------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.56.txz ===== Message from ca_root_nss-3.56: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/curl-7.72.0.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/libuv-1.39.0.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/rhash-1.3.9.txz Installing /packages/All/liblz4-1.9.2_1,1.txz Installing /packages/All/lzo2-2.10_1.txz Installing /packages/All/libarchive-3.4.3,1.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/cmake-3.18.2.txz SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> diamond-2.0.4 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> diamond-2.0.4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by diamond-2.0.4 for building SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> diamond-2.0.4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by diamond-2.0.4 for building => SHA256 Checksum OK for bbuchfink-diamond-v2.0.4_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> diamond-2.0.4 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by diamond-2.0.4 for building ===> Extracting for diamond-2.0.4 => SHA256 Checksum OK for bbuchfink-diamond-v2.0.4_GH0.tar.gz. Extracted Memory Use: 7.10M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for diamond-2.0.4 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> diamond-2.0.4 depends on file: /usr/local/bin/cmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> diamond-2.0.4 depends on file: /usr/local/bin/cmake - found ===> Configuring for diamond-2.0.4 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/diamond/.build -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS -- Build files have been written to: /construction/biology/diamond/.build SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for diamond-2.0.4 /usr/local/bin/cmake -S/construction/biology/diamond/diamond-2.0.4 -B/construction/biology/diamond/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/diamond/.build/CMakeFiles /construction/biology/diamond/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_generic.dir/all --- --- CMakeFiles/arch_avx2.dir/all --- --- CMakeFiles/arch_sse4_1.dir/all --- /usr/bin/make -f CMakeFiles/arch_sse4_1.dir/build.make CMakeFiles/arch_sse4_1.dir/depend --- CMakeFiles/arch_generic.dir/all --- /usr/bin/make -f CMakeFiles/arch_generic.dir/build.make CMakeFiles/arch_generic.dir/depend --- CMakeFiles/arch_avx2.dir/all --- /usr/bin/make -f CMakeFiles/arch_avx2.dir/build.make CMakeFiles/arch_avx2.dir/depend --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_sse4_1.dir/depend --- cd /construction/biology/diamond/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/diamond/diamond-2.0.4 /construction/biology/diamond/diamond-2.0.4 /construction/biology/diamond/.build /construction/biology/diamond/.build /construction/biology/diamond/.build/CMakeFiles/arch_sse4_1.dir/DependInfo.cmake --- CMakeFiles/arch_avx2.dir/all --- --- CMakeFiles/arch_avx2.dir/depend --- cd /construction/biology/diamond/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/diamond/diamond-2.0.4 /construction/biology/diamond/diamond-2.0.4 /construction/biology/diamond/.build /construction/biology/diamond/.build /construction/biology/diamond/.build/CMakeFiles/arch_avx2.dir/DependInfo.cmake --- CMakeFiles/arch_generic.dir/all --- --- CMakeFiles/arch_generic.dir/depend --- cd /construction/biology/diamond/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/diamond/diamond-2.0.4 /construction/biology/diamond/diamond-2.0.4 /construction/biology/diamond/.build /construction/biology/diamond/.build /construction/biology/diamond/.build/CMakeFiles/arch_generic.dir/DependInfo.cmake --- CMakeFiles/arch_sse4_1.dir/all --- Scanning dependencies of target arch_sse4_1 /usr/bin/make -f CMakeFiles/arch_sse4_1.dir/build.make CMakeFiles/arch_sse4_1.dir/build --- CMakeFiles/arch_avx2.dir/all --- Scanning dependencies of target arch_avx2 /usr/bin/make -f CMakeFiles/arch_avx2.dir/build.make CMakeFiles/arch_avx2.dir/build --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_swipe.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/search/collision.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/search/stage1.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/search/stage2.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/tools/benchmark.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe.cpp.o --- [ 1%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe.cpp.o --- CMakeFiles/arch_avx2.dir/all --- --- CMakeFiles/arch_avx2.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- [ 2%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe.cpp.o --- /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -std=gnu++11 -o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/dp/swipe/swipe.cpp --- CMakeFiles/arch_sse4_1.dir/src/tools/benchmark.cpp.o --- [ 2%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/tools/benchmark.cpp.o --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o --- [ 3%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o --- /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -std=gnu++11 -o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/dp/swipe/banded_3frame_swipe.cpp --- CMakeFiles/arch_sse4_1.dir/src/tools/benchmark.cpp.o --- /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -std=gnu++11 -o CMakeFiles/arch_sse4_1.dir/src/tools/benchmark.