[package - main-armv7-default][biology/hhsuite] Failed for hhsuite-3.3.0_1 in build
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Date: Wed, 07 Sep 2022 22:27:28 UTC
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: yuri@FreeBSD.org
Log URL: http://ampere2.nyi.freebsd.org/data/main-armv7-default/p1774365e01b3_sf46bea05f/logs/hhsuite-3.3.0_1.log
Build URL: http://ampere2.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=p1774365e01b3_sf46bea05f
Log:
=>> Building biology/hhsuite
build started at Wed Sep 7 22:26:13 UTC 2022
port directory: /usr/ports/biology/hhsuite
package name: hhsuite-3.3.0_1
building for: FreeBSD main-armv7-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400066 arm
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> hhsuite-3.3.0_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[main-armv7-default-job-06] Installing pkg-1.18.4...
[main-armv7-default-job-06] Extracting pkg-1.18.4: .......... done
===> hhsuite-3.3.0_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of hhsuite-3.3.0_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by hhsuite-3.3.0_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by hhsuite-3.3.0_1 for building
=> SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by hhsuite-3.3.0_1 for building
===> Extracting for hhsuite-3.3.0_1
=> SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for hhsuite-3.3.0_1
===> Applying FreeBSD patches for hhsuite-3.3.0_1 from /usr/ports/biology/hhsuite/files
===========================================================================
=======================<phase: build-depends >============================
===> hhsuite-3.3.0_1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-3.23.3.pkg
[main-armv7-default-job-06] Installing cmake-3.23.3...
[main-armv7-default-job-06] `-- Installing curl-7.85.0...
[main-armv7-default-job-06] | `-- Installing ca_root_nss-3.81...
[main-armv7-default-job-06] | `-- Extracting ca_root_nss-3.81: .......... done
[main-armv7-default-job-06] | `-- Installing libnghttp2-1.48.0...
[main-armv7-default-job-06] | `-- Extracting libnghttp2-1.48.0: .......... done
[main-armv7-default-job-06] | `-- Installing libpsl-0.21.1_4...
<snip>
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
=====
Message from openmpi-4.1.4:
--
===> NOTICE:
The openmpi port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> hhsuite-3.3.0_1 depends on shared library: libmpi.so - found (/usr/local/mpi/openmpi/lib/libmpi.so)
===> Returning to build of hhsuite-3.3.0_1
===========================================================================
=======================<phase: configure >============================
===> Configuring for hhsuite-3.3.0_1
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build
-- The C compiler identification is Clang 14.0.5
-- The CXX compiler identification is Clang 14.0.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Compiler is clang(++)
-- Looking for fmemopen
-- Looking for fmemopen - found
-- Found MPI_C: /usr/local/mpi/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/local/mpi/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- xxd not found, using xxdi.pl instead
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
BOOST_PYTHON_SUFFIX
CMAKE_COLOR_MAKEFILE
CMAKE_CXX_FLAGS_DEBUG
CMAKE_C_FLAGS_DEBUG
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
Python_ADDITIONAL_VERSIONS
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/biology/hhsuite/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for hhsuite-3.3.0_1
[ 0% 2/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -MF src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o.d -o src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/a3m_extract.cpp
[ 1% 3/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -MF src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o.d -o src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/a3m_compress.cpp
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/a3m_compress.cpp:504:26: warning: 'ptr_fun<int, int>' is deprecated [-Wdeprecated-declarations]
std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
^
/usr/include/c++/v1/__functional/pointer_to_unary_function.h:37:1: note: 'ptr_fun<int, int>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
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# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/usr/include/c++/v1/__config:1007:48: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
^
1 warning generated.
