[package - 114amd64-default][biology/mmseqs2] Failed for MMseqs2-13.45111_1 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Tue, 29 Jun 2021 02:42:20 GMT
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.

Maintainer:     jwb_at_FreeBSD.org
Log URL:        http://beefy9.nyi.freebsd.org/data/114amd64-default/1ac2d7ea8e41/logs/MMseqs2-13.45111_1.log
Build URL:      http://beefy9.nyi.freebsd.org/build.html?mastername=114amd64-default&build=1ac2d7ea8e41
Log:

=>> Building biology/mmseqs2
build started at Tue Jun 29 02:41:34 UTC 2021
port directory: /usr/ports/biology/mmseqs2
package name: MMseqs2-13.45111_1
building for: FreeBSD 114amd64-default-job-02 11.4-RELEASE-p11 FreeBSD 11.4-RELEASE-p11 amd64
maintained by: jwb_at_FreeBSD.org
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=======================<phase: check-sanity   >============================
===>  License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   MMseqs2-13.45111_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.16.3.txz
[114amd64-default-job-02] Installing pkg-1.16.3...
[114amd64-default-job-02] Extracting pkg-1.16.3: .......... done
===>   MMseqs2-13.45111_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of MMseqs2-13.45111_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by MMseqs2-13.45111_1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by MMseqs2-13.45111_1 for building
=> SHA256 Checksum OK for soedinglab-MMseqs2-13-45111_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by MMseqs2-13.45111_1 for building
===>  Extracting for MMseqs2-13.45111_1
=> SHA256 Checksum OK for soedinglab-MMseqs2-13-45111_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for MMseqs2-13.45111_1
===>  Applying FreeBSD patches for MMseqs2-13.45111_1 from /usr/ports/biology/mmseqs2/files
===========================================================================
=======================<phase: build-depends  >============================
===>   MMseqs2-13.45111_1 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-3.20.4.txz
[114amd64-default-job-02] Installing cmake-3.20.4...
[114amd64-default-job-02] `-- Installing curl-7.77.0...
[114amd64-default-job-02] |   `-- Installing ca_root_nss-3.63...
[114amd64-default-job-02] |   `-- Extracting ca_root_nss-3.63: ........ done
[114amd64-default-job-02] |   `-- Installing libnghttp2-1.43.0...
[114amd64-default-job-02] |   `-- Extracting libnghttp2-1.43.0: .......... done
[114amd64-default-job-02] `-- Extracting curl-7.77.0: .......... done
[114amd64-default-job-02] `-- Installing expat-2.4.1...
[114amd64-default-job-02] `-- Extracting expat-2.4.1: .......... done
[114amd64-default-job-02] `-- Installing jsoncpp-1.9.4...
[114amd64-default-job-02] `-- Extracting jsoncpp-1.9.4: .......... done
[114amd64-default-job-02] `-- Installing libarchive-3.5.1,1...
[114amd64-default-job-02] |   `-- Installing liblz4-1.9.3,1...
[114amd64-default-job-02] |   `-- Extracting liblz4-1.9.3,1: .......... done
[114amd64-default-job-02] `-- Extracting libarchive-3.5.1,1: .......... done
[114amd64-default-job-02] `-- Installing libuv-1.41.0...
[114amd64-default-job-02] `-- Extracting libuv-1.41.0: .......... done
<snip>
as they require additional dependencies. They are available as:

py38-gdbm       databases/py-gdbm_at_py38
py38-sqlite3    databases/py-sqlite3_at_py38
py38-tkinter    x11-toolkits/py-tkinter_at_py38
===>   MMseqs2-13.45111_1 depends on executable: ninja - found
===>   Returning to build of MMseqs2-13.45111_1
===>   MMseqs2-13.45111_1 depends on executable: gcc10 - not found
===>   Installing existing package /packages/All/gcc10-10.3.0.txz
[114amd64-default-job-02] Installing gcc10-10.3.0...
[114amd64-default-job-02] `-- Installing binutils-2.33.1_4,1...
[114amd64-default-job-02] `-- Extracting binutils-2.33.1_4,1: .......... done
[114amd64-default-job-02] `-- Installing gmp-6.2.1...
[114amd64-default-job-02] `-- Extracting gmp-6.2.1: .......... done
[114amd64-default-job-02] `-- Installing mpc-1.2.0...
[114amd64-default-job-02] |   `-- Installing mpfr-4.1.0...
[114amd64-default-job-02] |   `-- Extracting mpfr-4.1.0: .......... done
[114amd64-default-job-02] `-- Extracting mpc-1.2.0: ......... done
[114amd64-default-job-02] Extracting gcc10-10.3.0: .......... done
=====
Message from gcc10-10.3.0:

