[package - 124amd64-quarterly][science/code_saturne] Failed for code_saturne-8.0.0 in configure
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Date: Tue, 21 Nov 2023 02:34:58 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: thierry@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy2/data/124amd64-quarterly/d479b4559172/logs/code_saturne-8.0.0.log
Build URL: https://pkg-status.freebsd.org/beefy2/build.html?mastername=124amd64-quarterly&build=d479b4559172
Log:
=>> Building science/code_saturne
build started at Tue Nov 21 02:31:28 UTC 2023
port directory: /usr/ports/science/code_saturne
package name: code_saturne-8.0.0
building for: FreeBSD 124amd64-quarterly-job-09 12.4-RELEASE-p7 FreeBSD 12.4-RELEASE-p7 amd64
maintained by: thierry@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 3701 Oct 3 01:01 /usr/ports/science/code_saturne/Makefile
Ports top last git commit: d479b4559
Ports top unclean checkout: no
Port dir last git commit: 2195304f9
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.3.0-1258-gbc38e2e6
Host OSVERSION: 1500000
Jail OSVERSION: 1204000
Job Id: 09
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PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for code_saturne-8.0.0:
DOCS=on: Build and/or install documentation
====> Support of METIS: you can only select none or one of them
METIS=on: Support of METIS
PARMETIS=off: Support of ParMETIS
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
thierry@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--without-salome --without-salome-yacs --without-salome-kernel --without-salome-gui --enable-python --with-blas=yes --with-blas-type=BLAS --with-blas-include=/usr/local/include/cblas --with-blas-lib=/usr/local/lib --with-hypre="/usr/local" --with-mpi --with-mumps="/usr/local" --with-petsc="/usr/local" --with-scotch-include="/usr/local/include" --with-metis-include="/usr/local/include" --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
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c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" DEFAULT_AUTOCONF=2.71 CMAKE_PREFIX_PATH="/usr/local" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
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al/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" DEFAULT_AUTOCONF=2.71 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -D__XSI_VISIBLE -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-I/usr/local/include -I/usr/local/include/libxml2 -DLIBICONV_PLUG -isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -B/usr/local/bin -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -D__XSI_VISIBLE -Wno-error=incompatible-function-pointer-types -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -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"
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al RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/code_saturne" EXAMPLESDIR="share/examples/code_saturne" DATADIR="share/code_saturne" WWWDIR="www/code_saturne" ETCDIR="etc/code_saturne"
--End PLIST_SUB--
--SUB_LIST--
DOCS="" NO_DOCS="@comment " METIS="" NO_METIS="@comment " PARMETIS="@comment " NO_PARMETIS="" PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/code_saturne DOCSDIR=/usr/local/share/doc/code_saturne EXAMPLESDIR=/usr/local/share/examples/code_saturne WWWDIR=/usr/local/www/code_saturne ETCDIR=/usr/local/etc/code_saturne
--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) 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) 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 GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> code_saturne-8.0.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.8.pkg
[124amd64-quarterly-job-09] Installing pkg-1.20.8...
[124amd64-quarterly-job-09] Extracting pkg-1.20.8: .......... done
===> code_saturne-8.0.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of code_saturne-8.0.0
===========================================================================
=======================<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 GPLv2 accepted by the user
===> Fetching all distfiles required by code_saturne-8.0.0 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by code_saturne-8.0.0 for building
=> SHA256 Checksum OK for code_saturne-8.0.0.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 GPLv2 accepted by the user
===> Fetching all distfiles required by code_saturne-8.0.0 for building
===> Extracting for code_saturne-8.0.0
=> SHA256 Checksum OK for code_saturne-8.0.0.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 code_saturne-8.0.0
===> Applying FreeBSD patches for code_saturne-8.0.0 from /usr/ports/science/code_saturne/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> code_saturne-8.0.0 depends on package: py39-mpi4py>0 - not found
===> Installing existing package /packages/All/py39-mpi4py-3.1.4_2.pkg
[124amd64-quarterly-job-09] Installing py39-mpi4py-3.1.4_2...
[124amd64-quarterly-job-09] `-- Installing openmpi-4.1.5_1...
[124amd64-quarterly-job-09] | `-- Installing gcc12-12.2.0_6...
[124amd64-quarterly-job-09] | | `-- Installing binutils-2.40_4,1...
[124amd64-quarterly-job-09] | | `-- Installing gettext-runtime-0.22_1...
[124amd64-quarterly-job-09] | | | `-- Installing indexinfo-0.3.1...
[124amd64-quarterly-job-09] | | | `-- Extracting indexinfo-0.3.1: .... done
[124amd64-quarterly-job-09] | | `-- Extracting gettext-runtime-0.22_1: .......... done
[124amd64-quarterly-job-09] | | `-- Installing zstd-1.5.5...
[124amd64-quarterly-job-09] | | | `-- Installing liblz4-1.9.4,1...
