[package - 133releng-armv7-default][biology/gcta] Failed for gcta-1.94.1_2 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Wed, 04 Sep 2024 18:51:35 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:     jwb@FreeBSD.org
Log URL:        https://pkg-status.freebsd.org/ampere3/data/133releng-armv7-default/1b6eada811a7/logs/gcta-1.94.1_2.log
Build URL:      https://pkg-status.freebsd.org/ampere3/build.html?mastername=133releng-armv7-default&build=1b6eada811a7
Log:

=>> Building biology/gcta
build started at Wed Sep  4 18:50:26 UTC 2024
port directory: /usr/ports/biology/gcta
package name: gcta-1.94.1_2
building for: FreeBSD 133releng-armv7-default-job-08 13.3-RELEASE-p5 FreeBSD 13.3-RELEASE-p5 1303001 arm
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root  wheel  1581 Jun 27 01:08 /usr/ports/biology/gcta/Makefile
Ports top last git commit: 1b6eada811a
Ports top unclean checkout: no
Port dir last git commit: 84a6e7ec36e
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500019
Jail OSVERSION: 1303001
Job Id: 08

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=======================<phase: check-sanity   >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   gcta-1.94.1_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.21.3.pkg
[133releng-armv7-default-job-08] Installing pkg-1.21.3...
[133releng-armv7-default-job-08] Extracting pkg-1.21.3: .......... done
===>   gcta-1.94.1_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of gcta-1.94.1_2
===========================================================================
=======================<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 GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.94.1_2 for building
===========================================================================
=======================<phase: checksum       >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.94.1_2 for building
=> SHA256 Checksum OK for jianyangqt-gcta-v1.94.1_GH0.tar.gz.
=> SHA256 Checksum OK for zhilizheng-plink-ng-3744540_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 GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.94.1_2 for building
===>  Extracting for gcta-1.94.1_2
=> SHA256 Checksum OK for jianyangqt-gcta-v1.94.1_GH0.tar.gz.
=> SHA256 Checksum OK for zhilizheng-plink-ng-3744540_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 gcta-1.94.1_2
===>  Applying FreeBSD patches for gcta-1.94.1_2 from /usr/ports/biology/gcta/files
===========================================================================
=======================<phase: build-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   gcta-1.94.1_2 depends on package: boost-libs>0 - not found
===>   Installing existing package /packages/All/boost-libs-1.84.0.pkg
[133releng-armv7-default-job-08] Installing boost-libs-1.84.0...
[133releng-armv7-default-job-08] `-- Installing icu-74.2_1,1...
[133releng-armv7-default-job-08] `-- Extracting icu-74.2_1,1: .......... done
[133releng-armv7-default-job-08] Extracting boost-libs-1.84.0: .......... 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.
===>   gcta-1.94.1_2 depends on package: boost-libs>0 - found
===>   Returning to build of gcta-1.94.1_2
===>   gcta-1.94.1_2 depends on package: spectra>0 - not found
===>   Installing existing package /packages/All/spectra-1.0.1_1.pkg
[133releng-armv7-default-job-08] Installing spectra-1.0.1_1...
[133releng-armv7-default-job-08] `-- Installing eigen-3.4.0_3...
[133releng-armv7-default-job-08] |   `-- Installing blas-3.12.0_1...
[133releng-armv7-default-job-08] |   | `-- Installing gcc13-13.2.0_4...
[133releng-armv7-default-job-08] |   |   `-- Installing binutils-2.40_7,1...
[133releng-armv7-default-job-08] |   |   | `-- Installing indexinfo-0.3.1...
[133releng-armv7-default-job-08] |   |   | `-- Extracting indexinfo-0.3.1: .... done
[133releng-armv7-default-job-08] |   |   | `-- Installing zstd-1.5.6...
[133releng-armv7-default-job-08] |   |   |   `-- Installing liblz4-1.10.0,1...
[133releng-armv7-default-job-08] |   |   |   `-- Extracting liblz4-1.10.0,1: .......... done
[133releng-armv7-default-job-08] |   |   | `-- Extracting zstd-1.5.6: .......... done
[133releng-armv7-default-job-08] |   |   `-- Extracting binutils-2.40_7,1: .......... done
[133releng-armv7-default-job-08] |   |   `-- Installing gmp-6.3.0...
[133releng-armv7-default-job-08] |   |   `-- Extracting gmp-6.3.0: .......... done
[133releng-armv7-default-job-08] |   |   `-- Installing mpc-1.3.1_1...
[133releng-armv7-default-job-08] |   |   | `-- Installing mpfr-4.2.1,1...
[133releng-armv7-default-job-08] |   |   | `-- Extracting mpfr-4.2.1,1: .......... done
[133releng-armv7-default-job-08] |   |   `-- Extracting mpc-1.3.1_1: ......... done
[133releng-armv7-default-job-08] |   | `-- Extracting gcc13-13.2.0_4: .......... done
[133releng-armv7-default-job-08] |   `-- Extracting blas-3.12.0_1: ........ done
[133releng-armv7-default-job-08] |   `-- Installing lapack-3.12.0_2...
[133releng-armv7-default-job-08] |   `-- Extracting lapack-3.12.0_2: .......... done
[133releng-armv7-default-job-08] `-- Extracting eigen-3.4.0_3: .......... done
[133releng-armv7-default-job-08] Extracting spectra-1.0.1_1: .......... done
=====
Message from gcc13-13.2.0_4:

