[package - 140releng-armv7-default][biology/seqwish] Failed for seqwish-0.7.10 in configure

From: <pkg-fallout_at_FreeBSD.org>
Date: Mon, 26 Aug 2024 15:30:07 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/ampere3/data/140releng-armv7-default/60a177caf143/logs/seqwish-0.7.10.log
Build URL:      https://pkg-status.freebsd.org/ampere3/build.html?mastername=140releng-armv7-default&build=60a177caf143
Log:

=>> Building biology/seqwish
build started at Mon Aug 26 15:30:01 UTC 2024
port directory: /usr/ports/biology/seqwish
package name: seqwish-0.7.10
building for: FreeBSD 140releng-armv7-default-job-01 14.0-RELEASE-p9 FreeBSD 14.0-RELEASE-p9 1400097 arm
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 840 May 21 01:01 /usr/ports/biology/seqwish/Makefile
Ports top last git commit: 60a177caf14
Ports top unclean checkout: no
Port dir last git commit: 04eb409d363
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1-30-g79e3edcd
Host OSVERSION: 1500019
Jail OSVERSION: 1400097
Job Id: 01

---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400097
UNAME_v=FreeBSD 14.0-RELEASE-p9 1400097
UNAME_r=14.0-RELEASE-p9
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=3.4.1-30-g79e3edcd
MASTERMNT=/usr/local/poudriere/data/.m/140releng-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/140releng-armv7-default/01/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=140releng-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/140releng-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.1-30-g79e3edcd
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-0.7.10:
     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 " 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=14.0 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---
# 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--
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-0.7.10 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.21.3.pkg
[140releng-armv7-default-job-01] Installing pkg-1.21.3...
[140releng-armv7-default-job-01] Extracting pkg-1.21.3: .......... done
===>   seqwish-0.7.10 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of seqwish-0.7.10
===========================================================================
=======================<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-0.7.10 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-0.7.10 for building
=> SHA256 Checksum OK for seqwish-v0.7.10.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-0.7.10 for building
===>  Extracting for seqwish-0.7.10
=> SHA256 Checksum OK for seqwish-v0.7.10.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-0.7.10
===>  Applying FreeBSD patches for seqwish-0.7.10 from /usr/ports/biology/seqwish/files
===========================================================================
=======================<phase: build-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   seqwish-0.7.10 depends on file: /usr/local/bin/cmake - not found
===>   Installing existing package /packages/All/cmake-core-3.30.2.pkg
[140releng-armv7-default-job-01] Installing cmake-core-3.30.2...
[140releng-armv7-default-job-01] `-- Installing expat-2.6.2...
[140releng-armv7-default-job-01] `-- Extracting expat-2.6.2: .......... done
[140releng-armv7-default-job-01] `-- Installing jsoncpp-1.9.5...
[140releng-armv7-default-job-01] `-- Extracting jsoncpp-1.9.5: .......... done
[140releng-armv7-default-job-01] `-- Installing libuv-1.48.0...
[140releng-armv7-default-job-01] `-- Extracting libuv-1.48.0: .......... done
[140releng-armv7-default-job-01] `-- Installing rhash-1.4.4_1...
[140releng-armv7-default-job-01] |   `-- Installing gettext-runtime-0.22.5...
[140releng-armv7-default-job-01] |   | `-- Installing indexinfo-0.3.1...
[140releng-armv7-default-job-01] |   | `-- Extracting indexinfo-0.3.1: .... done
[140releng-armv7-default-job-01] |   `-- Extracting gettext-runtime-0.22.5: .......... done
[140releng-armv7-default-job-01] `-- Extracting rhash-1.4.4_1: .......... done
[140releng-armv7-default-job-01] Extracting cmake-core-3.30.2: .......... done
===>   seqwish-0.7.10 depends on file: /usr/local/bin/cmake - found
===>   Returning to build of seqwish-0.7.10
===========================================================================
=======================<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-0.7.10
===>  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 16.0.6
-- The CXX compiler identification is Clang 16.0.6
-- 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 - 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:73 (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-5zZ1xE'
    
    Run Build Command(s): /usr/local/bin/cmake -E env VERBOSE=1 /usr/bin/make -f Makefile cmTC_8a798/fast
    /usr/bin/make  -f CMakeFiles/cmTC_8a798.dir/build.make CMakeFiles/cmTC_8a798.dir/build
    Building CXX object CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o
    /usr/bin/c++   -O2 -pipe -fstack-protector-strong -fno-strict-aliasing  -fopenmp -MD -MT CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o -MF CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o.d -o CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o -c /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-5zZ1xE/testCXXCompiler.cxx
    Linking CXX executable cmTC_8a798
    /usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_8a798.dir/link.txt --verbose=1
    /usr/bin/c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing  -fopenmp  CMakeFiles/cmTC_8a798.dir/testCXXCompiler.cxx.o -o cmTC_8a798
    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[1]: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-5zZ1xE
    *** Error code 1
    
    Stop.
    make: stopped in /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/CMakeScratch/TryCompile-5zZ1xE
    
    

  

  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