=>> Building biology/mmseqs2 build started at Wed Apr 3 16:02:37 BST 2024 port directory: /usr/ports/biology/mmseqs2 package name: MMseqs2-13.45111_2 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1126 Mar 8 2023 /usr/ports/biology/mmseqs2/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git 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core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> MMseqs2-13.45111_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> MMseqs2-13.45111_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of MMseqs2-13.45111_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by MMseqs2-13.45111_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by MMseqs2-13.45111_2 for building => SHA256 Checksum OK for soedinglab-MMseqs2-13-45111_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by MMseqs2-13.45111_2 for building ===> Extracting for MMseqs2-13.45111_2 => SHA256 Checksum OK for soedinglab-MMseqs2-13-45111_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for MMseqs2-13.45111_2 ===> Applying FreeBSD patches for MMseqs2-13.45111_2 from /usr/ports/biology/mmseqs2/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> MMseqs2-13.45111_2 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.28.3.pkg [pkg-builder.dan.net.uk] Installing cmake-core-3.28.3... [pkg-builder.dan.net.uk] `-- Installing expat-2.6.1... [pkg-builder.dan.net.uk] `-- Extracting expat-2.6.1: .......... done [pkg-builder.dan.net.uk] `-- Installing jsoncpp-1.9.5... [pkg-builder.dan.net.uk] `-- Extracting jsoncpp-1.9.5: .......... done [pkg-builder.dan.net.uk] `-- Installing libuv-1.48.0... [pkg-builder.dan.net.uk] `-- Extracting libuv-1.48.0: .......... done [pkg-builder.dan.net.uk] `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing rhash-1.4.4_1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] `-- Extracting rhash-1.4.4_1: .......... done [pkg-builder.dan.net.uk] Extracting cmake-core-3.28.3: .......... done ===> MMseqs2-13.45111_2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of MMseqs2-13.45111_2 ===> MMseqs2-13.45111_2 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [pkg-builder.dan.net.uk] Installing ninja-1.11.1,2... [pkg-builder.dan.net.uk] `-- Installing python39-3.9.18_1... [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpdecimal-2.5.1... [pkg-builder.dan.net.uk] | `-- Extracting mpdecimal-2.5.1: .......... done [pkg-builder.dan.net.uk] | `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] | `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] `-- Extracting python39-3.9.18_1: .......... done [pkg-builder.dan.net.uk] Extracting ninja-1.11.1,2: ..... done ===== Message from python39-3.9.18_1: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> MMseqs2-13.45111_2 depends on executable: ninja - found ===> Returning to build of MMseqs2-13.45111_2 ===> MMseqs2-13.45111_2 depends on package: perl5>=5.36<5.37 - not found ===> Installing existing package /packages/All/perl5-5.36.3_1.pkg [pkg-builder.dan.net.uk] Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] Extracting perl5-5.36.3_1: .......... done ===> MMseqs2-13.45111_2 depends on package: perl5>=5.36<5.37 - found ===> Returning to build of MMseqs2-13.45111_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> MMseqs2-13.45111_2 depends on shared library: libzstd.so - not found ===> Installing existing package /packages/All/zstd-1.5.5_1.pkg [pkg-builder.dan.net.uk] Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] Extracting zstd-1.5.5_1: .......... done ===> MMseqs2-13.45111_2 depends on shared library: libzstd.so - found (/usr/local/lib/libzstd.so) ===> Returning to build of MMseqs2-13.45111_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for MMseqs2-13.45111_2 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is Clang 14.0.5 -- The C compiler identification is Clang 14.0.5 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /ccache/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /ccache/libexec/ccache/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Source Directory: /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111 -- Project Directory: /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111 -- Compiler is clang(++) -- Performing Test HAVE_AVX2_EXTENSIONS -- Performing Test HAVE_AVX2_EXTENSIONS - Success -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_SSE4_2_EXTENSIONS -- Performing Test HAVE_SSE4_2_EXTENSIONS - Success -- Performing Test HAVE_SSE4_1_EXTENSIONS -- Performing Test HAVE_SSE4_1_EXTENSIONS - Success -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success -- Performing Test HAVE_SSE2_EXTENSIONS -- Performing Test HAVE_SSE2_EXTENSIONS - Success -- Performing Test HAVE_SSE_EXTENSIONS -- Performing Test HAVE_SSE_EXTENSIONS - Success -- Found ZSTD: /usr/local/lib/libzstd.a CMake Deprecation Warning at lib/tinyexpr/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- xxd not found, using xxdi.pl instead -- ShellCheck disabled -- Performing Test HAVE_POSIX_FADVISE -- Performing Test HAVE_POSIX_FADVISE - Success -- Performing Test HAVE_POSIX_MADVISE -- Performing Test HAVE_POSIX_MADVISE - Success -- OMPTL sorting fallback -- Found ZLIB -- Performing Test HAVE_ZLIB_CHECK -- Performing Test HAVE_ZLIB_CHECK - Success -- ZLIB works -- Found BZLIB -- Performing Test HAVE_BZLIB_CHECK -- Performing Test HAVE_BZLIB_CHECK - Success -- BZLIB works -- Found OpenMP -- Configuring done (7.1s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: 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-I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/ksw2 -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/xxhash -O2 -pipe -march=x86-64 -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -march=x86-64 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fsigned-char -D_WITH_GETLINE -std=c++1y -stdlib=libc++ -w -MD -MT lib/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o -MF lib/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o.d -o lib/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o -c /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/alp/njn_ioutil.cpp [ 10% 24/228] /ccache/libexec/ccache/c++ -I/usr/local/include -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/tinyexpr -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/microtar -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/simde -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/simd -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/gzstream -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/alp -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/cacode -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/ksw2 -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/xxhash -O2 -pipe -march=x86-64 -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -march=x86-64 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -fsigned-char -D_WITH_GETLINE -std=c++1y -stdlib=libc++ -MD -MT lib/ksw2/CMakeFiles/ksw2.dir/ksw2_extz2_sse.cpp.o -MF lib/ksw2/CMakeFiles/ksw2.dir/ksw2_extz2_sse.cpp.o.d -o lib/ksw2/CMakeFiles/ksw2.dir/ksw2_extz2_sse.cpp.o -c /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/ksw2/ksw2_extz2_sse.cpp [ 10% 25/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/resources && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true CovSeqidQscPercMinDiag.lib && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl CovSeqidQscPercMinDiag.lib > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiag.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiag.lib.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiag.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiag.lib.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiag.lib.h [ 11% 26/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/resources && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true CovSeqidQscPercMinDiagTargetCov.lib && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl CovSeqidQscPercMinDiagTargetCov.lib > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiagTargetCov.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiagTargetCov.lib.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiagTargetCov.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiagTargetCov.lib.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/CovSeqidQscPercMinDiagTargetCov.lib.h [ 11% 27/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/resources && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true ExpOpt3_8_polished.cs32.lib && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl ExpOpt3_8_polished.cs32.lib > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/ExpOpt3_8_polished.cs32.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/ExpOpt3_8_polished.cs32.lib.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/ExpOpt3_8_polished.cs32.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/ExpOpt3_8_polished.cs32.lib.