[package - 130releng-armv6-quarterly][biology/gcta] Failed for gcta-1.26.0_3 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Mon, 18 Apr 2022 13:34:39 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://beefy8.nyi.freebsd.org/data/130releng-armv6-quarterly/10f9cea52df2/logs/gcta-1.26.0_3.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=130releng-armv6-quarterly&build=10f9cea52df2
Log:
=>> Building biology/gcta
build started at Mon Apr 18 13:34:01 UTC 2022
port directory: /usr/ports/biology/gcta
package name: gcta-1.26.0_3
building for: FreeBSD 130releng-armv6-quarterly-job-11 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 1300139 arm
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-21-g883afb07
Host OSVERSION: 1400050
Jail OSVERSION: 1300139
Job Id: 11
---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1300139
UNAME_v=FreeBSD 13.0-RELEASE-p11 1300139
UNAME_r=13.0-RELEASE-p11
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
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-21-g883afb07
MASTERMNT=/usr/local/poudriere/data/.m/130releng-armv6-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/130releng-armv6-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=130releng-armv6-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/130releng-armv6-quarterly/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 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 NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lopenblas -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -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=13.0 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---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv6
ARCH=${MACHINE_ARCH}
#### /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_9d218390=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-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_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv6
OPSYS=FreeBSD
_OSRELEASE=13.0-RELEASE-p11
OSREL=13.0
OSVERSION=1300139
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
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-1.17.5_1.pkg
[130releng-armv6-quarterly-job-11] Installing pkg-1.17.5_1...
[130releng-armv6-quarterly-job-11] Extracting pkg-1.17.5_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.
===========================================================================
=======================<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-armv6-quarterly-job-11] Installing eigen-3.3.9_1...
[130releng-armv6-quarterly-job-11] `-- Installing blas-3.10.0...
[130releng-armv6-quarterly-job-11] | `-- Installing gcc10-10.3.0...
[130releng-armv6-quarterly-job-11] | | `-- Installing binutils-2.37_2,1...
[130releng-armv6-quarterly-job-11] | | `-- Installing gettext-runtime-0.21...
[130releng-armv6-quarterly-job-11] | | | `-- Installing indexinfo-0.3.1...
[130releng-armv6-quarterly-job-11] | | | `-- Extracting indexinfo-0.3.1: .... done
[130releng-armv6-quarterly-job-11] | | `-- Extracting gettext-runtime-0.21: .......... done
[130releng-armv6-quarterly-job-11] | | `-- Extracting binutils-2.37_2,1: .......... done
[130releng-armv6-quarterly-job-11] | | `-- Installing gmp-6.2.1...
[130releng-armv6-quarterly-job-11] | | `-- Extracting gmp-6.2.1: .......... done
[130releng-armv6-quarterly-job-11] | | `-- Installing mpc-1.2.1...
[130releng-armv6-quarterly-job-11] | | `-- Installing mpfr-4.1.0_1...
[130releng-armv6-quarterly-job-11] | | `-- Extracting mpfr-4.1.0_1: .......... done
[130releng-armv6-quarterly-job-11] | | `-- Extracting mpc-1.2.1: ......... done
[130releng-armv6-quarterly-job-11] | `-- Extracting gcc10-10.3.0: .......... done
[130releng-armv6-quarterly-job-11] `-- Extracting blas-3.10.0: ........ done
[130releng-armv6-quarterly-job-11] `-- Installing lapack-3.10.0_1...
[130releng-armv6-quarterly-job-11] `-- Extracting lapack-3.10.0_1: .......... done
[130releng-armv6-quarterly-job-11] 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-armv6-quarterly-job-11] Installing gmake-4.3_2...
[130releng-armv6-quarterly-job-11] 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
[130releng-armv6-quarterly-job-11] Installing openblas-0.3.20,1...
[130releng-armv6-quarterly-job-11] Extracting openblas-0.3.20,1: .......... 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