[package - 132arm64-default][biology/seqwish] Failed for seqwish-0.7.9 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sat, 11 May 2024 16:36:10 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/ampere3/data/132arm64-default/aeab170c7654/logs/seqwish-0.7.9.log
Build URL:      https://pkg-status.freebsd.org/ampere3/build.html?mastername=132arm64-default&build=aeab170c7654
Log:

=>> Building biology/seqwish
build started at Sat May 11 16:34:44 UTC 2024
port directory: /usr/ports/biology/seqwish
package name: seqwish-0.7.9
building for: FreeBSD 132arm64-default-job-06 13.2-RELEASE-p11 FreeBSD 13.2-RELEASE-p11 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root  wheel  839 Nov  7  2023 /usr/ports/biology/seqwish/Makefile
Ports top last git commit: aeab170c765
Ports top unclean checkout: no
Port dir last git commit: 25d04c675ed
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500018
Jail OSVERSION: 1302001
Job Id: 06

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---Begin OPTIONS List---
===> The following configuration options are available for seqwish-0.7.9:
     OPENMP=on: Parallel processing support via OpenMP
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work  XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache  HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work  XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache  HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/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 PREFIX=/usr/local  LOCALBASE=/usr/local  CC="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -fno-strict-aliasing "  CPP="cpp" CPPFLAGS=""  LDFLAGS=" -fstack-protector-strong " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing  -fopenmp " BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -
m 0644"  BSD_INSTALL_MAN="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
 CMAKE_BUILD_TYPE="release" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqwish"  EXAMPLESDIR="share/examples/seqwish"  DATADIR="share/seqwish"  WWWDIR="www/seqwish"  ETCDIR="etc/seqwish"
--End PLIST_SUB--

--SUB_LIST--
 PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/seqwish DOCSDIR=/usr/local/share/doc/seqwish EXAMPLESDIR=/usr/local/share/examples/seqwish  WWWDIR=/usr/local/www/seqwish ETCDIR=/usr/local/etc/seqwish
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
####  ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
# failed mirror and then fails rather then trying another.  It *does*
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MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
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--Resource limits--
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--End resource limits--
=======================<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
===>   seqwish-0.7.9 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.21.2.pkg
[132arm64-default-job-06] Installing pkg-1.21.2...
[132arm64-default-job-06] Extracting pkg-1.21.2: .......... done
===>   seqwish-0.7.9 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of seqwish-0.7.9
===========================================================================
=======================<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 seqwish-0.7.9 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 seqwish-0.7.9 for building
=> SHA256 Checksum OK for seqwish-v0.7.9.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 seqwish-0.7.9 for building
===>  Extracting for seqwish-0.7.9
=> SHA256 Checksum OK for seqwish-v0.7.9.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 seqwish-0.7.9
===>  Applying FreeBSD patches for seqwish-0.7.9 from /usr/ports/biology/seqwish/files
===========================================================================
=======================<phase: build-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   seqwish-0.7.9 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-core-3.28.3.pkg
[132arm64-default-job-06] Installing cmake-core-3.28.3...
[132arm64-default-job-06] `-- Installing expat-2.6.2...
[132arm64-default-job-06] `-- Extracting expat-2.6.2: .......... done
[132arm64-default-job-06] `-- Installing jsoncpp-1.9.5...
[132arm64-default-job-06] `-- Extracting jsoncpp-1.9.5: .......... done
[132arm64-default-job-06] `-- Installing libuv-1.48.0...
[132arm64-default-job-06] `-- Extracting libuv-1.48.0: .......... done
[132arm64-default-job-06] `-- Installing rhash-1.4.4_1...
[132arm64-default-job-06] |   `-- Installing gettext-runtime-0.22.5...
[132arm64-default-job-06] |   | `-- Installing indexinfo-0.3.1...
[132arm64-default-job-06] |   | `-- Extracting indexinfo-0.3.1: .... done
[132arm64-default-job-06] |   `-- Extracting gettext-runtime-0.22.5: .......... done
[132arm64-default-job-06] `-- Extracting rhash-1.4.4_1: .......... done
[132arm64-default-job-06] Extracting cmake-core-3.28.3: .......... done
===>   seqwish-0.7.9 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of seqwish-0.7.9
===========================================================================
=======================<phase: lib-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure      >============================
<snip>
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Performing Test HAVE_INLINE
-- Performing Test HAVE_INLINE - Success
-- Performing Test HAVE___INLINE
-- Performing Test HAVE___INLINE - Success
-- Performing Test HAVE___INLINE__
-- Performing Test HAVE___INLINE__ - Success
-- Performing Test HAVE___DECLSPEC_DLLEXPORT_
-- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed
-- Performing Test HAVE___DECLSPEC_DLLIMPORT_
-- Performing Test HAVE___DECLSPEC_DLLIMPORT_ - Failed
-- Check size of uint8_t
-- Check size of uint8_t - done
-- Check size of int32_t
-- Check size of int32_t - done
-- Looking for PRId32
-- Looking for PRId32 - found
-- Check size of int64_t
-- Check size of int64_t - done
-- Looking for PRId64
-- Looking for PRId64 - found
CMake Warning (dev) at external/googletest/googletest/CMakeLists.txt:47 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    PROJECT_VERSION
    PROJECT_VERSION_MAJOR
    PROJECT_VERSION_MINOR
    PROJECT_VERSION_PATCH
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Deprecation Warning at external/googletest/googletest/CMakeLists.txt:48 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


