 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/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/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/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/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/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/eigenlib.o src/eigenlib.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/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/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/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/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/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/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/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 -isystem /usr/local/include -c -o src/varcov.o src/varcov.cpp src/lmm.cpp: In function 'void CalcPab(size_t, size_t, const gsl_vector*, const gsl_matrix*, const gsl_vector*, gsl_matrix*)': src/lmm.cpp:281:10: warning: unused variable 'n_index' [-Wunused-variable] size_t n_index = (n_cvt + 2 + 1) * (n_cvt + 2) / 2; // result size ^~~~~~~ src/lmm.cpp:282:8: warning: unused variable 'ni_test' [-Wunused-variable] auto ni_test = Uab->size1; // inds ^~~~~~~ src/lmm.cpp: In function 'double LogL_dev1(double, void*)': src/lmm.cpp:596:8: warning: unused variable 'Uab' [-Wunused-variable] auto Uab = p->Uab; ^~~ src/lmm.cpp:597:8: warning: unused variable 'ab' [-Wunused-variable] auto ab = p->ab; ^~ 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_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/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 src/mathfunc.cpp: In function 'bool isMatrixIllConditioned(const gsl_vector*, double)': src/mathfunc.cpp:390:8: warning: unused variable 'absmin' [-Wunused-variable] auto absmin = get<0>(t); ^~~~~~ 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/ldr.o src/debug.o src/gzstream.o src/lm.o src/main.o src/lmm.o src/eigenlib.o src/bslmm.o src/bslmmdap.o src/mathfunc.o src/prdt.o src/lapack.o src/gemma.o src/logistic.o src/vc.o src/varcov.o src/fastblas.o src/gemma_io.o src/mvlmm.o src/param.o -lopenblas -pthread -L/usr/local/lib -L/usr/local/lib -lgsl -lz gmake[1]: Leaving directory '/construction/biology/gemma/GEMMA-0.98.1' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for gemma-0.98.1_4 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/gemma/GEMMA-0.98.1' 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-0.98.1' (cd /construction/biology/gemma/GEMMA-0.98.1/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) Error: /usr/local/bin/gemma is linked to /usr/local/lib/libopenblas.so which does not have a SONAME. math/openblas needs to be fixed. Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for gemma-0.98.1_4 file sizes/checksums [20]: . done packing files [20]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 14 FEB 2020 at 03:15:06 UTC Duration: 00:07:30