[package - 131releng-armv7-quarterly][biology/hhsuite] Failed for hhsuite-3.3.0_1 in build
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Date: Sat, 01 Oct 2022 00:14:52 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://ampere1.nyi.freebsd.org/data/131releng-armv7-quarterly/26ab9c488ede/logs/hhsuite-3.3.0_1.log
Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=131releng-armv7-quarterly&build=26ab9c488ede
Log:
=>> Building biology/hhsuite
build started at Sat Oct 1 00:14:17 UTC 2022
port directory: /usr/ports/biology/hhsuite
package name: hhsuite-3.3.0_1
building for: FreeBSD 131releng-armv7-quarterly-job-03 13.1-RELEASE-p2 FreeBSD 13.1-RELEASE-p2 1301000 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-1.18.3.pkg
[131releng-armv7-quarterly-job-03] Installing pkg-1.18.3...
[131releng-armv7-quarterly-job-03] Extracting pkg-1.18.3: .......... 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-3.23.2.pkg
[131releng-armv7-quarterly-job-03] Installing cmake-3.23.2...
[131releng-armv7-quarterly-job-03] `-- Installing curl-7.85.0...
[131releng-armv7-quarterly-job-03] | `-- Installing ca_root_nss-3.78...
[131releng-armv7-quarterly-job-03] | `-- Extracting ca_root_nss-3.78: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing libnghttp2-1.48.0...
[131releng-armv7-quarterly-job-03] | `-- Extracting libnghttp2-1.48.0: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing libpsl-0.21.1_4...
[131releng-armv7-quarterly-job-03] | | `-- Installing gettext-runtime-0.21...
[131releng-armv7-quarterly-job-03] | | `-- Installing indexinfo-0.3.1...
[131releng-armv7-quarterly-job-03] | | `-- Extracting indexinfo-0.3.1: .... done
[131releng-armv7-quarterly-job-03] | | `-- Extracting gettext-runtime-0.21: .......... done
[131releng-armv7-quarterly-job-03] | | `-- Installing libidn2-2.3.2...
[131releng-armv7-quarterly-job-03] | | `-- Installing libunistring-1.0...
[131releng-armv7-quarterly-job-03] | | `-- Extracting libunistring-1.0: .......... done
[131releng-armv7-quarterly-job-03] | | `-- Extracting libidn2-2.3.2: .......... done
[131releng-armv7-quarterly-job-03] | `-- Extracting libpsl-0.21.1_4: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing libssh2-1.10.0,3...
[131releng-armv7-quarterly-job-03] | `-- Extracting libssh2-1.10.0,3: .......... done
[131releng-armv7-quarterly-job-03] `-- Extracting curl-7.85.0: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing expat-2.4.8...
[131releng-armv7-quarterly-job-03] `-- Extracting expat-2.4.8: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing jsoncpp-1.9.5...
[131releng-armv7-quarterly-job-03] `-- Extracting jsoncpp-1.9.5: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing libarchive-3.6.1,1...
[131releng-armv7-quarterly-job-03] | `-- Installing liblz4-1.9.3,1...
[131releng-armv7-quarterly-job-03] | `-- Extracting liblz4-1.9.3,1: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing zstd-1.5.2...
[131releng-armv7-quarterly-job-03] | `-- Extracting zstd-1.5.2: .......... done
[131releng-armv7-quarterly-job-03] `-- Extracting libarchive-3.6.1,1: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing libuv-1.42.0...
[131releng-armv7-quarterly-job-03] `-- Extracting libuv-1.42.0: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing rhash-1.4.3...
[131releng-armv7-quarterly-job-03] `-- Extracting rhash-1.4.3: .......... done
[131releng-armv7-quarterly-job-03] Extracting cmake-3.23.2: .......... done
=====
Message from ca_root_nss-3.78:
--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
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
===> hhsuite-3.3.0_1 depends on file: /usr/local/bin/cmake - found
===> Returning to build of hhsuite-3.3.0_1
===> hhsuite-3.3.0_1 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.10.2,2.pkg
[131releng-armv7-quarterly-job-03] Installing ninja-1.10.2,2...
[131releng-armv7-quarterly-job-03] `-- Installing python39-3.9.14...
[131releng-armv7-quarterly-job-03] | `-- Installing libffi-3.4.2...
[131releng-armv7-quarterly-job-03] | `-- Extracting libffi-3.4.2: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing mpdecimal-2.5.1...