[124amd64-quarterly-job-09] | | | `-- Extracting liblz4-1.9.4,1: .......... done
[124amd64-quarterly-job-09] | | `-- Extracting zstd-1.5.5: .......... done
[124amd64-quarterly-job-09] | | `-- Extracting binutils-2.40_4,1: .......... done
[124amd64-quarterly-job-09] | | `-- Installing gmp-6.3.0...
[124amd64-quarterly-job-09] | | `-- Extracting gmp-6.3.0: .......... done
[124amd64-quarterly-job-09] | | `-- Installing mpc-1.3.1_1...
[124amd64-quarterly-job-09] | | `-- Installing mpfr-4.2.1,1...
[124amd64-quarterly-job-09] | | `-- Extracting mpfr-4.2.1,1: .......... done
[124amd64-quarterly-job-09] | | `-- Extracting mpc-1.3.1_1: ......... done
[124amd64-quarterly-job-09] | `-- Extracting gcc12-12.2.0_6: .......... done
[124amd64-quarterly-job-09] | `-- Installing hwloc2-2.8.0...
<snip>
===> NOTICE:
The mpich port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> code_saturne-8.0.0 depends on shared library: libpetsc.so - found (/usr/local/lib/libpetsc.so)
===> Returning to build of code_saturne-8.0.0
===> code_saturne-8.0.0 depends on shared library: libHYPRE.so - not found
===> Installing existing package /packages/All/hypre-2.29.0_1.pkg
[124amd64-quarterly-job-09] Installing hypre-2.29.0_1...
[124amd64-quarterly-job-09] Extracting hypre-2.29.0_1: .......... done
===> code_saturne-8.0.0 depends on shared library: libHYPRE.so - found (/usr/local/lib/libHYPRE.so)
===> Returning to build of code_saturne-8.0.0
===> code_saturne-8.0.0 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so)
===> code_saturne-8.0.0 depends on shared library: libscotch.so - not found
===> Installing existing package /packages/All/scotch-6.0.4.a7_4.pkg
[124amd64-quarterly-job-09] Installing scotch-6.0.4.a7_4...
[124amd64-quarterly-job-09] Extracting scotch-6.0.4.a7_4: .......... done
===> code_saturne-8.0.0 depends on shared library: libscotch.so - found (/usr/local/lib/libscotch.so)
===> Returning to build of code_saturne-8.0.0
===> code_saturne-8.0.0 depends on shared library: libsmumps.so - not found
===> Installing existing package /packages/All/mumps-edf-5.1.2.a7_4.pkg
[124amd64-quarterly-job-09] Installing mumps-edf-5.1.2.a7_4...
[124amd64-quarterly-job-09] Extracting mumps-edf-5.1.2.a7_4: .......... done
===> code_saturne-8.0.0 depends on shared library: libsmumps.so - found (/usr/local/lib/libsmumps.so)
===> Returning to build of code_saturne-8.0.0
===> code_saturne-8.0.0 depends on shared library: libcblas.so - not found
===> Installing existing package /packages/All/cblas-3.11.0_1.pkg
[124amd64-quarterly-job-09] Installing cblas-3.11.0_1...
[124amd64-quarterly-job-09] Extracting cblas-3.11.0_1: .......... done
===> code_saturne-8.0.0 depends on shared library: libcblas.so - found (/usr/local/lib/libcblas.so)
===> Returning to build of code_saturne-8.0.0
===> code_saturne-8.0.0 depends on shared library: libmedC.so - not found
===> Installing existing package /packages/All/fr-med-4.0.0_3.pkg
[124amd64-quarterly-job-09] Installing fr-med-4.0.0_3...
[124amd64-quarterly-job-09] `-- Installing hdf5-110-1.10.10...
