[package - 130releng-armv7-quarterly][biology/hhsuite] Failed for hhsuite-3.3.0 in build
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Date: Sat, 12 Mar 2022 22:22:44 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://beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/1b4a6a151c20/logs/hhsuite-3.3.0.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=1b4a6a151c20
Log:
=>> Building biology/hhsuite
build started at Sat Mar 12 22:21:41 UTC 2022
port directory: /usr/ports/biology/hhsuite
package name: hhsuite-3.3.0
building for: FreeBSD 130releng-armv7-quarterly-job-01 13.0-RELEASE-p7 FreeBSD 13.0-RELEASE-p7 1300139 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 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5.pkg
[130releng-armv7-quarterly-job-01] Installing pkg-1.17.5...
[130releng-armv7-quarterly-job-01] Extracting pkg-1.17.5: .......... 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-3.22.1.pkg
[130releng-armv7-quarterly-job-01] Installing cmake-3.22.1...
[130releng-armv7-quarterly-job-01] `-- Installing curl-7.80.0...
[130releng-armv7-quarterly-job-01] | `-- Installing ca_root_nss-3.71...
[130releng-armv7-quarterly-job-01] | `-- Extracting ca_root_nss-3.71: ........ done
[130releng-armv7-quarterly-job-01] | `-- Installing libnghttp2-1.46.0...
[130releng-armv7-quarterly-job-01] | `-- Extracting libnghttp2-1.46.0: .......... done
[130releng-armv7-quarterly-job-01] | `-- Installing libssh2-1.10.0,3...
[130releng-armv7-quarterly-job-01] | `-- Extracting libssh2-1.10.0,3: .......... done
[130releng-armv7-quarterly-job-01] `-- Extracting curl-7.80.0: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing expat-2.4.7...
[130releng-armv7-quarterly-job-01] `-- Extracting expat-2.4.7: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing jsoncpp-1.9.5...
[130releng-armv7-quarterly-job-01] `-- Extracting jsoncpp-1.9.5: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing libarchive-3.5.2,1...
[130releng-armv7-quarterly-job-01] | `-- Installing liblz4-1.9.3,1...
[130releng-armv7-quarterly-job-01] | `-- Extracting liblz4-1.9.3,1: .......... done
[130releng-armv7-quarterly-job-01] | `-- Installing zstd-1.5.0...
[130releng-armv7-quarterly-job-01] | `-- Extracting zstd-1.5.0: .......... done
[130releng-armv7-quarterly-job-01] `-- Extracting libarchive-3.5.2,1: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing libuv-1.42.0...
[130releng-armv7-quarterly-job-01] `-- Extracting libuv-1.42.0: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing rhash-1.4.2...
[130releng-armv7-quarterly-job-01] | `-- Installing gettext-runtime-0.21...
[130releng-armv7-quarterly-job-01] | | `-- Installing indexinfo-0.3.1...
[130releng-armv7-quarterly-job-01] | | `-- Extracting indexinfo-0.3.1: .... done
[130releng-armv7-quarterly-job-01] | `-- Extracting gettext-runtime-0.21: .......... done
[130releng-armv7-quarterly-job-01] `-- Extracting rhash-1.4.2: .......... done
[130releng-armv7-quarterly-job-01] Extracting cmake-3.22.1: .......... done
=====
Message from ca_root_nss-3.71:
--
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 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.pkg
[130releng-armv7-quarterly-job-01] Installing ninja-1.10.2,2...
[130releng-armv7-quarterly-job-01] `-- Installing python38-3.8.12_1...
[130releng-armv7-quarterly-job-01] | `-- Installing libffi-3.3_1...
[130releng-armv7-quarterly-job-01] | `-- Extracting libffi-3.3_1: .......... done
[130releng-armv7-quarterly-job-01] | `-- Installing mpdecimal-2.5.1...
[130releng-armv7-quarterly-job-01] | `-- Extracting mpdecimal-2.5.1: .......... done
[130releng-armv7-quarterly-job-01] | `-- Installing readline-8.1.1...
[130releng-armv7-quarterly-job-01] | `-- Extracting readline-8.1.1: .......... done
[130releng-armv7-quarterly-job-01] `-- Extracting python38-3.8.12_1: .......... done
[130releng-armv7-quarterly-job-01] Extracting ninja-1.10.2,2: ........ done
=====
Message from python38-3.8.12_1:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py38-gdbm databases/py-gdbm@py38
py38-sqlite3 databases/py-sqlite3@py38
py38-tkinter x11-toolkits/py-tkinter@py38
===> 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/python3.8 - 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.pkg
[130releng-armv7-quarterly-job-01] Installing perl5-5.32.1_1...
[130releng-armv7-quarterly-job-01] 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-4.1.1.pkg
[130releng-armv7-quarterly-job-01] Installing openmpi-4.1.1...
[130releng-armv7-quarterly-job-01] `-- Installing gcc10-10.3.0...
[130releng-armv7-quarterly-job-01] | `-- Installing binutils-2.37_2,1...
[130releng-armv7-quarterly-job-01] | `-- Extracting binutils-2.37_2,1: .......... done
[130releng-armv7-quarterly-job-01] | `-- Installing gmp-6.2.1...
[130releng-armv7-quarterly-job-01] | `-- Extracting gmp-6.2.1: .......... done
[130releng-armv7-quarterly-job-01] | `-- Installing mpc-1.2.1...
[130releng-armv7-quarterly-job-01] | | `-- Installing mpfr-4.1.0_1...
[130releng-armv7-quarterly-job-01] | | `-- Extracting mpfr-4.1.0_1: .......... done
[130releng-armv7-quarterly-job-01] | `-- Extracting mpc-1.2.1: ......... done
[130releng-armv7-quarterly-job-01] `-- Extracting gcc10-10.3.0: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing hwloc2-2.5.0...
[130releng-armv7-quarterly-job-01] | `-- Installing level-zero-1.7.4...
[130releng-armv7-quarterly-job-01] | `-- Extracting level-zero-1.7.4: .......... done
[130releng-armv7-quarterly-job-01] | `-- Installing libpciaccess-0.16...
[130releng-armv7-quarterly-job-01] | | `-- Installing pciids-20211124...
[130releng-armv7-quarterly-job-01] | | `-- Extracting pciids-20211124: ..... done
[130releng-armv7-quarterly-job-01] | `-- Extracting libpciaccess-0.16: ......... done
[130releng-armv7-quarterly-job-01] | `-- Installing libxml2-2.9.12...
[130releng-armv7-quarterly-job-01] | `-- Extracting libxml2-2.9.12: .......... done
[130releng-armv7-quarterly-job-01] `-- Extracting hwloc2-2.5.0: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing libevent-2.1.12...
[130releng-armv7-quarterly-job-01] `-- Extracting libevent-2.1.12: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing libltdl-2.4.6...
[130releng-armv7-quarterly-job-01] `-- Extracting libltdl-2.4.6: .......... done
[130releng-armv7-quarterly-job-01] `-- Installing munge-0.5.14_1...
[130releng-armv7-quarterly-job-01] `-- Extracting munge-0.5.14_1: ......... done
[130releng-armv7-quarterly-job-01] Extracting openmpi-4.1.1: .......... done
=====
Message from gcc10-10.3.0:
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc10
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> 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 11.0.1
-- The CXX compiler identification is Clang 11.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /nxb-bin/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: /nxb-bin/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% 1/98] 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
[ 2% 2/98] /nxb-bin/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 -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
FAILED: src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o
/nxb-bin/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 -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
c++: error: the clang compiler does not support '-march=native'
ninja: build stopped: subcommand failed.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/hhsuite