[package - 140releng-armv7-quarterly][biology/gcta] Failed for gcta-1.26.0_4 in build
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Date: Sun, 03 Dec 2023 16:09:02 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/140releng-armv7-quarterly/1121637d9005/logs/gcta-1.26.0_4.log
Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=140releng-armv7-quarterly&build=1121637d9005
Log:
=>> Building biology/gcta
build started at Sun Dec 3 16:08:43 UTC 2023
port directory: /usr/ports/biology/gcta
package name: gcta-1.26.0_4
building for: FreeBSD 140releng-armv7-quarterly-job-09 14.0-RELEASE FreeBSD 14.0-RELEASE 1400097 arm
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 977 Oct 5 01:01 /usr/ports/biology/gcta/Makefile
Ports top last git commit: 1121637d9
Ports top unclean checkout: no
Port dir last git commit: 46c5200e9
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.3.0-1258-gbc38e2e6
Host OSVERSION: 1500000
Jail OSVERSION: 1400097
Job Id: 09
---Begin Environment---
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SAVED_TERM=
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POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gcta/work/.cache HOME=/wrkdirs/usr/ports/biology/gcta/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gcta/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gcta/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"
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gcta/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gcta/work/.cache HOME=/wrkdirs/usr/ports/biology/gcta/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gcta/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gcta/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lopenblas -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/wrkdirs/usr/ports/biology/gcta/work/eigen-3.3.9 -fopenmp -isys
tem /usr/local/include " MANPREFIX="/usr/local" 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--
OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gcta" EXAMPLESDIR="share/examples/gcta" DATADIR="share/gcta" WWWDIR="www/gcta" ETCDIR="etc/gcta"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gcta DOCSDIR=/usr/local/share/doc/gcta EXAMPLESDIR=/usr/local/share/examples/gcta WWWDIR=/usr/local/www/gcta ETCDIR=/usr/local/etc/gcta
--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*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 1048576
stack size (kbytes, -s) 1048576
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<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-1.26.0_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.8.pkg
[140releng-armv7-quarterly-job-09] Installing pkg-1.20.8...
[140releng-armv7-quarterly-job-09] Extracting pkg-1.20.8: .......... done
===> gcta-1.26.0_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<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-1.26.0_4 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-1.26.0_4 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>============================
===== 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-1.26.0_4 for building
===> Extracting for gcta-1.26.0_4
=> 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 >============================
===== 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-1.26.0_4
===> Converting DOS text files to UNIX text files
===> Applying FreeBSD patches for gcta-1.26.0_4 from /usr/ports/biology/gcta/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gcta-1.26.0_4 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[140releng-armv7-quarterly-job-09] Installing gmake-4.3_2...
[140releng-armv7-quarterly-job-09] `-- Installing gettext-runtime-0.22_1...
[140releng-armv7-quarterly-job-09] | `-- Installing indexinfo-0.3.1...
[140releng-armv7-quarterly-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[140releng-armv7-quarterly-job-09] `-- Extracting gettext-runtime-0.22_1: .......... done
[140releng-armv7-quarterly-job-09] Extracting gmake-4.3_2: .......... done
===> gcta-1.26.0_4 depends on package: gmake>=4.3 - found
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gcta-1.26.0_4 depends on shared library: libopenblas.so - not found
===> Installing existing package /packages/All/openblas-0.3.20,2.pkg
[140releng-armv7-quarterly-job-09] Installing openblas-0.3.20,2...
[140releng-armv7-quarterly-job-09] `-- Installing gcc12-12.2.0_6...
[140releng-armv7-quarterly-job-09] | `-- Installing binutils-2.40_4,1...
[140releng-armv7-quarterly-job-09] | | `-- Installing zstd-1.5.5...
[140releng-armv7-quarterly-job-09] | | `-- Installing liblz4-1.9.4,1...
[140releng-armv7-quarterly-job-09] | | `-- Extracting liblz4-1.9.4,1: .......... done
[140releng-armv7-quarterly-job-09] | | `-- Extracting zstd-1.5.5: .......... done
[140releng-armv7-quarterly-job-09] | `-- Extracting binutils-2.40_4,1: .......... done
[140releng-armv7-quarterly-job-09] | `-- Installing gmp-6.3.0...
[140releng-armv7-quarterly-job-09] | `-- Extracting gmp-6.3.0: .......... done
[140releng-armv7-quarterly-job-09] | `-- Installing mpc-1.3.1_1...
[140releng-armv7-quarterly-job-09] | | `-- Installing mpfr-4.2.1,1...
[140releng-armv7-quarterly-job-09] | | `-- Extracting mpfr-4.2.1,1: .......... done
[140releng-armv7-quarterly-job-09] | `-- Extracting mpc-1.3.1_1: ......... done
[140releng-armv7-quarterly-job-09] `-- Extracting gcc12-12.2.0_6: .......... done
[140releng-armv7-quarterly-job-09] Extracting openblas-0.3.20,2: .......... done
=====
Message from gcc12-12.2.0_6:
--
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_4 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so)
===> Returning to build of gcta-1.26.0_4
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for gcta-1.26.0_4
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for gcta-1.26.0_4
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
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
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>
^~~~~~~
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 data.cpp
1 error generated.
gmake[1]: *** [Makefile:72: eigen_func.o] Error 1
gmake[1]: *** Waiting for unfinished jobs....
1 error generated.
gmake[1]: *** [Makefile:72: bivar_reml.o] Error 1
In file included from data.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>
^~~~~~~
1 error generated.
gmake[1]: *** [Makefile:72: data.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