[package - main-armv7-default][biology/fastani] Failed for fastani-1.34 in build
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Date: Thu, 24 Oct 2024 05:51:49 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/ampere2/data/main-armv7-default/p94c4ac6b071b_sc87b3f0006/logs/fastani-1.34.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p94c4ac6b071b_sc87b3f0006
Log:
=>> Building biology/fastani
build started at Thu Oct 24 05:51:36 UTC 2024
port directory: /usr/ports/biology/fastani
package name: fastani-1.34
building for: FreeBSD main-armv7-default-job-06 15.0-CURRENT FreeBSD 15.0-CURRENT 1500025 arm
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 597 Sep 28 01:02 /usr/ports/biology/fastani/Makefile
Ports top last git commit: 94c4ac6b071
Ports top unclean checkout: no
Port dir last git commit: 89f62deb8a9
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1500025
Job Id: 06
!!! Jail is newer than host. (Jail: 1500025, Host: 1500023) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500025
UNAME_v=FreeBSD 15.0-CURRENT 1500025
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/06/.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--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastani/work/.cache HOME=/wrkdirs/usr/ports/biology/fastani/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastani/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastani/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--
NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastani/work/.cache HOME=/wrkdirs/usr/ports/biology/fastani/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastani/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastani/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/fastani/work/stage 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 " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0
644" 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/fastani" EXAMPLESDIR="share/examples/fastani" DATADIR="share/fastani" WWWDIR="www/fastani" ETCDIR="etc/fastani"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fastani DOCSDIR=/usr/local/share/doc/fastani EXAMPLESDIR=/usr/local/share/examples/fastani WWWDIR=/usr/local/www/fastani ETCDIR=/usr/local/etc/fastani
--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 APACHE20 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> fastani-1.34 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-armv7-default-job-06] Installing pkg-1.21.3...
[main-armv7-default-job-06] Extracting pkg-1.21.3: .......... done
===> fastani-1.34 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of fastani-1.34
===========================================================================
=======================<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 APACHE20 accepted by the user
===> Fetching all distfiles required by fastani-1.34 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License APACHE20 accepted by the user
===> Fetching all distfiles required by fastani-1.34 for building
=> SHA256 Checksum OK for ParBLiSS-FastANI-v1.34_GH0.tar.gz.
=> SHA256 Checksum OK for catchorg-Catch2-359542d_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 APACHE20 accepted by the user
===> Fetching all distfiles required by fastani-1.34 for building
===> Extracting for fastani-1.34
=> SHA256 Checksum OK for ParBLiSS-FastANI-v1.34_GH0.tar.gz.
=> SHA256 Checksum OK for catchorg-Catch2-359542d_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 fastani-1.34
===> Applying FreeBSD patches for fastani-1.34 from /usr/ports/biology/fastani/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> fastani-1.34 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.30.5.pkg
[main-armv7-default-job-06] Installing cmake-core-3.30.5...
[main-armv7-default-job-06] `-- Installing expat-2.6.3...
[main-armv7-default-job-06] `-- Extracting expat-2.6.3: .......... done
[main-armv7-default-job-06] `-- Installing jsoncpp-1.9.6_1...
[main-armv7-default-job-06] `-- Extracting jsoncpp-1.9.6_1: .......... done
[main-armv7-default-job-06] `-- Installing libuv-1.49.1...
[main-armv7-default-job-06] `-- Extracting libuv-1.49.1: .......... done
[main-armv7-default-job-06] `-- Installing rhash-1.4.4_1...
[main-armv7-default-job-06] | `-- Installing gettext-runtime-0.22.5...
[main-armv7-default-job-06] | | `-- Installing indexinfo-0.3.1...
[main-armv7-default-job-06] | | `-- Extracting indexinfo-0.3.1: .... done
[main-armv7-default-job-06] | `-- Extracting gettext-runtime-0.22.5: .......... done
[main-armv7-default-job-06] `-- Extracting rhash-1.4.4_1: .......... done
[main-armv7-default-job-06] Extracting cmake-core-3.30.5: .......... done
===> fastani-1.34 depends on file: /usr/local/bin/cmake - found
===> Returning to build of fastani-1.34
===> fastani-1.34 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.11.1,4.pkg
[main-armv7-default-job-06] Installing ninja-1.11.1,4...
[main-armv7-default-job-06] `-- Installing python311-3.11.10...
[main-armv7-default-job-06] | `-- Installing libffi-3.4.6...
[main-armv7-default-job-06] | `-- Extracting libffi-3.4.6: .......... done
[main-armv7-default-job-06] | `-- Installing mpdecimal-4.0.0...
[main-armv7-default-job-06] | `-- Extracting mpdecimal-4.0.0: .......... done
[main-armv7-default-job-06] | `-- Installing readline-8.2.13_2...
[main-armv7-default-job-06] | `-- Extracting readline-8.2.13_2: .......... done
[main-armv7-default-job-06] `-- Extracting python311-3.11.10: .......... done
[main-armv7-default-job-06] 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
===> fastani-1.34 depends on executable: ninja - found
===> Returning to build of fastani-1.34
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> fastani-1.34 depends on shared library: libgsl.so - not found
===> Installing existing package /packages/All/gsl-2.7.1_1.pkg
[main-armv7-default-job-06] Installing gsl-2.7.1_1...
[main-armv7-default-job-06] Extracting gsl-2.7.1_1: .......... done
===> fastani-1.34 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
===> Returning to build of fastani-1.34
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for fastani-1.34
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/fastani/work/.build
-- The CXX compiler identification is Clang 18.1.6
-- 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
-- Found ZLIB: /usr/lib/libz.so (found suitable version "1.3.1", minimum required is "1.1")
Using zlib library v1.3.1
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND)
NOTE: OpenMP not found; Compiling as a single threaded app...
-- Found GSL: /usr/local/include (found suitable version "2.7.1", minimum required is "1.6")
GSL v2.7.1 Found:
-- Configuring done (1.5s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_COLOR_MAKEFILE
CMAKE_C_COMPILER
CMAKE_C_FLAGS
CMAKE_C_FLAGS_DEBUG
CMAKE_C_FLAGS_RELEASE
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/fastani/work/.build
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for fastani-1.34
[ 33% 2/3] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/main.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/main.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/main.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/main.cpp
[ 66% 2/3] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp
FAILED: CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o
/usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp
/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp:11:10: fatal error: 'omp.h' file not found
11 | #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/fastani