[package - main-armv7-default][biology/gcta] Failed for gcta-1.94.1_2 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Sat, 05 Oct 2024 15:56:52 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/ampere2/data/main-armv7-default/p4a16d2e85dd9_sb7cbf741d/logs/gcta-1.94.1_2.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p4a16d2e85dd9_sb7cbf741d
Log:
=>> Building biology/gcta
build started at Sat Oct 5 15:56:00 UTC 2024
port directory: /usr/ports/biology/gcta
package name: gcta-1.94.1_2
building for: FreeBSD main-armv7-default-job-01 15.0-CURRENT FreeBSD 15.0-CURRENT 1500023 arm
maintained by: jwb@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1581 Jun 22 01:01 /usr/ports/biology/gcta/Makefile
Ports top last git commit: 4a16d2e85dd
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: 1500023
Jail OSVERSION: 1500023
Job Id: 01
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500023
UNAME_v=FreeBSD 15.0-CURRENT 1500023
UNAME_r=15.0-CURRENT
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
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-armv7-default/01/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
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--
EIGEN3_INCLUDE_DIR=/usr/local/include/eigen3 BOOST_INCLUDE_DIR=/usr/local/include/boost OPENBLAS=/usr/local SPECTRA_INCLUDE_DIR=/usr/local/include/Spectra 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--
NINJA_STATUS="[%p %s/%t] " 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 DESTDIR=/wrkdirs/usr/ports/biology/gcta/work/stage 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=" -fopenmp -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict
-aliasing -isystem /usr/local/include " 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--
CMAKE_BUILD_TYPE="release" OSREL=15.0 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---
# 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
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--
ulimit: can't get limit: Invalid argument
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
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-1.94.1_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-armv7-default-job-01] Installing pkg-1.21.3...
[main-armv7-default-job-01] 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
[main-armv7-default-job-01] Installing boost-libs-1.84.0...
[main-armv7-default-job-01] `-- Installing icu-74.2_1,1...
[main-armv7-default-job-01] `-- Extracting icu-74.2_1,1: .......... done
[main-armv7-default-job-01] 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
[main-armv7-default-job-01] Installing spectra-1.0.1_1...
[main-armv7-default-job-01] `-- Installing eigen-3.4.0_3...
[main-armv7-default-job-01] | `-- Installing blas-3.12.0_1...
[main-armv7-default-job-01] | | `-- Installing gcc13-13.3.0...
[main-armv7-default-job-01] | | `-- Installing binutils-2.43,1...
[main-armv7-default-job-01] | | | `-- Installing indexinfo-0.3.1...
[main-armv7-default-job-01] | | | `-- Extracting indexinfo-0.3.1: .... done
[main-armv7-default-job-01] | | | `-- Installing zstd-1.5.6...
[main-armv7-default-job-01] | | | `-- Installing liblz4-1.10.0,1...
[main-armv7-default-job-01] | | | `-- Extracting liblz4-1.10.0,1: .......... done
[main-armv7-default-job-01] | | | `-- Extracting zstd-1.5.6: .......... done
[main-armv7-default-job-01] | | `-- Extracting binutils-2.43,1: .......... done
[main-armv7-default-job-01] | | `-- Installing gmp-6.3.0...
[main-armv7-default-job-01] | | `-- Extracting gmp-6.3.0: .......... done
[main-armv7-default-job-01] | | `-- Installing mpc-1.3.1_1...
[main-armv7-default-job-01] | | | `-- Installing mpfr-4.2.1,1...
[main-armv7-default-job-01] | | | `-- Extracting mpfr-4.2.1,1: .......... done
[main-armv7-default-job-01] | | `-- Extracting mpc-1.3.1_1: ......... done
[main-armv7-default-job-01] | | `-- Extracting gcc13-13.3.0: .......... done
[main-armv7-default-job-01] | `-- Extracting blas-3.12.0_1: ........ done
[main-armv7-default-job-01] | `-- Installing lapack-3.12.0_2...
[main-armv7-default-job-01] | `-- Extracting lapack-3.12.0_2: .......... done
[main-armv7-default-job-01] `-- Extracting eigen-3.4.0_3: .......... done
[main-armv7-default-job-01] Extracting spectra-1.0.1_1: .......... done
=====
Message from gcc13-13.3.0:
--
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/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-3.30.3_1.pkg
[main-armv7-default-job-01] Installing cmake-core-3.30.3_1...
[main-armv7-default-job-01] `-- Installing expat-2.6.3...
[main-armv7-default-job-01] `-- Extracting expat-2.6.3: .......... done
[main-armv7-default-job-01] `-- Installing jsoncpp-1.9.6_1...
[main-armv7-default-job-01] `-- Extracting jsoncpp-1.9.6_1: .......... done
[main-armv7-default-job-01] `-- Installing libuv-1.49.0...
[main-armv7-default-job-01] `-- Extracting libuv-1.49.0: .......... done
[main-armv7-default-job-01] `-- Installing rhash-1.4.4_1...
[main-armv7-default-job-01] | `-- Installing gettext-runtime-0.22.5...
[main-armv7-default-job-01] | `-- Extracting gettext-runtime-0.22.5: .......... done
[main-armv7-default-job-01] `-- Extracting rhash-1.4.4_1: .......... done
[main-armv7-default-job-01] Extracting cmake-core-3.30.3_1: .......... 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
[main-armv7-default-job-01] Installing ninja-1.11.1,4...
[main-armv7-default-job-01] `-- Installing python311-3.11.10...
[main-armv7-default-job-01] | `-- Installing libffi-3.4.6...
[main-armv7-default-job-01] | `-- Extracting libffi-3.4.6: .......... done
[main-armv7-default-job-01] | `-- Installing mpdecimal-4.0.0...
[main-armv7-default-job-01] | `-- Extracting mpdecimal-4.0.0: .......... done
[main-armv7-default-job-01] | `-- Installing readline-8.2.13...
[main-armv7-default-job-01] | `-- Extracting readline-8.2.13: .......... done
[main-armv7-default-job-01] `-- Extracting python311-3.11.10: .......... done
[main-armv7-default-job-01] Extracting ninja-1.11.1,4: ........ done
=====
Message from python311-3.11.10:
--
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
[main-armv7-default-job-01] Installing gsl-2.7.1_1...
[main-armv7-default-job-01] 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
[main-armv7-default-job-01] Installing openblas-0.3.27,2...
[main-armv7-default-job-01] 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
[main-armv7-default-job-01] Installing sqlite3-3.46.1,1...
[main-armv7-default-job-01] `-- Installing libedit-3.1.20240808,1...
[main-armv7-default-job-01] `-- Extracting libedit-3.1.20240808,1: .......... done
[main-armv7-default-job-01] 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 18.1.6
-- The CXX compiler identification is Clang 18.1.6
-- 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 Clang18.1.6
-- ARCHITECTURE:arm
-- Configuring done (1.4s)
-- 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 making "build" in /usr/ports/biology/gcta