[131releng-armv7-quarterly-job-03] | `-- Extracting mpdecimal-2.5.1: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing readline-8.1.2...
[131releng-armv7-quarterly-job-03] | `-- Extracting readline-8.1.2: .......... done
[131releng-armv7-quarterly-job-03] `-- Extracting python39-3.9.14: .......... done
[131releng-armv7-quarterly-job-03] Extracting ninja-1.10.2,2: ........ done
=====
Message from python39-3.9.14:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> hhsuite-3.3.0_1 depends on executable: ninja - found
===> Returning to build of hhsuite-3.3.0_1
===> hhsuite-3.3.0_1 depends on file: /usr/local/bin/python3.9 - found
===> hhsuite-3.3.0_1 depends on package: perl5>=5.32.r0<5.33 - not found
===> Installing existing package /packages/All/perl5-5.32.1_1.pkg
[131releng-armv7-quarterly-job-03] Installing perl5-5.32.1_1...
[131releng-armv7-quarterly-job-03] Extracting perl5-5.32.1_1: .......... done
===> hhsuite-3.3.0_1 depends on package: perl5>=5.32.r0<5.33 - found
===> Returning to build of hhsuite-3.3.0_1
===========================================================================
=======================<phase: lib-depends >============================
===> hhsuite-3.3.0_1 depends on shared library: libmpi.so - not found
===> Installing existing package /packages/All/openmpi-4.1.4.pkg
[131releng-armv7-quarterly-job-03] Installing openmpi-4.1.4...
[131releng-armv7-quarterly-job-03] `-- Installing gcc11-11.3.0...
[131releng-armv7-quarterly-job-03] | `-- Installing binutils-2.37_2,1...
[131releng-armv7-quarterly-job-03] | `-- Extracting binutils-2.37_2,1: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing gmp-6.2.1...
[131releng-armv7-quarterly-job-03] | `-- Extracting gmp-6.2.1: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing mpc-1.2.1...
[131releng-armv7-quarterly-job-03] | | `-- Installing mpfr-4.1.0_1...
[131releng-armv7-quarterly-job-03] | | `-- Extracting mpfr-4.1.0_1: .......... done
[131releng-armv7-quarterly-job-03] | `-- Extracting mpc-1.2.1: ......... done
[131releng-armv7-quarterly-job-03] `-- Extracting gcc11-11.3.0: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing hwloc2-2.7.0_2...
[131releng-armv7-quarterly-job-03] | `-- Installing level-zero-1.8.1...
[131releng-armv7-quarterly-job-03] | `-- Extracting level-zero-1.8.1: .......... done
[131releng-armv7-quarterly-job-03] | `-- Installing libpciaccess-0.16...
[131releng-armv7-quarterly-job-03] | | `-- Installing pciids-20220518...
[131releng-armv7-quarterly-job-03] | | `-- Extracting pciids-20220518: ..... done
[131releng-armv7-quarterly-job-03] | `-- Extracting libpciaccess-0.16: ......... done
[131releng-armv7-quarterly-job-03] | `-- Installing libxml2-2.9.13_2...
[131releng-armv7-quarterly-job-03] | `-- Extracting libxml2-2.9.13_2: .......... done
[131releng-armv7-quarterly-job-03] `-- Extracting hwloc2-2.7.0_2: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing libevent-2.1.12...
[131releng-armv7-quarterly-job-03] `-- Extracting libevent-2.1.12: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing libltdl-2.4.7...
[131releng-armv7-quarterly-job-03] `-- Extracting libltdl-2.4.7: .......... done
[131releng-armv7-quarterly-job-03] `-- Installing munge-0.5.14_1...
[131releng-armv7-quarterly-job-03] `-- Extracting munge-0.5.14_1: ......... done
[131releng-armv7-quarterly-job-03] Extracting openmpi-4.1.4: .......... done
=====
Message from gcc11-11.3.0:
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc11
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 13.0.0
-- The CXX compiler identification is Clang 13.0.0
-- 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
[ 1% 2/98] /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 -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 -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
FAILED: src/CMakeFiles/A3M_COMPRESS.dir/a3m_compress.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 -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 -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
c++: error: the clang compiler does not support '-march=native'
[ 2% 2/98] /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 -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 -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
FAILED: src/CMakeFiles/a3m_extract.dir/a3m_extract.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 -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 -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
c++: error: the clang compiler does not support '-march=native'
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