[package - 130releng-armv7-quarterly][biology/gcta] Failed for gcta-1.26.0_3 in build
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Date: Mon, 03 Jan 2022 15:33:18 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: http://beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/725c54a5a087/logs/gcta-1.26.0_3.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=725c54a5a087
Log:
=>> Building biology/gcta
build started at Mon Jan 3 15:32:47 UTC 2022
port directory: /usr/ports/biology/gcta
package name: gcta-1.26.0_3
building for: FreeBSD 130releng-armv7-quarterly-job-02 13.0-RELEASE-p5 FreeBSD 13.0-RELEASE-p5 1300139 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-1.17.5.pkg
[130releng-armv7-quarterly-job-02] Installing pkg-1.17.5...
[130releng-armv7-quarterly-job-02] Extracting pkg-1.17.5: .......... 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.
===========================================================================
=======================<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.
/usr/bin/unzip -d /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src /portdistfiles/gcta_1.26.0_src.zip
Archive: /portdistfiles/gcta_1.26.0_src.zip
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/bivar_reml.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/cdflib.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/CommFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/CommFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/Copyright.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/data.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/dcdflib.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/dcdflib.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/edata.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/eigen_func.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/eigen_func.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/ejma.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/est_hsq.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/gbat.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/gcta.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/GNU_General_Public_License_v3.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/grm.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/gwas_simu.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/HowToCompile.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/ipmpar.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/joint_meta.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/ld.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/Makefile
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/mkl.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/mlm_assoc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/option.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/popu_genet.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/raw_geno.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/read_imput.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/README.txt
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/reml_within_family.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/sbat.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/StatFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/StatFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/StrFunc.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/StrFunc.h
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/UnusedCode.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/zfstream.cpp
extracting: /wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src/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 file: /usr/local/libdata/pkgconfig/eigen3.pc - not found
===> Installing existing package /packages/All/eigen-3.3.9_1.pkg
[130releng-armv7-quarterly-job-02] Installing eigen-3.3.9_1...
[130releng-armv7-quarterly-job-02] `-- Installing blas-3.10.0...
[130releng-armv7-quarterly-job-02] | `-- Installing gcc10-10.3.0...
[130releng-armv7-quarterly-job-02] | | `-- Installing binutils-2.37_2,1...
[130releng-armv7-quarterly-job-02] | | `-- Installing gettext-runtime-0.21...
[130releng-armv7-quarterly-job-02] | | | `-- Installing indexinfo-0.3.1...
[130releng-armv7-quarterly-job-02] | | | `-- Extracting indexinfo-0.3.1: .... done
[130releng-armv7-quarterly-job-02] | | `-- Extracting gettext-runtime-0.21: .......... done
[130releng-armv7-quarterly-job-02] | | `-- Extracting binutils-2.37_2,1: .......... done
[130releng-armv7-quarterly-job-02] | | `-- Installing gmp-6.2.1...
[130releng-armv7-quarterly-job-02] | | `-- Extracting gmp-6.2.1: .......... done
[130releng-armv7-quarterly-job-02] | | `-- Installing mpc-1.2.1...
[130releng-armv7-quarterly-job-02] | | `-- Installing mpfr-4.1.0_1...
[130releng-armv7-quarterly-job-02] | | `-- Extracting mpfr-4.1.0_1: .......... done
[130releng-armv7-quarterly-job-02] | | `-- Extracting mpc-1.2.1: ......... done
[130releng-armv7-quarterly-job-02] | `-- Extracting gcc10-10.3.0: .......... done
[130releng-armv7-quarterly-job-02] `-- Extracting blas-3.10.0: ........ done
[130releng-armv7-quarterly-job-02] `-- Installing lapack-3.10.0_1...
[130releng-armv7-quarterly-job-02] `-- Extracting lapack-3.10.0_1: .......... done
[130releng-armv7-quarterly-job-02] Extracting eigen-3.3.9_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.
===> gcta-1.26.0_3 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found
===> Returning to build of gcta-1.26.0_3
===> gcta-1.26.0_3 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[130releng-armv7-quarterly-job-02] Installing gmake-4.3_2...
[130releng-armv7-quarterly-job-02] 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-0.3.16,1.pkg
[130releng-armv7-quarterly-job-02] Installing openblas-0.3.16,1...
[130releng-armv7-quarterly-job-02] Extracting openblas-0.3.16,1: .......... done
===> 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_src'
/nxb-bin/usr/bin/c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -fopenmp -isystem /usr/local/include -c bivar_reml.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 /usr/local/include/eigen3/Eigen/Dense:1:
/usr/local/include/eigen3/Eigen/Core:266:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
gmake[1]: *** [Makefile:72: bivar_reml.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gcta/work/gcta_1.26.0_src'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/gcta