[package - 131releng-armv7-quarterly][biology/gcta] Failed for gcta-1.26.0_3 in build
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Date: Tue, 09 May 2023 19:55:57 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/ampere1/data/131releng-armv7-quarterly/9d8ed9a40e2a/logs/gcta-1.26.0_3.log
Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=131releng-armv7-quarterly&build=9d8ed9a40e2a
Log:
=>> Building biology/gcta
build started at Tue May 9 19:55:33 UTC 2023
port directory: /usr/ports/biology/gcta
package name: gcta-1.26.0_3
building for: FreeBSD 131releng-armv7-quarterly-job-04 13.1-RELEASE-p7 FreeBSD 13.1-RELEASE-p7 1301000 arm
maintained by: jwb@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> gcta-1.26.0_3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[131releng-armv7-quarterly-job-04] Installing pkg-1.19.1_1...
[131releng-armv7-quarterly-job-04] Extracting pkg-1.19.1_1: .......... done
===> gcta-1.26.0_3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gcta-1.26.0_3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_3 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_3 for building
=> SHA256 Checksum OK for gcta_1.26.0_src.zip.
=> SHA256 Checksum OK for eigen-3.3.9.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by gcta-1.26.0_3 for building
===> Extracting for gcta-1.26.0_3
=> SHA256 Checksum OK for gcta_1.26.0_src.zip.
=> SHA256 Checksum OK for eigen-3.3.9.tar.gz.
Archive: /portdistfiles/gcta_1.26.0_src.zip
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/bivar_reml.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/cdflib.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/CommFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/CommFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/Copyright.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/data.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/dcdflib.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/dcdflib.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/edata.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/eigen_func.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/eigen_func.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ejma.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/est_hsq.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gbat.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gcta.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/GNU_General_Public_License_v3.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/grm.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/gwas_simu.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/HowToCompile.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ipmpar.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/joint_meta.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/ld.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/Makefile
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/mkl.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/mlm_assoc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/option.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/popu_genet.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/raw_geno.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/read_imput.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/README.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/reml_within_family.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/sbat.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StatFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StatFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StrFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/StrFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/UnusedCode.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/zfstream.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0/zfstream.h
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for gcta-1.26.0_3
===> Converting DOS text files to UNIX text files
===> Applying FreeBSD patches for gcta-1.26.0_3 from /usr/ports/biology/gcta/files
===========================================================================
=======================<phase: build-depends >============================
===> gcta-1.26.0_3 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[131releng-armv7-quarterly-job-04] Installing gmake-4.3_2...
[131releng-armv7-quarterly-job-04] `-- Installing gettext-runtime-0.21.1...
[131releng-armv7-quarterly-job-04] | `-- Installing indexinfo-0.3.1...
[131releng-armv7-quarterly-job-04] | `-- Extracting indexinfo-0.3.1: .... done
[131releng-armv7-quarterly-job-04] `-- Extracting gettext-runtime-0.21.1: .......... done
[131releng-armv7-quarterly-job-04] Extracting gmake-4.3_2: .......... done
===> gcta-1.26.0_3 depends on package: gmake>=4.3 - found
===> Returning to build of gcta-1.26.0_3
===========================================================================
=======================<phase: lib-depends >============================
===> gcta-1.26.0_3 depends on shared library: libopenblas.so - not found
===> Installing existing package /packages/All/openblas-0.3.20,1.pkg
[131releng-armv7-quarterly-job-04] Installing openblas-0.3.20,1...
[131releng-armv7-quarterly-job-04] `-- Installing gcc12-12.2.0_5...
[131releng-armv7-quarterly-job-04] | `-- Installing binutils-2.40_3,1...
[131releng-armv7-quarterly-job-04] | | `-- Installing zstd-1.5.4...
[131releng-armv7-quarterly-job-04] | | `-- Installing liblz4-1.9.4,1...
[131releng-armv7-quarterly-job-04] | | `-- Extracting liblz4-1.9.4,1: .......... done
[131releng-armv7-quarterly-job-04] | | `-- Extracting zstd-1.5.4: .......... done
[131releng-armv7-quarterly-job-04] | `-- Extracting binutils-2.40_3,1: .......... done
[131releng-armv7-quarterly-job-04] | `-- Installing gmp-6.2.1...
[131releng-armv7-quarterly-job-04] | `-- Extracting gmp-6.2.1: .......... done
[131releng-armv7-quarterly-job-04] | `-- Installing mpc-1.2.1...
[131releng-armv7-quarterly-job-04] | | `-- Installing mpfr-4.2.0,1...
[131releng-armv7-quarterly-job-04] | | `-- Extracting mpfr-4.2.0,1: .......... done
[131releng-armv7-quarterly-job-04] | `-- Extracting mpc-1.2.1: ......... done
[131releng-armv7-quarterly-job-04] `-- Extracting gcc12-12.2.0_5: .......... done
[131releng-armv7-quarterly-job-04] Extracting openblas-0.3.20,1: .......... done
=====
Message from gcc12-12.2.0_5:
--
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/gcc12
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> gcta-1.26.0_3 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===> Returning to build of gcta-1.26.0_3
===========================================================================
=======================<phase: configure >============================
===> Configuring for gcta-1.26.0_3
===========================================================================
=======================<phase: build >============================
===> Building for gcta-1.26.0_3
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0'
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c bivar_reml.cpp
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c CommFunc.cpp
In file included from bivar_reml.cpp:13:
In file included from ./gcta.h:26:
In file included from ./StatFunc.h:19:
In file included from /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Dense:1:
/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Core:266:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isystem /usr/local/include -c eigen_func.cpp
1 error generated.
gmake[1]: *** [Makefile:72: bivar_reml.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
In file included from eigen_func.cpp:11:
In file included from ./eigen_func.h:20:
In file included from ./StatFunc.h:19:
In file included from /wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Dense:1:
/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9/Eigen/Core:266:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
gmake[1]: *** [Makefile:72: eigen_func.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gcta/work/gcta-1.26.0'
===> 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