[package - 131releng-armv7-default][biology/gcta] Failed for gcta-1.26.0_3 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Fri, 11 Nov 2022 16:12:23 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://ampere3.nyi.freebsd.org/data/131releng-armv7-default/0f24e88b3aa7/logs/gcta-1.26.0_3.log
Build URL:      http://ampere3.nyi.freebsd.org/build.html?mastername=131releng-armv7-default&build=0f24e88b3aa7
Log:

=>> Building biology/gcta
build started at Fri Nov 11 16:11:59 UTC 2022
port directory: /usr/ports/biology/gcta
package name: gcta-1.26.0_3
building for: FreeBSD 131releng-armv7-default-job-07 13.1-RELEASE-p3 FreeBSD 13.1-RELEASE-p3 1301000 arm
maintained by: jwb@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400063
Jail OSVERSION: 1301000
Job Id: 07

---Begin Environment---
SHELL=/bin/csh
OSVERSION=1301000
UNAME_v=FreeBSD 13.1-RELEASE-p3 1301000
UNAME_r=13.1-RELEASE-p3
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-21-g883afb07
MASTERMNT=/usr/local/poudriere/data/.m/131releng-armv7-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=131releng-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---

---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
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 -isystem /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=13.1 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
#### /usr/local/etc/poudriere.d/make.conf ####
# 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 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_53255a77=yes
CC_OUTPUT_921dbbb2_911cfe02=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=armv7
OPSYS=FreeBSD
_OSRELEASE=13.1-RELEASE-p3
OSREL=13.1
OSVERSION=1301000
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
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)  1024
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   >============================
===>  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-1.18.4.pkg
[131releng-armv7-default-job-07] Installing pkg-1.18.4...
[131releng-armv7-default-job-07] Extracting pkg-1.18.4: .......... 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-default-job-07] Installing gmake-4.3_2...
[131releng-armv7-default-job-07] `-- Installing gettext-runtime-0.21...
[131releng-armv7-default-job-07] |   `-- Installing indexinfo-0.3.1...
[131releng-armv7-default-job-07] |   `-- Extracting indexinfo-0.3.1: .... done
[131releng-armv7-default-job-07] `-- Extracting gettext-runtime-0.21: .......... done
[131releng-armv7-default-job-07] 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-default-job-07] Installing openblas-0.3.20,1...
[131releng-armv7-default-job-07] `-- Installing gcc11-11.3.0_2...
[131releng-armv7-default-job-07] |   `-- Installing binutils-2.37_4,1...
[131releng-armv7-default-job-07] |   `-- Extracting binutils-2.37_4,1: .......... done
[131releng-armv7-default-job-07] |   `-- Installing gmp-6.2.1...
[131releng-armv7-default-job-07] |   `-- Extracting gmp-6.2.1: .......... done
[131releng-armv7-default-job-07] |   `-- Installing mpc-1.2.1...
[131releng-armv7-default-job-07] |   | `-- Installing mpfr-4.1.0_1...
[131releng-armv7-default-job-07] |   | `-- Extracting mpfr-4.1.0_1: .......... done
[131releng-armv7-default-job-07] |   `-- Extracting mpc-1.2.1: ......... done
[131releng-armv7-default-job-07] `-- Extracting gcc11-11.3.0_2: .......... done
[131releng-armv7-default-job-07] Extracting openblas-0.3.20,1: .......... done
=====
Message from gcc11-11.3.0_2:

--
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/gcc11

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