[package - 122powerpc64-quarterly][biology/hhsuite] Failed for hhsuite-3.3.0 in build
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Date: Sun, 27 Jun 2021 03:24:13 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://foul1.nyi.freebsd.org/data/122powerpc64-quarterly/3a6240c21278/logs/hhsuite-3.3.0.log
Build URL: http://foul1.nyi.freebsd.org/build.html?mastername=122powerpc64-quarterly&build=3a6240c21278
Log:
=>> Building biology/hhsuite
build started at Sun Jun 27 03:22:46 UTC 2021
port directory: /usr/ports/biology/hhsuite
package name: hhsuite-3.3.0
building for: FreeBSD 122powerpc64-quarterly-job-10 12.2-RELEASE FreeBSD 12.2-RELEASE powerpc
maintained by: yuri@FreeBSD.org
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CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
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CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11"
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CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x"
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CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14"
CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17"
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11"
CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14"
CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17"
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--End resource limits--
=======================<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
[122powerpc64-quarterly-job-10] Installing pkg-1.16.3...
[122powerpc64-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
/usr/bin/sed -i.bak -e 's/-msse -msse2/-D_ARCH_PWR8 -DNO_WARN_X86_INTRINSICS -maltivec -mpower8-vector -mvsx/g' /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/CMakeLists.txt
===========================================================================
=======================<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
[122powerpc64-quarterly-job-10] Installing cmake-3.19.6...
[122powerpc64-quarterly-job-10] `-- Installing curl-7.76.0...
[122powerpc64-quarterly-job-10] | `-- Installing ca_root_nss-3.63...
[122powerpc64-quarterly-job-10] | `-- Extracting ca_root_nss-3.63: ........ done
[122powerpc64-quarterly-job-10] | `-- Installing libnghttp2-1.43.0...
[122powerpc64-quarterly-job-10] | | `-- Installing gcc10-10.2.0_1...
[122powerpc64-quarterly-job-10] | | `-- Installing binutils-2.33.1_4,1...
[122powerpc64-quarterly-job-10] | | | `-- Installing gettext-runtime-0.21...
[122powerpc64-quarterly-job-10] | | | `-- Installing indexinfo-0.3.1...
[122powerpc64-quarterly-job-10] | | | `-- Extracting indexinfo-0.3.1: .... done
[122powerpc64-quarterly-job-10] | | | `-- Extracting gettext-runtime-0.21: .......... done
[122powerpc64-quarterly-job-10] | | `-- Extracting binutils-2.33.1_4,1: .......... done
[122powerpc64-quarterly-job-10] | | `-- Installing gcc9-9.3.0_3...
[122powerpc64-quarterly-job-10] | | | `-- Installing gmp-6.2.1...
[122powerpc64-quarterly-job-10] | | | `-- Extracting gmp-6.2.1: .......... done
[122powerpc64-quarterly-job-10] | | | `-- Installing mpc-1.2.0...
[122powerpc64-quarterly-job-10] | | | `-- Installing mpfr-4.1.0...
<snip>
audited for trustworthiness or RFC 3647 compliance.
Assessment and verification of trust is the complete responsibility of the
system administrator.
This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.
This enables SSL Certificate Verification by client software without manual
intervention.
If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.
* /etc/ssl/cert.pem
* /usr/local/etc/ssl/cert.pem
* /usr/local/openssl/cert.pem
=====
Message from gcc9-9.3.0_3:
--
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/gcc9
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
=====
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 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
[122powerpc64-quarterly-job-10] Installing ninja-1.10.2,2...
[122powerpc64-quarterly-job-10] `-- Installing python37-3.7.10...
[122powerpc64-quarterly-job-10] | `-- Installing libffi-3.3_1...
[122powerpc64-quarterly-job-10] | `-- Extracting libffi-3.3_1: .......... done
[122powerpc64-quarterly-job-10] | `-- Installing readline-8.1.0...