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[ 3% 5/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -MF src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o.d -o src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/a3m_reduce.cpp
[ 4% 6/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -MF src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o.d -o src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/a3m_database_reduce.cpp
[ 5% 7/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -MF src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o.d -o src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/a3m_database_extract.cpp
[ 6% 8/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -MF src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o.d -o src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/a3m_database_filter.cpp
[ 7% 9/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -MF src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o.d -o src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs/log.cc
[ 8% 10/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -MF src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o.d -o src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs/aa.cc
[ 9% 11/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -MF src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o.d -o src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs/as.cc
[ 10% 12/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -MF src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o.d -o src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs/assert_helpers.cc
[ 11% 13/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -MF src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o.d -o src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs/blosum_matrix.cc
[ 12% 14/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -MF src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o.d -o src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs/getopt_pp.cc
[ 13% 15/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex.c
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex.c:291:55: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
fprintf(stderr, "Failed to allocate %ld bytes\n", nbytes);
~~~ ^~~~~~
%zu
1 warning generated.
[ 14% 16/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -MF src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o.d -o src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs/application.cc
[ 15% 17/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -MF lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffutil.c
[ 16% 18/106] : && /usr/local/bin/cmake -E rm -f lib/ffindex/src/libffindex.a && /usr/bin/llvm-ar qc lib/ffindex/src/libffindex.a lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o lib/ffindex/src/CMakeFiles/ffindex.dir/ffutil.c.o && /usr/bin/llvm-ranlib lib/ffindex/src/libffindex.a && :
[ 16% 19/106] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -o src/a3m_extract lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a && :
[ 17% 20/106] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -o src/a3m_reduce lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a && :
[ 18% 21/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -UHAVE_MPI -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:76: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
~~~ ^~~~~~~~~~~~~
%zu
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:91: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
~~~ ^~~~~~~~~~~~~
%zu
2 warnings generated.
[ 19% 22/106] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -o src/a3m_database_reduce lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a && :
[ 20% 23/106] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -o src/a3m_database_extract lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a && :
[ 21% 24/106] : && /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o -o src/a3m_database_filter lib/ffindex/src/libffindex.a src/libA3M_COMPRESS.a && :
[ 22% 25/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o lib/ffindex/src/ffindex_apply lib/ffindex/src/libffindex.a && :
[ 23% 26/106] : && /usr/local/bin/cmake -E rm -f src/cs/libCS_OBJECTS.a && /usr/bin/llvm-ar qc src/cs/libCS_OBJECTS.a src/cs/CMakeFiles/CS_OBJECTS.dir/aa.cc.o src/cs/CMakeFiles/CS_OBJECTS.dir/as.cc.o src/cs/CMakeFiles/CS_OBJECTS.dir/assert_helpers.cc.o src/cs/CMakeFiles/CS_OBJECTS.dir/blosum_matrix.cc.o src/cs/CMakeFiles/CS_OBJECTS.dir/getopt_pp.cc.o src/cs/CMakeFiles/CS_OBJECTS.dir/log.cc.o src/cs/CMakeFiles/CS_OBJECTS.dir/application.cc.o && /usr/bin/llvm-ranlib src/cs/libCS_OBJECTS.a && :
[ 24% 27/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_reduce.c
[ 25% 28/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o lib/ffindex/src/ffindex_reduce lib/ffindex/src/libffindex.a && :
[ 26% 29/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -I/usr/local/mpi/openmpi/include -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_MPI=1 -fexceptions -pthread -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:76: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
~~~ ^~~~~~~~~~~~~
%zu
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:91: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat]
fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
~~~ ^~~~~~~~~~~~~
%zu
2 warnings generated.
