[package - 140i386-quarterly][biology/spoa] Failed for spoa-4.1.0 in build
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Date: Thu, 25 Apr 2024 01:56:11 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: https://pkg-status.freebsd.org/beefy19/data/140i386-quarterly/7b15f345a8c7/logs/spoa-4.1.0.log
Build URL: https://pkg-status.freebsd.org/beefy19/build.html?mastername=140i386-quarterly&build=7b15f345a8c7
Log:
=>> Building biology/spoa
build started at Thu Apr 25 01:55:59 UTC 2024
port directory: /usr/ports/biology/spoa
package name: spoa-4.1.0
building for: FreeBSD 140i386-quarterly-job-02 14.0-RELEASE-p6 FreeBSD 14.0-RELEASE-p6 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1372 Apr 8 19:19 /usr/ports/biology/spoa/Makefile
Ports top last git commit: 7b15f345a
Ports top unclean checkout: no
Port dir last git commit: b3aa1ea86
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1400097
Job Id: 02
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--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/spoa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/spoa/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/spoa/work/.cache HOME=/wrkdirs/usr/ports/biology/spoa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/spoa/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/spoa/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
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NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/spoa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/spoa/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/spoa/work/.cache HOME=/wrkdirs/usr/ports/biology/spoa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/spoa/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/spoa/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/spoa/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lz -lcpu_features -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -
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--End PLIST_SUB--
--SUB_LIST--
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ARCH=${MACHINE_ARCH}
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
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GID=0
UID=0
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=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> spoa-4.1.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.2.pkg
[140i386-quarterly-job-02] Installing pkg-1.21.2...
[140i386-quarterly-job-02] Extracting pkg-1.21.2: .......... done
===> spoa-4.1.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of spoa-4.1.0
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by spoa-4.1.0 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by spoa-4.1.0 for building
=> SHA256 Checksum OK for rvaser-spoa-4.1.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by spoa-4.1.0 for building
===> Extracting for spoa-4.1.0
=> SHA256 Checksum OK for rvaser-spoa-4.1.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for spoa-4.1.0
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> spoa-4.1.0 depends on package: bioparser>0 - not found
===> Installing existing package /packages/All/bioparser-3.1.0.pkg
[140i386-quarterly-job-02] Installing bioparser-3.1.0...
[140i386-quarterly-job-02] `-- Installing biosoup-0.11.0_1...
[140i386-quarterly-job-02] `-- Extracting biosoup-0.11.0_1: .......... done
[140i386-quarterly-job-02] Extracting bioparser-3.1.0: .......... done
===> spoa-4.1.0 depends on package: bioparser>0 - found
===> Returning to build of spoa-4.1.0
===> spoa-4.1.0 depends on package: biosoup>0 - found
===> spoa-4.1.0 depends on package: cereal>0 - not found
===> Installing existing package /packages/All/cereal-1.3.2_1.pkg
[140i386-quarterly-job-02] Installing cereal-1.3.2_1...
[140i386-quarterly-job-02] `-- Installing boost-libs-1.84.0...
[140i386-quarterly-job-02] | `-- Installing icu-74.2_1,1...
[140i386-quarterly-job-02] | `-- Extracting icu-74.2_1,1: .......... done
[140i386-quarterly-job-02] `-- Extracting boost-libs-1.84.0: .......... done
[140i386-quarterly-job-02] Extracting cereal-1.3.2_1: .......... done
=====
Message from boost-libs-1.84.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> spoa-4.1.0 depends on package: cereal>0 - found
===> Returning to build of spoa-4.1.0
===> spoa-4.1.0 depends on package: simde>0 - not found
===> Installing existing package /packages/All/simde-0.8.0.pkg
[140i386-quarterly-job-02] Installing simde-0.8.0...
[140i386-quarterly-job-02] Extracting simde-0.8.0: .......... done
===> spoa-4.1.0 depends on package: simde>0 - found
===> Returning to build of spoa-4.1.0
===> spoa-4.1.0 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.28.3.pkg
[140i386-quarterly-job-02] Installing cmake-core-3.28.3...
[140i386-quarterly-job-02] `-- Installing expat-2.6.2...
[140i386-quarterly-job-02] `-- Extracting expat-2.6.2: .......... done
[140i386-quarterly-job-02] `-- Installing jsoncpp-1.9.5...
[140i386-quarterly-job-02] `-- Extracting jsoncpp-1.9.5: .......... done
[140i386-quarterly-job-02] `-- Installing libuv-1.48.0...
[140i386-quarterly-job-02] `-- Extracting libuv-1.48.0: .......... done
[140i386-quarterly-job-02] `-- Installing rhash-1.4.4_1...
[140i386-quarterly-job-02] | `-- Installing gettext-runtime-0.22.5...
[140i386-quarterly-job-02] | | `-- Installing indexinfo-0.3.1...
[140i386-quarterly-job-02] | | `-- Extracting indexinfo-0.3.1: .... done
[140i386-quarterly-job-02] | `-- Extracting gettext-runtime-0.22.5: .......... done
[140i386-quarterly-job-02] `-- Extracting rhash-1.4.4_1: .......... done
[140i386-quarterly-job-02] Extracting cmake-core-3.28.3: .......... done
===> spoa-4.1.0 depends on file: /usr/local/bin/cmake - found
===> Returning to build of spoa-4.1.0
===> spoa-4.1.0 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.11.1,2.pkg
[140i386-quarterly-job-02] Installing ninja-1.11.1,2...