--
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/gcc10

For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===>   MMseqs2-13.45111_1 depends on executable: gcc10 - found
===>   Returning to build of MMseqs2-13.45111_1
===>   MMseqs2-13.45111_1 depends on file: /usr/local/bin/as - found
===>   MMseqs2-13.45111_1 depends on package: perl5>=5.32.r0<5.33 - not found
===>   Installing existing package /packages/All/perl5-5.32.1_1.txz
[114amd64-default-job-02] Installing perl5-5.32.1_1...
[114amd64-default-job-02] Extracting perl5-5.32.1_1: .......... done
===>   MMseqs2-13.45111_1 depends on package: perl5>=5.32.r0<5.33 - found
===>   Returning to build of MMseqs2-13.45111_1
===========================================================================
=======================<phase: lib-depends    >============================
===>   MMseqs2-13.45111_1 depends on shared library: libzstd.so - not found
===>   Installing existing package /packages/All/zstd-1.5.0.txz
[114amd64-default-job-02] Installing zstd-1.5.0...
[114amd64-default-job-02] Extracting zstd-1.5.0: .......... done
===>   MMseqs2-13.45111_1 depends on shared library: libzstd.so - found (/usr/local/lib/libzstd.so)
===>   Returning to build of MMseqs2-13.45111_1
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for MMseqs2-13.45111_1
===>  Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build
-- The CXX compiler identification is GNU 10.3.0
-- The C compiler identification is GNU 10.3.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/local/bin/g++10 - 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: /usr/local/bin/gcc10 - 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 GNU 
-- Performing Test HAVE_AVX2_EXTENSIONS
-- Performing Test HAVE_AVX2_EXTENSIONS - Failed
-- Performing Test HAVE_AVX_EXTENSIONS
-- Performing Test HAVE_AVX_EXTENSIONS - Failed
-- 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  
-- 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
-- Performing Test ATOMIC_LIBRARY_NATIVE
-- Performing Test ATOMIC_LIBRARY_NATIVE - Failed
-- Performing Test ATOMIC_LIBRARY_LIB
-- Performing Test ATOMIC_LIBRARY_LIB - Success
-- Found Atomic: atomic  
-- IPS4O sorting works
-- 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
-- Generating done
CMake Warning:
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    CMAKE_VERBOSE_MAKEFILE
    THREADS_HAVE_PTHREAD_ARG