--
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/gcc13

For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===>   gcta-1.94.1_2 depends on package: spectra>0 - found
===>   Returning to build of gcta-1.94.1_2
===>   gcta-1.94.1_2 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-core-3.30.2.pkg
[133releng-armv7-default-job-08] Installing cmake-core-3.30.2...
[133releng-armv7-default-job-08] `-- Installing expat-2.6.2...
[133releng-armv7-default-job-08] `-- Extracting expat-2.6.2: .......... done
[133releng-armv7-default-job-08] `-- Installing jsoncpp-1.9.5...
[133releng-armv7-default-job-08] `-- Extracting jsoncpp-1.9.5: .......... done
[133releng-armv7-default-job-08] `-- Installing libuv-1.48.0...
[133releng-armv7-default-job-08] `-- Extracting libuv-1.48.0: .......... done
[133releng-armv7-default-job-08] `-- Installing rhash-1.4.4_1...
[133releng-armv7-default-job-08] |   `-- Installing gettext-runtime-0.22.5...
[133releng-armv7-default-job-08] |   `-- Extracting gettext-runtime-0.22.5: .......... done
[133releng-armv7-default-job-08] `-- Extracting rhash-1.4.4_1: .......... done
[133releng-armv7-default-job-08] Extracting cmake-core-3.30.2: .......... done
===>   gcta-1.94.1_2 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of gcta-1.94.1_2
===>   gcta-1.94.1_2 depends on executable: ninja - not found
===>   Installing existing package /packages/All/ninja-1.11.1,4.pkg
[133releng-armv7-default-job-08] Installing ninja-1.11.1,4...
[133releng-armv7-default-job-08] `-- Installing python311-3.11.9_1...
[133releng-armv7-default-job-08] |   `-- Installing libffi-3.4.6...
[133releng-armv7-default-job-08] |   `-- Extracting libffi-3.4.6: .......... done
[133releng-armv7-default-job-08] |   `-- Installing mpdecimal-4.0.0...
[133releng-armv7-default-job-08] |   `-- Extracting mpdecimal-4.0.0: .......... done
[133releng-armv7-default-job-08] |   `-- Installing readline-8.2.10...
[133releng-armv7-default-job-08] |   `-- Extracting readline-8.2.10: .......... done
[133releng-armv7-default-job-08] `-- Extracting python311-3.11.9_1: .......... done
[133releng-armv7-default-job-08] Extracting ninja-1.11.1,4: ........ done
=====
Message from python311-3.11.9_1:

--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

py311-gdbm       databases/py-gdbm@py311
py311-sqlite3    databases/py-sqlite3@py311
py311-tkinter    x11-toolkits/py-tkinter@py311
===>   gcta-1.94.1_2 depends on executable: ninja - found
===>   Returning to build of gcta-1.94.1_2
===>   gcta-1.94.1_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found
===========================================================================
=======================<phase: lib-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   gcta-1.94.1_2 depends on shared library: libgsl.so - not found
===>   Installing existing package /packages/All/gsl-2.7.1_1.pkg
[133releng-armv7-default-job-08] Installing gsl-2.7.1_1...
[133releng-armv7-default-job-08] Extracting gsl-2.7.1_1: .......... done
===>   gcta-1.94.1_2 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
===>   Returning to build of gcta-1.94.1_2
===>   gcta-1.94.1_2 depends on shared library: libopenblas.so - not found
===>   Installing existing package /packages/All/openblas-0.3.27,2.pkg
[133releng-armv7-default-job-08] Installing openblas-0.3.27,2...
[133releng-armv7-default-job-08] Extracting openblas-0.3.27,2: .......... done
===>   gcta-1.94.1_2 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===>   Returning to build of gcta-1.94.1_2
===>   gcta-1.94.1_2 depends on shared library: libsqlite3.so - not found
===>   Installing existing package /packages/All/sqlite3-3.46.1,1.pkg
[133releng-armv7-default-job-08] Installing sqlite3-3.46.1,1...
[133releng-armv7-default-job-08] `-- Installing libedit-3.1.20240808,1...
[133releng-armv7-default-job-08] `-- Extracting libedit-3.1.20240808,1: .......... done
[133releng-armv7-default-job-08] Extracting sqlite3-3.46.1,1: .......... done
===>   gcta-1.94.1_2 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so)
===>   Returning to build of gcta-1.94.1_2
===>   gcta-1.94.1_2 depends on shared library: libzstd.so - found (/usr/local/lib/libzstd.so)
===========================================================================
=======================<phase: configure      >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  Configuring for gcta-1.94.1_2
===>  Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/gcta/work/.build
CMake Deprecation Warning at CMakeLists.txt:1 (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.