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/ExpOpt3_8_polished.cs32.lib.h [ 12% 28/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/resources && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true Library255_may17.lib && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl Library255_may17.lib > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/Library255_may17.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/Library255_may17.lib.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/Library255_may17.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/Library255_may17.lib.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/Library255_may17.lib.h [ 12% 29/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true PAM30.out && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl PAM30.out > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/PAM30.out.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/PAM30.out.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/PAM30.out.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/PAM30.out.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/PAM30.out.h [ 13% 30/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true VTML40.out && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl VTML40.out > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML40.out.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML40.out.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML40.out.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML40.out.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML40.out.h [ 13% 31/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true VTML80.out && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl VTML80.out > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML80.out.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML80.out.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML80.out.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML80.out.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/VTML80.out.h [ 14% 32/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true blastn.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl blastn.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastn.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastn.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastn.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastn.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastn.sh.h [ 14% 33/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true blastp.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl blastp.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastp.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastp.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastp.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastp.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastp.sh.h [ 14% 34/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true blastpgp.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl blastpgp.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastpgp.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastpgp.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastpgp.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastpgp.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blastpgp.sh.h [ 15% 35/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true blosum62.out && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl blosum62.out > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blosum62.out.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blosum62.out.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blosum62.out.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blosum62.out.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/blosum62.out.h [ 15% 36/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true cascaded_clustering.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl cascaded_clustering.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cascaded_clustering.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cascaded_clustering.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cascaded_clustering.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cascaded_clustering.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cascaded_clustering.sh.h [ 16% 37/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true clustering.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl clustering.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/clustering.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/clustering.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/clustering.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/clustering.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/clustering.sh.h [ 16% 38/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true createindex.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl createindex.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createindex.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createindex.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createindex.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createindex.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createindex.sh.h [ 17% 39/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true createtaxdb.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl createtaxdb.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createtaxdb.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createtaxdb.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createtaxdb.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createtaxdb.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/createtaxdb.sh.h [ 17% 40/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/resources && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true cs219.lib && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl cs219.lib > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cs219.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cs219.lib.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cs219.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cs219.lib.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/cs219.lib.h [ 17% 41/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true databases.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl databases.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/databases.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/databases.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/databases.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/databases.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/databases.sh.h [ 18% 42/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true easycluster.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl easycluster.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easycluster.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easycluster.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easycluster.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easycluster.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easycluster.sh.h [ 18% 43/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true easyrbh.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl easyrbh.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easyrbh.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easyrbh.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easyrbh.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easyrbh.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easyrbh.sh.h [ 19% 44/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true easysearch.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl easysearch.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easysearch.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easysearch.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easysearch.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easysearch.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easysearch.sh.h [ 19% 45/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true easytaxonomy.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl easytaxonomy.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easytaxonomy.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easytaxonomy.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easytaxonomy.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easytaxonomy.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/easytaxonomy.sh.h [ 20% 46/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true enrich.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl enrich.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/enrich.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/enrich.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/enrich.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/enrich.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/enrich.sh.h [ 20% 47/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/resources && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true krona_prelude.html && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl krona_prelude.html > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/krona_prelude.html.