[122powerpc64-quarterly-job-10] | `-- Extracting readline-8.1.0: .......... done
[122powerpc64-quarterly-job-10] `-- Extracting python37-3.7.10: .......... done
[122powerpc64-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@py37
py37-sqlite3 databases/py-sqlite3@py37
py37-tkinter x11-toolkits/py-tkinter@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 executable: gcc10 - found
===> hhsuite-3.3.0 depends on file: /usr/local/bin/as - 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
[122powerpc64-quarterly-job-10] Installing perl5-5.32.1_1...
[122powerpc64-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
[122powerpc64-quarterly-job-10] Installing openmpi-4.1.0_1...
[122powerpc64-quarterly-job-10] `-- Installing hwloc2-2.4.1...
[122powerpc64-quarterly-job-10] | `-- Installing libpciaccess-0.16...
[122powerpc64-quarterly-job-10] | | `-- Installing pciids-20210223...
[122powerpc64-quarterly-job-10] | | `-- Extracting pciids-20210223: ..... done
[122powerpc64-quarterly-job-10] | `-- Extracting libpciaccess-0.16: ......... done
[122powerpc64-quarterly-job-10] | `-- Installing libxml2-2.9.10_4...
[122powerpc64-quarterly-job-10] | `-- Extracting libxml2-2.9.10_4: .......... done
[122powerpc64-quarterly-job-10] `-- Extracting hwloc2-2.4.1: .......... done
[122powerpc64-quarterly-job-10] `-- Installing libevent-2.1.12...
[122powerpc64-quarterly-job-10] `-- Extracting libevent-2.1.12: .......... done
[122powerpc64-quarterly-job-10] `-- Installing libltdl-2.4.6...
[122powerpc64-quarterly-job-10] `-- Extracting libltdl-2.4.6: .......... done
[122powerpc64-quarterly-job-10] `-- Installing munge-0.5.14_1...
[122powerpc64-quarterly-job-10] `-- Extracting munge-0.5.14_1: ......... done
[122powerpc64-quarterly-job-10] `-- Installing slurm-wlm-20.02.1_6...
[122powerpc64-quarterly-job-10] | `-- Installing hdf-szip-2.1.1...
[122powerpc64-quarterly-job-10] | `-- Extracting hdf-szip-2.1.1: .......... done
[122powerpc64-quarterly-job-10] | `-- Installing hdf5-1.10.6,1...
[122powerpc64-quarterly-job-10] | `-- Extracting hdf5-1.10.6,1: .......... done
[122powerpc64-quarterly-job-10] | `-- Installing json-c-0.15_1...
[122powerpc64-quarterly-job-10] | `-- Extracting json-c-0.15_1: .......... done
[122powerpc64-quarterly-job-10] | `-- Installing libsysinfo-0.0.3_2...
[122powerpc64-quarterly-job-10] | `-- Extracting libsysinfo-0.0.3_2: ......... done
[122powerpc64-quarterly-job-10] | `-- Installing lua52-5.2.4...
[122powerpc64-quarterly-job-10] | | `-- Installing libedit-3.1.20210216,1...
[122powerpc64-quarterly-job-10] | | `-- Extracting libedit-3.1.20210216,1: .......... done
[122powerpc64-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'.
[122powerpc64-quarterly-job-10] `-- Extracting slurm-wlm-20.02.1_6: .......... done
[122powerpc64-quarterly-job-10] Extracting openmpi-4.1.0_1: .......... done
===> 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 GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- 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
-- 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
-- Compiler is GNU
-- 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 (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
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
[1/98] /usr/local/bin/gcc10 -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 -Wl,-rpath=/usr/local/lib/gcc10 -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -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
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[25/98] : && /usr/local/bin/gcc10 -std=c99 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -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 && :
[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.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
[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/local/bin/g++10 -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 -Wl,-rpath=/usr/local/lib/gcc10 -Wl,-rpath=/usr/local/lib/gcc10 -std=c++0x -fsigned-char -msse2 -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -Wl,-rpath=/usr/local/lib/gcc10 -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
FAILED: src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o
/usr/local/bin/g++10 -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 -Wl,-rpath=/usr/local/lib/gcc10 -Wl,-rpath=/usr/local/lib/gcc10 -std=c++0x -fsigned-char -msse2 -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -Wl,-rpath=/usr/local/lib/gcc10 -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
g++10: error: unrecognized command-line option '-msse2'
[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.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
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