-- The C compiler identification is Clang 17.0.6
-- The CXX compiler identification is Clang 17.0.6
-- 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
FreeBSD, Linux and Mac are supported.
Compiling by Clang17.0.6
-- ARCHITECTURE:arm
-- Configuring done (3.4s)
-- Generating done (0.1s)
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_COLOR_MAKEFILE
    CMAKE_MODULE_LINKER_FLAGS
    CMAKE_SHARED_LINKER_FLAGS
    CMAKE_VERBOSE_MAKEFILE
    FETCHCONTENT_FULLY_DISCONNECTED
    THREADS_HAVE_PTHREAD_ARG


-- Build files have been written to: /wrkdirs/usr/ports/biology/gcta/work/.build
===========================================================================
=======================<phase: build          >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  Building for gcta-1.94.1_2
[  1% 3/67] /usr/bin/c++  -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/grm.dir/src/GRM.cpp.o -MF CMakeFiles/grm.dir/src/GRM.cpp.o.d -o CMakeFiles/grm.dir/src/GRM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/GRM.cpp
FAILED: CMakeFiles/grm.dir/src/GRM.cpp.o 
/usr/bin/c++  -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/grm.dir/src/GRM.cpp.o -MF CMakeFiles/grm.dir/src/GRM.cpp.o.d -o CMakeFiles/grm.dir/src/GRM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/GRM.cpp
/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/GRM.cpp:32:10: fatal error: 'omp.h' file not found
   32 | #include <omp.h>
      |          ^~~~~~~
1 error generated.
[  2% 3/67] /usr/bin/c++  -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/covar.dir/src/Covar.cpp.o -MF CMakeFiles/covar.dir/src/Covar.cpp.o.d -o CMakeFiles/covar.dir/src/Covar.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp
FAILED: CMakeFiles/covar.dir/src/Covar.cpp.o 
/usr/bin/c++  -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/covar.dir/src/Covar.cpp.o -MF CMakeFiles/covar.dir/src/Covar.cpp.o.d -o CMakeFiles/covar.dir/src/Covar.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp
In file included from /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/Covar.cpp:26:
In file included from /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/StatLib.h:19:
In file included from /usr/local/include/eigen3/Eigen/Eigen:1:
In file included from /usr/local/include/eigen3/Eigen/Dense:1:
/usr/local/include/eigen3/Eigen/Core:70:10: fatal error: 'omp.h' file not found
   70 | #include <omp.h>
      |          ^~~~~~~
1 error generated.
[  4% 3/67] /usr/bin/c++  -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -MF CMakeFiles/fastfam.dir/src/FastFAM.cpp.o.d -o CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/FastFAM.cpp
FAILED: CMakeFiles/fastfam.dir/src/FastFAM.cpp.o 
/usr/bin/c++  -I/wrkdirs/usr/ports/biology/gcta/work/.build -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1 -I/usr/local/include/eigen3 -I/usr/local/include/Spectra -I/usr/local/include/boost -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0 -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/submods/plink-ng/2.0/simde -I/wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include  -DNDEBUG -DNDEBUG -std=gnu++14 -fopenmp -MD -MT CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -MF CMakeFiles/fastfam.dir/src/FastFAM.cpp.o.d -o CMakeFiles/fastfam.dir/src/FastFAM.cpp.o -c /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/FastFAM.cpp
In file included from /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/src/FastFAM.cpp:18:
In file included from /wrkdirs/usr/ports/biology/gcta/work/gcta-1.94.1/include/FastFAM.h:27:
In file included from /usr/local/include/eigen3/Eigen/Dense:1:
/usr/local/include/eigen3/Eigen/Core:70:10: fatal error: 'omp.h' file not found
   70 | #include <omp.h>
      |          ^~~~~~~
1 error generated.
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/gcta