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/tools/benchmark.cpp --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o --- /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -std=gnu++11 -o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/swipe_wrapper.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/dp/swipe/swipe_wrapper.cpp --- CMakeFiles/arch_sse4_1.dir/src/search/collision.cpp.o --- [ 4%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/search/collision.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -std=gnu++11 -o CMakeFiles/arch_sse4_1.dir/src/search/collision.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/search/collision.cpp --- CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_swipe.cpp.o --- [ 4%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_swipe.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -std=gnu++11 -o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_swipe.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/dp/swipe/banded_swipe.cpp --- CMakeFiles/arch_avx2.dir/all --- [ 4%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/swipe/banded_3frame_swipe.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -std=gnu++11 -o CMakeFiles/arch_avx2.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/dp/swipe/banded_3frame_swipe.cpp --- CMakeFiles/arch_sse4_1.dir/all --- --- CMakeFiles/arch_sse4_1.dir/src/search/stage2.cpp.o --- [ 5%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/search/stage2.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -std=gnu++11 -o CMakeFiles/arch_sse4_1.dir/src/search/stage2.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/search/stage2.cpp --- CMakeFiles/arch_sse4_1.dir/src/search/stage1.cpp.o --- [ 6%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/search/stage1.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -std=gnu++11 -o CMakeFiles/arch_sse4_1.dir/src/search/stage1.cpp.o -c 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/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -std=gnu++11 -o CMakeFiles/arch_avx2.dir/src/dp/scan_diags.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/dp/scan_diags.cpp --- CMakeFiles/arch_avx2.dir/src/dp/ungapped_simd.cpp.o --- /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized 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/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -std=gnu++11 -o CMakeFiles/arch_generic.dir/src/util/tantan.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/util/tantan.cpp --- CMakeFiles/arch_generic.dir/src/dp/scan_diags.cpp.o --- /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option 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--- CMakeFiles/arch_avx2.dir/all --- [ 25%] Built target arch_avx2 --- CMakeFiles/diamond.dir/all --- /usr/bin/make -f CMakeFiles/diamond.dir/build.make CMakeFiles/diamond.dir/depend --- CMakeFiles/diamond.dir/depend --- cd /construction/biology/diamond/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/diamond/diamond-2.0.4 /construction/biology/diamond/diamond-2.0.4 /construction/biology/diamond/.build /construction/biology/diamond/.build /construction/biology/diamond/.build/CMakeFiles/diamond.dir/DependInfo.cmake Scanning dependencies of target diamond /usr/bin/make -f CMakeFiles/diamond.dir/build.make CMakeFiles/diamond.dir/build --- CMakeFiles/diamond.dir/src/run/main.cpp.o --- --- CMakeFiles/diamond.dir/src/basic/config.cpp.o --- --- CMakeFiles/diamond.dir/src/basic/score_matrix.cpp.o --- --- CMakeFiles/diamond.dir/src/data/queries.cpp.o --- --- CMakeFiles/diamond.dir/src/data/reference.cpp.o --- --- 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CMakeFiles/diamond.dir/src/data/seed_array.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/data/seed_array.cpp --- CMakeFiles/diamond.dir/src/output/paf_format.cpp.o --- [ 68%] Building CXX object CMakeFiles/diamond.dir/src/output/paf_format.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/output/paf_format.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/output/paf_format.cpp --- CMakeFiles/diamond.dir/src/util/system/system.cpp.o --- [ 69%] Building CXX object CMakeFiles/diamond.dir/src/util/system/system.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -I/construction/biology/diamond/diamond-2.0.4/src/lib -pipe -O2 -fno-strict-aliasing -std=gnu++11 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -pipe -O2 -fno-strict-aliasing -std=gnu++11 -o CMakeFiles/diamond.dir/src/util/system/system.cpp.o -c /construction/biology/diamond/diamond-2.0.4/src/util/system/system.cpp /construction/biology/diamond/diamond-2.0.4/src/util/system/system.cpp:18:16: fatal error: sys/sysinfo.h: No such file or directory #include ^~~~~~~~~~~~~~~ compilation terminated. *** [CMakeFiles/diamond.dir/src/util/system/system.cpp.o] Error code 1 make[3]: stopped in /construction/biology/diamond/.build 1 error make[3]: stopped in /construction/biology/diamond/.build *** [CMakeFiles/diamond.dir/all] Error code 2 make[2]: stopped in /construction/biology/diamond/.build 1 error make[2]: stopped in /construction/biology/diamond/.build *** [all] Error code 2 make[1]: stopped in /construction/biology/diamond/.build 1 error make[1]: stopped in /construction/biology/diamond/.build ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /xports/biology/diamond FAILED 00:01:40