[ 27% 30/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_build.c
[ 28% 31/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta.c
[ 29% 32/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o lib/ffindex/src/ffindex_build lib/ffindex/src/libffindex.a && :
[ 30% 33/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o lib/ffindex/src/ffindex_from_fasta lib/ffindex/src/libffindex.a && :
[ 31% 34/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_get.c
[ 32% 35/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o lib/ffindex/src/ffindex_get lib/ffindex/src/libffindex.a && :
[ 33% 36/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_modify.c
[ 33% 37/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o lib/ffindex/src/ffindex_modify lib/ffindex/src/libffindex.a && :
[ 34% 38/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_unpack.c
[ 35% 39/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_order.c
[ 36% 40/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o lib/ffindex/src/ffindex_unpack lib/ffindex/src/libffindex.a && :
[ 37% 41/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o -o lib/ffindex/src/ffindex_order lib/ffindex/src/libffindex.a && :
[ 38% 42/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta_with_split.c
[ 39% 43/106] /usr/bin/cc -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -I/usr/local/mpi/openmpi/include -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc11 -Wl,-rpath -Wl,/usr/local/mpi/openmpi/lib -Wl,--enable-new-dtags -pthread -MD -MT lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o -MF lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o.d -o lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/mpq/mpq.c
cc: warning: -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc11: 'linker' input unused [-Wunused-command-line-argument]
cc: warning: -Wl,-rpath: 'linker' input unused [-Wunused-command-line-argument]
cc: warning: -Wl,/usr/local/mpi/openmpi/lib: 'linker' input unused [-Wunused-command-line-argument]
cc: warning: -Wl,--enable-new-dtags: 'linker' input unused [-Wunused-command-line-argument]
[ 40% 44/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o lib/ffindex/src/ffindex_from_fasta_with_split lib/ffindex/src/libffindex.a && :
[ 41% 45/106] : && /usr/local/bin/cmake -E rm -f lib/ffindex/src/mpq/libmpq.a && /usr/bin/llvm-ar qc lib/ffindex/src/mpq/libmpq.a lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o && /usr/bin/llvm-ranlib lib/ffindex/src/mpq/libmpq.a && :
[ 42% 46/106] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc11 -Wl,-rpath -Wl,/usr/local/mpi/openmpi/lib -Wl,--enable-new-dtags -pthread lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -o lib/ffindex/src/ffindex_apply_mpi -Wl,-rpath,/usr/local/mpi/openmpi/lib: lib/ffindex/src/libffindex.a lib/ffindex/src/mpq/libmpq.a /usr/local/mpi/openmpi/lib/libmpi.so && :
[ 43% 47/106] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl context_data.lib > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h
[ 44% 48/106] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl cs219.lib > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h
[ 45% 49/106] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl context_data.crf > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h
[ 46% 50/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbi
algorithm.cpp
FAILED: src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
/usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVITERBI_CELLOFF=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp:7:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbi.h:11:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhhit.h:19:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhhmm.h:8:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/util.h:23:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd/simd.h:316:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/sse4.1.h:31:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/ssse3.h:30:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/sse3.h:30:
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/sse2.h:6595:10: error: no member named 'neon_f64' in 'simde__m128d_private'
r_.neon_f64 = vnegq_f64(a_.neon_f64);
~~ ^
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/sse2.h:6595:34: error: no member named 'neon_f64' in 'simde__m128d_private'
r_.neon_f64 = vnegq_f64(a_.neon_f64);
~~ ^
2 errors generated.
[ 47% 50/106] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhbackwardalgorithm.cpp
FAILED: src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o
/usr/bin/c++ -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/generated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/.build/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -I/usr/local/mpi/openmpi/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -MF src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o.d -o src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhbackwardalgorithm.cpp
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:8:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhposteriordecoder.h:35:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhhmmsimd.h:5:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhhmm.h:8:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/util.h:23:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd/simd.h:316:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/sse4.1.h:31:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/ssse3.h:30:
In file included from /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/sse3.h:30:
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/sse2.h:6595:10: error: no member named 'neon_f64' in 'simde__m128d_private'
r_.neon_f64 = vnegq_f64(a_.neon_f64);
~~ ^
/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde/simde/x86/sse2.h:6595:34: error: no member named 'neon_f64' in 'simde__m128d_private'
r_.neon_f64 = vnegq_f64(a_.neon_f64);
~~ ^
2 errors generated.
ninja: build stopped: subcommand failed.
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/hhsuite