-- Build files have been written to: /wrkdirs/usr/ports/biology/mmseqs2/work/.build
===========================================================================
=======================<phase: build          >============================
===>  Building for MMseqs2-13.45111_1
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 -rpath=/usr/local/lib/gcc10 -fsigned-char -D_WITH_GETLINE -std=c++1y -w -MD -MT lib/alp/CMakeFiles/alp.dir/sls_basic.cpp.o -MF lib/alp/CMakeFiles/alp.dir/sls_basic.cpp.o.d -o lib/alp/CMakeFiles/alp.dir/sls_basic.cpp.o -c /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/alp/sls_basic.cpp
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 -rpath=/usr/local/lib/gcc10 -fsigned-char -D_WITH_GETLINE -std=c++1y -w -MD -MT lib/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o -MF lib/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o.d -o lib/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o -c /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/alp/sls_alp_data.cpp
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 -rpath=/usr/local/lib/gcc10 -fsigned-char -D_WITH_GETLINE -std=c++1y -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] /usr/local/bin/g++10  -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 -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/ips4o -O2 -pipe  -march=x86-64 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10  -Wl,-rpath=/usr/local/lib/gcc10 -O2 -pipe  -march=x86-64 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10  -Wl,
 -rpath=/usr/local/lib/gcc10 -fsigned-char -D_WITH_GETLINE -std=c++1y -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 > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/update_clustering.sh.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/update_clustering.sh.h > /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/update_clustering.sh.h.tmp && mv -f /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/update_clustering.sh.h.tmp /wrkdirs/usr/ports/biology/mmseqs2/work/.build/generated/update_clustering.sh.h
[ 28% 64/228] /usr/local/bin/g++10 -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -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 -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/ips4o -Igenerated -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment -I/wrkdirs/usr/
 ports/biology/mmseqs2/work/MMseqs2-13-45111/src/clustering -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/commons -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/multihit -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/prefiltering -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/linclust -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/taxonomy -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/util -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/. -O2 -pipe  -march=x86-64 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10  -Wl,-rpath=/usr/local/lib/gcc10 -O2 -pipe  -march=x86-64 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10  -Wl,-rpath=/usr/local/lib/gcc10   -fsigned-char -D_WITH_GETLINE -std=c++1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT src/CMakeFiles/mmseqs.dir/mmseqs.cpp.o -MF src/CMakeFiles/mmseqs.dir/mmseqs.cpp.o.d -o s
 rc/CMakeFiles/mmseqs.dir/mmseqs.cpp.o -c /wr!
 kdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/mmseqs.cpp
[ 28% 65/228] /usr/local/bin/g++10 -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -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 -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/ips4o -Igenerated -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment -I/wrkdirs/usr/
 ports/biology/mmseqs2/work/MMseqs2-13-45111/src/clustering -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/commons -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/multihit -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/prefiltering -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/linclust -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/taxonomy -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/util -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/. -O2 -pipe  -march=x86-64 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10  -Wl,-rpath=/usr/local/lib/gcc10 -O2 -pipe  -march=x86-64 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10  -Wl,-rpath=/usr/local/lib/gcc10  -fsigned-char -D_WITH_GETLINE -std=c++1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -MF src/CMakeFiles/mmseqs-f
 ramework.dir/alignment/Alignment.cpp.o.d -o !
 src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -c /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment/Alignment.cpp
FAILED: src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o 
/usr/local/bin/g++10 -DENABLE_IPS4O=1 -DHAVE_BZLIB=1 -DHAVE_POSIX_FADVISE=1 -DHAVE_POSIX_MADVISE=1 -DHAVE_ZLIB=1 -DOPENMP=1 -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 -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/lib/ips4o -Igenerated -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment -I/wrkdirs/usr/ports/biology/
 mmseqs2/work/MMseqs2-13-45111/src/clustering -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/commons -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/multihit -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/prefiltering -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/linclust -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/taxonomy -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/util -I/wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/. -O2 -pipe  -march=x86-64 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10  -Wl,-rpath=/usr/local/lib/gcc10 -O2 -pipe  -march=x86-64 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10  -Wl,-rpath=/usr/local/lib/gcc10  -fsigned-char -D_WITH_GETLINE -std=c++1y -pedantic -Wall -Wextra -Wdisabled-optimization -fno-exceptions -fopenmp -MD -MT src/CMakeFiles/mmseqs-framework.dir/alignment/Alignment.cpp.o -MF src/CMakeFiles/mmseqs-framework.dir/a
 lignment/Alignment.cpp.o.d -o src/CMakeFiles!
 /mmseqs-framework.dir/alignment/Alignment.cpp.o -c /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment/Alignment.cpp
In file included from /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment/StripedSmithWaterman.h:40,
                 from /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment/Matcher.h:17,
                 from /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment/Alignment.h:8,
                 from /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111/src/alignment/Alignment.cpp:1:
/usr/include/malloc.h:3:2: error: #error "<malloc.h> has been replaced by <stdlib.h>"
    3 | #error "<malloc.h> has been replaced by <stdlib.h>"
      |  ^~~~~
ninja: build stopped: subcommand failed.
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/mmseqs2
Received on Tue Jun 29 2021 - 02:42:20 UTC

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