------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/gmake-4.3.txz Installing /packages/All/gmp-6.2.0.txz Installing /packages/All/libltdl-2.4.6.txz Installing /packages/All/libunistring-0.9.10_1.txz Installing /packages/All/libffi-3.2.1_3.txz Installing /packages/All/boehm-gc-8.0.4_1.txz Installing /packages/All/boehm-gc-threaded-8.0.4_1.txz Installing /packages/All/ncurses-6.1.20190525.txz Installing /packages/All/readline-8.0.4.txz Installing /packages/All/guile2-2.2.7.txz Installing /packages/All/metis-5.1.0_8.txz Installing /packages/All/tbb-2020.2.txz Installing /packages/All/mpfr-4.0.2.txz Installing /packages/All/mpc-1.1.0_2.txz UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/binutils-2.33.1_2,1.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-0.3.9_2,1.txz Installing /packages/All/suitesparse-5.7.2_1.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/python37-3.7.7.txz ===== Message from python37-3.7.7: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 Installing /packages/All/py37-setuptools-44.0.0.txz Installing /packages/All/py37-numpy-1.16.5_5,1.txz Installing /packages/All/nlopt-2.6.2.txz Installing /packages/All/icu-67.1,1.txz Installing /packages/All/boost-libs-1.72.0_2.txz ===== Message from boost-libs-1.72.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:54 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bolt-lmm-2.3.4_4 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bolt-lmm-2.3.4_4 for building => SHA256 Checksum OK for BOLT-LMM_v2.3.4.tar.gz. SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bolt-lmm-2.3.4_4 for building ===> Extracting for bolt-lmm-2.3.4_4 ===> bolt-lmm-2.3.4_4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bolt-lmm-2.3.4_4 for building => SHA256 Checksum OK for BOLT-LMM_v2.3.4.tar.gz. Extracted Memory Use: 356.46M SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for bolt-lmm-2.3.4_4 ===> Applying ports patches for bolt-lmm-2.3.4_4 ===> Cleanly applied ports patch(es) patch-example_run__example.sh patch-example_run__example__reml2.sh patch-src_Makefile patch-src_StringUtils.cpp patch-src_Timer.cpp /usr/bin/env WRKSRC=/construction/biology/bolt-lmm/BOLT-LMM_v2.3.4 REWARNFILE=/construction/biology/bolt-lmm/reinplace_warnings.txt /xports/Tools/scripts/sed_checked.sh -e 's@ -lgfortran@@g' /construction/biology/bolt-lmm/BOLT-LMM_v2.3.4/src/Makefile SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> bolt-lmm-2.3.4_4 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> bolt-lmm-2.3.4_4 depends on shared library: libnlopt.so - found (/usr/local/lib/libnlopt.so) ===> bolt-lmm-2.3.4_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> bolt-lmm-2.3.4_4 depends on shared library: libboost_program_options.so - found (/usr/local/lib/libboost_program_options.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> bolt-lmm-2.3.4_4 depends on package: gmake>=4.3 - found ===> bolt-lmm-2.3.4_4 depends on shared library: libnlopt.so - found (/usr/local/lib/libnlopt.so) ===> bolt-lmm-2.3.4_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> bolt-lmm-2.3.4_4 depends on shared library: libboost_program_options.so - found (/usr/local/lib/libboost_program_options.so) ===> Configuring for bolt-lmm-2.3.4_4 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for bolt-lmm-2.3.4_4 gmake[2]: Entering directory '/construction/biology/bolt-lmm/BOLT-LMM_v2.3.4/src' g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o BoltMain.o -c BoltMain.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o Bolt.o -c Bolt.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o BoltParams.o -c BoltParams.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o BoltParEstCV.o -c BoltParEstCV.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o BoltReml.o -c BoltReml.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o CovariateBasis.o -c CovariateBasis.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o DataMatrix.o -c DataMatrix.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o FileUtils.o -c FileUtils.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o Jackknife.o -c Jackknife.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o LDscoreCalibration.o -c LDscoreCalibration.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o MapInterpolater.o -c MapInterpolater.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o MatrixUtils.o -c MatrixUtils.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o MemoryUtils.o -c MemoryUtils.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o NonlinearOptMulti.o -c NonlinearOptMulti.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o NumericUtils.o -c NumericUtils.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o PhenoBuilder.o -c PhenoBuilder.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o RestrictSnpSet.o -c RestrictSnpSet.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o SnpData.o -c SnpData.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o SnpInfo.o -c SnpInfo.cpp NonlinearOptMulti.cpp: In function 'std::vector > NonlinearOptMulti::constrainedNR(double&, boost::numeric::ublas::vector&, const std::vector >&, const boost::numeric::ublas::vector&, const boost::numeric::ublas::matrix&, double)': NonlinearOptMulti.cpp:230:21: warning: catching polymorphic type 'class nlopt::roundoff_limited' by value [-Wcatch-value=] catch (nlopt::roundoff_limited) { ^~~~~~~~~~~~~~~~ g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o SpectrumTools.o -c SpectrumTools.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o StatsUtils.o -c StatsUtils.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o StringUtils.o -c StringUtils.cpp g++ -pipe -O2 -fno-strict-aliasing -DUSE_SSE -O2 -DMEASURE_DGEMM -DVERBOSE -Wall -fopenmp -I/usr/local/include -I/usr/local/api -o Timer.o -c Timer.cpp g++ -fopenmp -o bolt BoltMain.o Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o -L/usr/local/lib -Wl,-rpath,/usr/local/lib -L/usr/local/.libs -Wl,-rpath,/usr/local/.libs -lnlopt -lboost_program_options -lboost_iostreams -lz -lopenblas -lpthread -lm gmake[2]: Leaving directory '/construction/biology/bolt-lmm/BOLT-LMM_v2.3.4/src' SUCCEEDED 00:00:36 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for bolt-lmm-2.3.4_4 ===> Generating temporary packing list install -s -m 555 /construction/biology/bolt-lmm/BOLT-LMM_v2.3.4/src/bolt /construction/biology/bolt-lmm/stage/usr/local/bin (cd /construction/biology/bolt-lmm/BOLT-LMM_v2.3.4/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/bolt-lmm/stage/usr/local/share/examples/bolt-lmm) (cd /construction/biology/bolt-lmm/BOLT-LMM_v2.3.4 && /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 tables /construction/biology/bolt-lmm/stage/usr/local/share/bolt-lmm) ====> 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 00:00:02 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for bolt-lmm-2.3.4_4 file sizes/checksums [40]: 0% file sizes/checksums [40]: 100% packing files [40]: 0% packing files [40]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:07:39 TOTAL TIME 00:09:27