------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/eigen-3.3.7.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/gsl-2.6.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_3,1.txz Installing /packages/All/gcc8-8.4.0.txz ===== Message from gcc8-8.4.0: -- 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-0.3.10,1.txz UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> gemma-0.98.1_5 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> gemma-0.98.1_5 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gemma-0.98.1_5 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> gemma-0.98.1_5 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gemma-0.98.1_5 for building => SHA256 Checksum OK for genetics-statistics-GEMMA-0.98.1_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> gemma-0.98.1_5 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by gemma-0.98.1_5 for building ===> Extracting for gemma-0.98.1_5 => SHA256 Checksum OK for genetics-statistics-GEMMA-0.98.1_GH0.tar.gz. Extracted Memory Use: 90.59M SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for gemma-0.98.1_5 ===> Applying ports patches for gemma-0.98.1_5 from /xports/biology/gemma/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> gemma-0.98.1_5 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> gemma-0.98.1_5 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> gemma-0.98.1_5 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> gemma-0.98.1_5 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> gemma-0.98.1_5 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> gemma-0.98.1_5 depends on package: gmake>=4.3 - found ===> gemma-0.98.1_5 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> gemma-0.98.1_5 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Configuring for gemma-0.98.1_5 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for gemma-0.98.1_5 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/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/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/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 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/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 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 -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/eigenlib.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-0.98.1' SUCCEEDED 00:00:35 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for gemma-0.98.1_5 ===> 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) 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-0.98.1_5 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 00:02:35 TOTAL TIME 00:03:38