[package - 122arm64-quarterly][biology/hhsuite] Failed for hhsuite-3.3.0 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sat, 26 Jun 2021 01:23:17 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:     yuri_at_FreeBSD.org
Log URL:        http://ampere1.nyi.freebsd.org/data/122arm64-quarterly/67383f941ca2/logs/hhsuite-3.3.0.log
Build URL:      http://ampere1.nyi.freebsd.org/build.html?mastername=122arm64-quarterly&build=67383f941ca2
Log:

=>> Building biology/hhsuite
build started at Sat Jun 26 01:22:40 UTC 2021
port directory: /usr/ports/biology/hhsuite
package name: hhsuite-3.3.0
building for: FreeBSD 122arm64-quarterly-job-10 12.2-RELEASE FreeBSD 12.2-RELEASE arm64
maintained by: yuri_at_FreeBSD.org
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=======================<phase: check-sanity   >============================
===>  License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   hhsuite-3.3.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.16.3.txz
[122arm64-quarterly-job-10] Installing pkg-1.16.3...
[122arm64-quarterly-job-10] Extracting pkg-1.16.3: .......... done
===>   hhsuite-3.3.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of hhsuite-3.3.0
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by hhsuite-3.3.0 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by hhsuite-3.3.0 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 for building
===>  Extracting for hhsuite-3.3.0
=> SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for hhsuite-3.3.0
===>  Applying FreeBSD patches for hhsuite-3.3.0 from /usr/ports/biology/hhsuite/files
===========================================================================
=======================<phase: build-depends  >============================
===>   hhsuite-3.3.0 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-3.19.6.txz
[122arm64-quarterly-job-10] Installing cmake-3.19.6...
[122arm64-quarterly-job-10] `-- Installing curl-7.76.0...
[122arm64-quarterly-job-10] |   `-- Installing ca_root_nss-3.63...
[122arm64-quarterly-job-10] |   `-- Extracting ca_root_nss-3.63: ........ done
[122arm64-quarterly-job-10] |   `-- Installing libnghttp2-1.43.0...
[122arm64-quarterly-job-10] |   `-- Extracting libnghttp2-1.43.0: .......... done
[122arm64-quarterly-job-10] `-- Extracting curl-7.76.0: .......... done
[122arm64-quarterly-job-10] `-- Installing expat-2.4.1...
[122arm64-quarterly-job-10] `-- Extracting expat-2.4.1: .......... done
[122arm64-quarterly-job-10] `-- Installing jsoncpp-1.9.4...
[122arm64-quarterly-job-10] `-- Extracting jsoncpp-1.9.4: .......... done
[122arm64-quarterly-job-10] `-- Installing libarchive-3.5.1,1...
[122arm64-quarterly-job-10] |   `-- Installing liblz4-1.9.3,1...
[122arm64-quarterly-job-10] |   `-- Extracting liblz4-1.9.3,1: .......... done
[122arm64-quarterly-job-10] `-- Extracting libarchive-3.5.1,1: .......... done
[122arm64-quarterly-job-10] `-- Installing libuv-1.41.0...
[122arm64-quarterly-job-10] `-- Extracting libuv-1.41.0: .......... done
[122arm64-quarterly-job-10] `-- Installing rhash-1.4.1...
[122arm64-quarterly-job-10] |   `-- Installing gettext-runtime-0.21...
<snip>

If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.

  * /etc/ssl/cert.pem
  * /usr/local/etc/ssl/cert.pem
  * /usr/local/openssl/cert.pem
===>   hhsuite-3.3.0 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of hhsuite-3.3.0
===>   hhsuite-3.3.0 depends on executable: ninja - not found
===>   Installing existing package /packages/All/ninja-1.10.2,2.txz
[122arm64-quarterly-job-10] Installing ninja-1.10.2,2...
[122arm64-quarterly-job-10] `-- Installing python37-3.7.10...
[122arm64-quarterly-job-10] |   `-- Installing libffi-3.3_1...
[122arm64-quarterly-job-10] |   `-- Extracting libffi-3.3_1: .......... done
[122arm64-quarterly-job-10] |   `-- Installing readline-8.1.0...
[122arm64-quarterly-job-10] |   `-- Extracting readline-8.1.0: .......... done
[122arm64-quarterly-job-10] `-- Extracting python37-3.7.10: .......... done
[122arm64-quarterly-job-10] Extracting ninja-1.10.2,2: ........ done
=====
Message from python37-3.7.10:

--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

py37-gdbm       databases/py-gdbm_at_py37
py37-sqlite3    databases/py-sqlite3_at_py37
py37-tkinter    x11-toolkits/py-tkinter_at_py37
===>   hhsuite-3.3.0 depends on executable: ninja - found
===>   Returning to build of hhsuite-3.3.0
===>   hhsuite-3.3.0 depends on file: /usr/local/bin/python3.7 - found
===>   hhsuite-3.3.0 depends on package: perl5>=5.32.r0<5.33 - not found
===>   Installing existing package /packages/All/perl5-5.32.1_1.txz
[122arm64-quarterly-job-10] Installing perl5-5.32.1_1...
[122arm64-quarterly-job-10] Extracting perl5-5.32.1_1: .......... done
===>   hhsuite-3.3.0 depends on package: perl5>=5.32.r0<5.33 - found
===>   Returning to build of hhsuite-3.3.0
===========================================================================
=======================<phase: lib-depends    >============================
===>   hhsuite-3.3.0 depends on shared library: libmpi.so - not found
===>   Installing existing package /packages/All/openmpi-4.1.0_1.txz
[122arm64-quarterly-job-10] Installing openmpi-4.1.0_1...
[122arm64-quarterly-job-10] `-- Installing gcc10-10.2.0_1...
[122arm64-quarterly-job-10] |   `-- Installing binutils-2.33.1_4,1...
[122arm64-quarterly-job-10] |   `-- Extracting binutils-2.33.1_4,1: .......... done
[122arm64-quarterly-job-10] |   `-- Installing gmp-6.2.1...
[122arm64-quarterly-job-10] |   `-- Extracting gmp-6.2.1: .......... done
[122arm64-quarterly-job-10] |   `-- Installing mpc-1.2.0...
[122arm64-quarterly-job-10] |   | `-- Installing mpfr-4.1.0...
[122arm64-quarterly-job-10] |   | `-- Extracting mpfr-4.1.0: .......... done
[122arm64-quarterly-job-10] |   `-- Extracting mpc-1.2.0: ......... done
[122arm64-quarterly-job-10] `-- Extracting gcc10-10.2.0_1: .......... done
[122arm64-quarterly-job-10] `-- Installing hwloc2-2.4.1...
[122arm64-quarterly-job-10] |   `-- Installing libpciaccess-0.16...
[122arm64-quarterly-job-10] |   | `-- Installing pciids-20210223...
[122arm64-quarterly-job-10] |   | `-- Extracting pciids-20210223: ..... done
[122arm64-quarterly-job-10] |   `-- Extracting libpciaccess-0.16: ......... done
[122arm64-quarterly-job-10] |   `-- Installing libxml2-2.9.10_4...
[122arm64-quarterly-job-10] |   `-- Extracting libxml2-2.9.10_4: .......... done
[122arm64-quarterly-job-10] `-- Extracting hwloc2-2.4.1: .......... done
[122arm64-quarterly-job-10] `-- Installing libevent-2.1.12...
[122arm64-quarterly-job-10] `-- Extracting libevent-2.1.12: .......... done
[122arm64-quarterly-job-10] `-- Installing libltdl-2.4.6...
[122arm64-quarterly-job-10] `-- Extracting libltdl-2.4.6: .......... done
[122arm64-quarterly-job-10] `-- Installing munge-0.5.14_1...
[122arm64-quarterly-job-10] `-- Extracting munge-0.5.14_1: ......... done
[122arm64-quarterly-job-10] `-- Installing slurm-wlm-20.02.1_6...
[122arm64-quarterly-job-10] |   `-- Installing hdf-szip-2.1.1...
[122arm64-quarterly-job-10] |   `-- Extracting hdf-szip-2.1.1: .......... done
[122arm64-quarterly-job-10] |   `-- Installing hdf5-1.10.6,1...
[122arm64-quarterly-job-10] |   `-- Extracting hdf5-1.10.6,1: .......... done
[122arm64-quarterly-job-10] |   `-- Installing json-c-0.15_1...
[122arm64-quarterly-job-10] |   `-- Extracting json-c-0.15_1: .......... done
[122arm64-quarterly-job-10] |   `-- Installing libsysinfo-0.0.3_2...
[122arm64-quarterly-job-10] |   `-- Extracting libsysinfo-0.0.3_2: ......... done
[122arm64-quarterly-job-10] |   `-- Installing lua52-5.2.4...
[122arm64-quarterly-job-10] |   | `-- Installing libedit-3.1.20210216,1...
[122arm64-quarterly-job-10] |   | `-- Extracting libedit-3.1.20210216,1: .......... done
[122arm64-quarterly-job-10] |   `-- Extracting lua52-5.2.4: ......... done
===> Creating groups.
Creating group 'slurm' with gid '468'.
===> Creating users
Creating user 'slurm' with uid '468'.
[122arm64-quarterly-job-10] `-- Extracting slurm-wlm-20.02.1_6: .......... done
[122arm64-quarterly-job-10] Extracting openmpi-4.1.0_1: .......... done
=====
Message from gcc10-10.2.0_1:

--
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.
===>   hhsuite-3.3.0 depends on shared library: libmpi.so - found (/usr/local/mpi/openmpi/lib/libmpi.so)
===>   Returning to build of hhsuite-3.3.0
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for hhsuite-3.3.0
===>  Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build
-- The C compiler identification is Clang 10.0.1
-- The CXX compiler identification is Clang 10.0.1
-- 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
-- Found OpenMP_C: -fopenmp=libomp (found version "4.5") 
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) 
-- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND) (found version "4.5")
-- 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
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    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
[1/98] /usr/bin/cc  -Igenerated -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
[2/98] /usr/bin/cc  -Igenerated -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
[3/98] /usr/bin/cc  -Igenerated -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
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[8/98] /usr/bin/cc  -Igenerated -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
[9/98] /usr/bin/cc  -Igenerated -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:172:106: warning: format specifies type 'long long' but the argument has type 'long' [-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));
                                                 ~~~~                                                    ^~~~~~~~~~~
                                                 %ld
1 warning generated.
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/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:106: warning: format specifies type 'long long' but the argument has type 'long' [-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));
                                                 ~~~~                                                    ^~~~~~~~~~~
                                                 %ld
1 warning generated.
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cc: warning: -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc10: '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]
[13/98] : && /usr/local/bin/cmake -E rm -f lib/ffindex/src/mpq/libmpq.a && /usr/bin/ar qc lib/ffindex/src/mpq/libmpq.a  lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o && /usr/bin/ranlib lib/ffindex/src/mpq/libmpq.a && :
[14/98] /usr/bin/cc  -Igenerated -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
[15/98] : && /usr/local/bin/cmake -E rm -f lib/ffindex/src/libffindex.a && /usr/bin/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/ranlib lib/ffindex/src/libffindex.a && :
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[17/98] : && /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 && :
[18/98] : && /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 && :
[19/98] : && /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 && :
[20/98] : && /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 && :
[21/98] : && /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 && :
[22/98] : && /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 && :
[23/98] : && /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 && :
[24/98] : && /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/gcc10 -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 && :
[25/98] : && /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 && :
[26/98] 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
[27/98] 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
[28/98] /usr/bin/c++  -Igenerated -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 -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -march=native -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp
FAILED: src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o 
/usr/bin/c++  -Igenerated -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 -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -march=native -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp
c++: error: the clang compiler does not support '-march=native'
[29/98] 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
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
Received on Sat Jun 26 2021 - 01:23:17 UTC

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