[package - 132releng-armv7-quarterly][biology/seqwish] Failed for seqwish-0.7.9 in configure
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Date: Sun, 25 Feb 2024 11:06:43 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere1/data/132releng-armv7-quarterly/941d96c740f7/logs/seqwish-0.7.9.log
Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=132releng-armv7-quarterly&build=941d96c740f7
Log:
=>> Building biology/seqwish
build started at Sun Feb 25 11:06:36 UTC 2024
port directory: /usr/ports/biology/seqwish
package name: seqwish-0.7.9
building for: FreeBSD 132releng-armv7-quarterly-job-07 13.2-RELEASE-p6 FreeBSD 13.2-RELEASE-p6 1302001 arm
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 839 Jan 16 01:02 /usr/ports/biology/seqwish/Makefile
Ports top last git commit: 941d96c74
Ports top unclean checkout: no
Port dir last git commit: 72cbe1a32
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-1-g1e9f97d6
Host OSVERSION: 1500006
Jail OSVERSION: 1302001
Job Id: 07
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1302001
UNAME_v=FreeBSD 13.2-RELEASE-p6 1302001
UNAME_r=13.2-RELEASE-p6
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=3.4.1-1-g1e9f97d6
MASTERMNT=/usr/local/poudriere/data/.m/132releng-armv7-quarterly/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/132releng-armv7-quarterly/07/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=132releng-armv7-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/132releng-armv7-quarterly/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-1-g1e9f97d6
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---
===> The following configuration options are available for seqwish-0.7.9:
OPENMP=on: Parallel processing support via OpenMP
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/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 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp " 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--
CMAKE_BUILD_TYPE="release" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqwish" EXAMPLESDIR="share/examples/seqwish" DATADIR="share/seqwish" WWWDIR="www/seqwish" ETCDIR="etc/seqwish"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqwish DOCSDIR=/usr/local/share/doc/seqwish EXAMPLESDIR=/usr/local/share/examples/seqwish WWWDIR=/usr/local/www/seqwish ETCDIR=/usr/local/etc/seqwish
--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) 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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> seqwish-0.7.9 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9.pkg
[132releng-armv7-quarterly-job-07] Installing pkg-1.20.9...
[132releng-armv7-quarterly-job-07] Extracting pkg-1.20.9: .......... done
===> seqwish-0.7.9 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of seqwish-0.7.9
===========================================================================
=======================<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 MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
=> SHA256 Checksum OK for seqwish-v0.7.9.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 MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
===> Extracting for seqwish-0.7.9
=> SHA256 Checksum OK for seqwish-v0.7.9.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 seqwish-0.7.9
===> Applying FreeBSD patches for seqwish-0.7.9 from /usr/ports/biology/seqwish/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> seqwish-0.7.9 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.28.1.pkg
[132releng-armv7-quarterly-job-07] Installing cmake-core-3.28.1...
[132releng-armv7-quarterly-job-07] `-- Installing expat-2.5.0...
[132releng-armv7-quarterly-job-07] `-- Extracting expat-2.5.0: .......... done
[132releng-armv7-quarterly-job-07] `-- Installing jsoncpp-1.9.5...
[132releng-armv7-quarterly-job-07] `-- Extracting jsoncpp-1.9.5: .......... done
[132releng-armv7-quarterly-job-07] `-- Installing libuv-1.47.0...
[132releng-armv7-quarterly-job-07] `-- Extracting libuv-1.47.0: .......... done
[132releng-armv7-quarterly-job-07] `-- Installing rhash-1.4.4...
[132releng-armv7-quarterly-job-07] | `-- Installing gettext-runtime-0.22.3...
[132releng-armv7-quarterly-job-07] | | `-- Installing indexinfo-0.3.1...
[132releng-armv7-quarterly-job-07] | | `-- Extracting indexinfo-0.3.1: .... done
[132releng-armv7-quarterly-job-07] | `-- Extracting gettext-runtime-0.22.3: .......... done
[132releng-armv7-quarterly-job-07] `-- Extracting rhash-1.4.4: .......... done
[132releng-armv7-quarterly-job-07] Extracting cmake-core-3.28.1: .......... done
===> seqwish-0.7.9 depends on file: /usr/local/bin/cmake - found
===> Returning to build of seqwish-0.7.9
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for seqwish-0.7.9
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/seqwish/work/.build
CMake Deprecation Warning at CMakeLists.txt:3 (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 14.0.5
-- The CXX compiler identification is Clang 14.0.5
-- 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 - failed
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ - broken
CMake Error at /usr/local/share/cmake/Modules/CMakeTestCXXCompiler.cmake:60 (message):
The C++ compiler
"/usr/bin/c++"
is not able to compile a simple test program.
It fails with the following output:
Change Dir: '/wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-3qx9zX'
Run Build Command(s): /usr/local/bin/cmake -E env VERBOSE=1 /usr/bin/make -f Makefile cmTC_de6dd/fast
/usr/bin/make -f CMakeFiles/cmTC_de6dd.dir/build.make CMakeFiles/cmTC_de6dd.dir/build
Building CXX object CMakeFiles/cmTC_de6dd.dir/testCXXCompiler.cxx.o
/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp -MD -MT CMakeFiles/cmTC_de6dd.dir/testCXXCompiler.cxx.o -MF CMakeFiles/cmTC_de6dd.dir/testCXXCompiler.cxx.o.d -o CMakeFiles/cmTC_de6dd.dir/testCXXCompiler.cxx.o -c /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-3qx9zX/testCXXCompiler.cxx
Linking CXX executable cmTC_de6dd
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_de6dd.dir/link.txt --verbose=1
/usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fopenmp CMakeFiles/cmTC_de6dd.dir/testCXXCompiler.cxx.o -o cmTC_de6dd
ld: error: unable to find library -lomp
c++: error: linker command failed with exit code 1 (use -v to see invocation)
*** Error code 1
Stop.
make[2]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-3qx9zX
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-3qx9zX
CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
CMakeLists.txt:6 (project)
-- Configuring incomplete, errors occurred!
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/seqwish