CMake Warning (dev) at external/googletest/googletest/cmake/internal_utils.cmake:211 (find_package):
  Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
  are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
  the cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  external/googletest/googletest/CMakeLists.txt:60 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) 
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Looking for C++ include cstdio
-- Looking for C++ include cstdio - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
-- Configuring done (9.6s)
-- Generating done (0.3s)
-- Build files have been written to: /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-configure
--- sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-build ---
[ 80%] Performing build step for 'sdsl-lite'
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/bin/make
[  0%] Building CXX object external/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
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[ 20%] Built target divsufsort
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[ 40%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o
[ 40%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o
[ 40%] Linking CXX static library libgtest.a
[ 40%] Built target gtest
[ 40%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o
[ 40%] Building CXX object external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/sdsl-lite/lib/construct_lcp.cpp:6:
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/lib/../include/sdsl/construct_lcp.hpp:130:53: warning: instantiation of variable 'sdsl::key_text_trait<'\b'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template]
    const char* KEY_TEXT = key_text_trait<t_width>::KEY_TEXT;
                                                    ^
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/sdsl-lite/lib/construct_lcp.cpp:209:25: note: in instantiation of function template specialization 'sdsl::construct_lcp_PHI<(unsigned char)'\b'>' requested here
                        construct_lcp_PHI<8>(config);
                        ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/lib/../include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here
    static const char* KEY_TEXT;
                       ^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/lib/../include/sdsl/construct_lcp.hpp:130:53: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\b'>::KEY_TEXT' is explicitly instantiated in another translation unit
    const char* KEY_TEXT = key_text_trait<t_width>::KEY_TEXT;
                                                    ^
[ 50%] Linking CXX static library libgtest_main.a
[ 50%] Built target gtest_main
[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o
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1 warning generated.
[ 60%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o
[ 60%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o
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[100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o
[100%] Linking CXX static library libsdsl.a
[100%] Built target sdsl
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-build
--- sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-install ---
[ 81%] No install step for 'sdsl-lite'
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/local/bin/cmake -E echo_append
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-install
--- CMakeFiles/sdsl-lite-complete ---
[ 82%] Completed 'sdsl-lite'
/usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/sdsl-lite-complete
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-done
[ 82%] Built target sdsl-lite
--- CMakeFiles/seqwish.dir/all ---
/usr/bin/make  -f CMakeFiles/seqwish.dir/build.make CMakeFiles/seqwish.dir/depend
--- CMakeFiles/seqwish.dir/depend ---
cd /wrkdirs/usr/ports/biology/seqwish/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9 /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9 /wrkdirs/usr/ports/biology/seqwish/work/.build /wrkdirs/usr/ports/biology/seqwish/work/.build /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/seqwish.dir/DependInfo.cmake
/usr/bin/make  -f CMakeFiles/seqwish.dir/build.make CMakeFiles/seqwish.dir/build
--- CMakeFiles/seqwish.dir/src/utils.cpp.o ---
--- CMakeFiles/seqwish.dir/src/tempfile.cpp.o ---
--- CMakeFiles/seqwish.dir/src/main.cpp.o ---
--- CMakeFiles/seqwish.dir/src/utils.cpp.o ---
[ 84%] Building CXX object CMakeFiles/seqwish.dir/src/utils.cpp.o
--- CMakeFiles/seqwish.dir/src/tempfile.cpp.o ---
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