[140i386-quarterly-job-02] `-- Installing python39-3.9.18_2...
[140i386-quarterly-job-02] | `-- Installing libffi-3.4.4_1...
[140i386-quarterly-job-02] | `-- Extracting libffi-3.4.4_1: .......... done
[140i386-quarterly-job-02] | `-- Installing mpdecimal-4.0.0...
[140i386-quarterly-job-02] | `-- Extracting mpdecimal-4.0.0: .......... done
[140i386-quarterly-job-02] | `-- Installing readline-8.2.10...
[140i386-quarterly-job-02] | `-- Extracting readline-8.2.10: .......... done
[140i386-quarterly-job-02] `-- Extracting python39-3.9.18_2: .......... done
[140i386-quarterly-job-02] Extracting ninja-1.11.1,2: ........ done
=====
Message from python39-3.9.18_2:
--
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
===> spoa-4.1.0 depends on executable: ninja - found
===> Returning to build of spoa-4.1.0
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> spoa-4.1.0 depends on shared library: libcpu_features.so - not found
===> Installing existing package /packages/All/cpu_features-0.7.0.pkg
[140i386-quarterly-job-02] Installing cpu_features-0.7.0...
[140i386-quarterly-job-02] Extracting cpu_features-0.7.0: .......... done
===> spoa-4.1.0 depends on shared library: libcpu_features.so - found (/usr/local/lib/libcpu_features.so)
===> Returning to build of spoa-4.1.0
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for spoa-4.1.0
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/spoa/work/.build
-- The CXX compiler identification is Clang 16.0.6
-- 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
-- Configuring done (0.5s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_COLOR_MAKEFILE
CMAKE_C_COMPILER
CMAKE_C_FLAGS
CMAKE_C_FLAGS_DEBUG
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
THREADS_HAVE_PTHREAD_ARG
spoa_build_executable
spoa_optimize_for_native
spoa_optimize_for_portability
-- Build files have been written to: /wrkdirs/usr/ports/biology/spoa/work/.build
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for spoa-4.1.0
[ 8% 3/12] /usr/bin/c++ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DSPOA_GENERATE_DISPATCH -DSPOA_USE_CEREAL -DSPOA_USE_SIMDE -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/include -I/wrkdirs/usr/ports/biology/spoa/work/.build -I/wrkdirs/usr/ports/biology/spoa/work/.build/_deps/simde-src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -DNDEBUG -std=c++11 -fPIC -MD -MT CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -MF CMakeFiles/spoa.dir/src/alignment_engine.cpp.o.d -o CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/src/alignment_engine.cpp
[ 16% 4/12] /usr/bin/c++ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DSPOA_GENERATE_DISPATCH -DSPOA_USE_CEREAL -DSPOA_USE_SIMDE -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/include -I/wrkdirs/usr/ports/biology/spoa/work/.build -I/wrkdirs/usr/ports/biology/spoa/work/.build/_deps/simde-src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -DNDEBUG -std=c++11 -fPIC -MD -MT CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o -MF CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o.d -o CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/
src/simd_alignment_engine_dispatcher.cpp
FAILED: CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o
/usr/bin/c++ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DSPOA_GENERATE_DISPATCH -DSPOA_USE_CEREAL -DSPOA_USE_SIMDE -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/include -I/wrkdirs/usr/ports/biology/spoa/work/.build -I/wrkdirs/usr/ports/biology/spoa/work/.build/_deps/simde-src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -DNDEBUG -std=c++11 -fPIC -MD -MT CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o -MF CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o.d -o CMakeFiles/spoa.dir/src/simd_alignment_engine_dispatcher.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/src/simd_ali
gnment_engine_dispatcher.cpp
In file included from /wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/src/simd_alignment_engine_dispatcher.cpp:3:
In file included from /wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/src/simd_alignment_engine_implementation.hpp:21:
In file included from /usr/local/include/simde/x86/sse4.1.h:27:
In file included from /usr/local/include/simde/x86/sse.h:34:
/usr/local/include/simde/x86/../simde-f16.h:96:11: error: _Float16 is not supported on this target
typedef _Float16 simde_float16;
^
1 error generated.
[ 25% 4/12] /usr/bin/c++ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DSPOA_GENERATE_DISPATCH -DSPOA_USE_CEREAL -DSPOA_USE_SIMDE -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/include -I/wrkdirs/usr/ports/biology/spoa/work/.build -I/wrkdirs/usr/ports/biology/spoa/work/.build/_deps/simde-src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -DNDEBUG -std=c++11 -fPIC -MD -MT CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o -MF CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o.d -o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/src/sisd_alignment_engine.cpp
[ 33% 4/12] /usr/bin/c++ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DSPOA_GENERATE_DISPATCH -DSPOA_USE_CEREAL -DSPOA_USE_SIMDE -DSTACK_LINE_READER_BUFFER_SIZE=1024 -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/include -I/wrkdirs/usr/ports/biology/spoa/work/.build -I/wrkdirs/usr/ports/biology/spoa/work/.build/_deps/simde-src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/cpu_features -isystem /usr/local/include -DNDEBUG -std=c++11 -fPIC -MD -MT CMakeFiles/spoa.dir/src/graph.cpp.o -MF CMakeFiles/spoa.dir/src/graph.cpp.o.d -o CMakeFiles/spoa.dir/src/graph.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.1.0/src/graph.cpp
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/spoa