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/krona_prelude.html.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/krona_prelude.html.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/krona_prelude.html.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/krona_prelude.html.h [ 21% 48/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/resources && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true libPolished_8.lib && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl libPolished_8.lib > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/libPolished_8.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/libPolished_8.lib.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/libPolished_8.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/libPolished_8.lib.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/libPolished_8.lib.h [ 21% 49/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true linclust.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl linclust.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linclust.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linclust.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linclust.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linclust.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linclust.sh.h [ 21% 50/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true linsearch.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl linsearch.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linsearch.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linsearch.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linsearch.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linsearch.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/linsearch.sh.h [ 22% 51/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true map.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl map.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/map.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/map.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/map.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/map.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/map.sh.h [ 22% 52/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true multihitdb.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl multihitdb.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitdb.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitdb.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitdb.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitdb.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitdb.sh.h [ 23% 53/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true multihitsearch.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl multihitsearch.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitsearch.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitsearch.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitsearch.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitsearch.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/multihitsearch.sh.h [ 23% 54/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true nucleotide.out && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl nucleotide.out > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide.out.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide.out.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide.out.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide.out.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide.out.h [ 24% 55/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true nucleotide_clustering.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl nucleotide_clustering.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide_clustering.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide_clustering.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide_clustering.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide_clustering.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/nucleotide_clustering.sh.h [ 24% 56/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true rbh.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl rbh.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/rbh.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/rbh.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/rbh.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/rbh.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/rbh.sh.h [ 25% 57/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/resources && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true result_viz_prelude.html.zst && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl result_viz_prelude.html.zst > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/result_viz_prelude.html.zst.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/result_viz_prelude.html.zst.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/result_viz_prelude.html.zst.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/result_viz_prelude.html.zst.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/result_viz_prelude.html.zst.h [ 25% 58/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true searchslicedtargetprofile.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl searchslicedtargetprofile.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchslicedtargetprofile.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchslicedtargetprofile.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchslicedtargetprofile.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchslicedtargetprofile.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchslicedtargetprofile.sh.h [ 25% 59/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true searchtargetprofile.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl searchtargetprofile.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchtargetprofile.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchtargetprofile.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchtargetprofile.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchtargetprofile.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/searchtargetprofile.sh.h [ 26% 60/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true taxonomy.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl taxonomy.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxonomy.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxonomy.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxonomy.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxonomy.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxonomy.sh.h [ 26% 61/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true taxpercontig.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl taxpercontig.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxpercontig.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxpercontig.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxpercontig.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxpercontig.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/taxpercontig.sh.h [ 27% 62/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true translated_search.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl translated_search.sh > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/translated_search.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/translated_search.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/translated_search.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/translated_search.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/translated_search.sh.h [ 27% 63/228] cd /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/data/workflow && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/checkshell.sh true update_clustering.sh && mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated && /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/cmake/xxdi.pl update_clustering.sh > 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=========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for MMseqs2-13.45111_2 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/mmseqs2/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/mmseqs2/work/stage/usr/local/bin/mmseqs -- Installing: /wrkdirs/usr/ports/biology/mmseqs2/work/stage/usr/local/util/bash-completion.sh /bin/mv /wrkdirs/usr/ports/biology/mmseqs2/work/stage/usr/local/util /wrkdirs/usr/ports/biology/mmseqs2/work/stage/usr/local/share/MMseqs2 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-03T15:02:37+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for MMseqs2-13.45111_2 ===> Building MMseqs2-13.45111_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for MMseqs2-13.45111_2 build of biology/mmseqs2 | MMseqs2-13.45111_2 ended at Wed Apr 3 16:37:09 BST 2024 build time: 00:34:32