[124amd64-quarterly-job-09] `-- Extracting hdf5-110-1.10.10: .......... done
[124amd64-quarterly-job-09] Extracting fr-med-4.0.0_3: .......... done
===> code_saturne-8.0.0 depends on shared library: libmedC.so - found (/usr/local/lib/libmedC.so)
===> Returning to build of code_saturne-8.0.0
===> code_saturne-8.0.0 depends on shared library: libmetis.so - found (/usr/local/lib/libmetis.so)
===> code_saturne-8.0.0 depends on shared library: libblas.so - found (/usr/local/lib/libblas.so)
===> code_saturne-8.0.0 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so)
===> code_saturne-8.0.0 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so)
===> code_saturne-8.0.0 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so)
===> code_saturne-8.0.0 depends on shared library: libmpich.so - found (/usr/local/lib/libmpich.so)
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for code_saturne-8.0.0
/usr/bin/sed -i.bak -e 's|/usr/bin/env python|/usr/local/bin/python3.9|' /wrkdirs/usr/ports/science/code_saturne/work/code_saturne-8.0.0/Makefile.am
/usr/bin/sed -i.bak -e 's|make -s|gmake -s|' /wrkdirs/usr/ports/science/code_saturne/work/code_saturne-8.0.0/m4/cs_petsc.m4
configure: loading site script /usr/ports/Templates/config.site
checking build system type... amd64-portbld-freebsd12.4
checking host system type... amd64-portbld-freebsd12.4
checking target system type... amd64-portbld-freebsd12.4
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
checking whether gmake supports nested variables... yes
checking how to create a pax tar archive... gnutar
checking whether to enable maintainer-specific portions of Makefiles... no
checking whether gmake supports nested variables... (cached) yes
configure: WARNING: no supported environment module commmand detected
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether cc accepts -g... yes
checking for cc option to enable C11 features... none needed
checking whether cc understands -c and -o together... yes
checking whether gmake supports the include directive... yes (GNU style)
checking dependency style of cc... gcc3
checking whether the compiler supports GNU C++... yes
checking whether c++ accepts -g... yes
checking for c++ option to enable C++11 features... none needed
checking dependency style of c++... gcc3
checking whether the compiler supports GNU Fortran... yes
checking whether gfortran12 accepts -g... yes
checking whether ln -s works... yes
checking for ranlib... /usr/local/bin/ranlib
checking for a sed that does not truncate output... (cached) /usr/local/bin/gsed
checking the archiver (/usr/local/bin/ar) interface... ar
configure: sourcing config/cs_auto_flags.sh (test for known compilers)
compiler 'cc' is clang
compiler 'c++' is clang
compiler 'gfortran12' is GNU gfortran-12.2.0
configure: WARNING: Not sure how to build shared lib for freebsd12.4; assuming Linux-like
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for stdio.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for strings.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for unistd.h... (cached) yes
checking for size_t... (cached) yes
checking for pid_t... (cached) yes
checking for _Bool... (cached) yes
checking for stdbool.h that conforms to C99... (cached) yes
checking for long long... (cached) yes
checking for unsigned long long... (cached) yes
checking for int32_t... (cached) yes
checking for int64_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for ptrdiff_t... (cached) yes
checking size of void *... 8
checking size of short... 2
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of float... 4
checking size of double... 8
checking how to get verbose linking output from gfortran12... -v
checking for Fortran libraries of gfortran12... -L/usr/local/lib -L/usr/local/lib/gcc12 -L/usr/local/bin -L/usr/local/lib/gcc12/gcc/x86_64-portbld-freebsd12.4/12.2.0 -L/usr/local/lib/gcc12/gcc/x86_64-portbld-freebsd12.4/12.2.0/../../../../../x86_64-portbld-freebsd12.4/lib -L/usr/local/lib/gcc12/gcc/x86_64-portbld-freebsd12.4/12.2.0/../../.. -lgfortran -lm -lssp_nonshared -lquadmath
checking for OpenMP (C)... yes
checking for OpenMP (Fortran)... no
checking whether /usr/local/bin/python3.9 version is >= "3.4"... yes
checking for /usr/local/bin/python3.9 version... 3.9
checking for /usr/local/bin/python3.9 platform... freebsd12
checking for GNU default /usr/local/bin/python3.9 prefix... ${prefix}
checking for GNU default /usr/local/bin/python3.9 exec_prefix... ${exec_prefix}
checking for /usr/local/bin/python3.9 script directory (pythondir)... ${PYTHON_PREFIX}/lib/python3.9/site-packages
checking for /usr/local/bin/python3.9 extension module directory (pyexecdir)... ${PYTHON_EXEC_PREFIX}/lib/python3.9/site-packages
checking for dlopen... dlopen
checking for legacy C BLAS... yes
checking how to run the C preprocessor... cpp
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for MPI (MPI compiler wrapper test)... no
checking for mpi.h... yes
checking for MPICH-3 or MPICH2... yes
checking for MPI I/O... yes
checking for MPI in place... yes
checking for MPI nonblocking barrier... yes
checking for ptscotch.h... yes
checking for PT-SCOTCH... yes
checking for hdf5.h... yes
checking for H5Fopen in -lhdf5-shared... no
checking for H5Fopen in -lhdf5-static... no
checking for H5Fopen in -lhdf5... yes
CGNS >= 3.1.0 headers found
checking for cg_coord_partial_write in -lcgns... yes
MED >= 3.0 headers found
configure: WARNING: no MED file MPI support
CCMIO headers not found
checking for freesteam/steam.h... no
checking for CoolProp library)... no
checking for Zlib... yes
checking size of z_off_t... 8
configure: WARNING: no MEDCoupling file support
configure: MUMPS_CPP=-I/usr/local/include
configure: MUMPS_LD=-L/usr/local/lib
configure: MUMPS_LIBS=-ldmumps -lsmumps -lmumps_common -lmpiseq -llapack -lgfortran -lm
configure: MUMPSRUNPATH=-R/usr/local/lib
ld-elf.so.1: Shared object "libreadline.so.8" not found, required by "bash"
gmake[1]: *** [/wrkdirs/usr/ports/science/code_saturne/work/code_saturne-8.0.0/build-aux/petsc-variables.makefile:4: getincludedirs] Error 1
ld-elf.so.1: Shared object "libreadline.so.8" not found, required by "bash"
gmake[1]: *** [/wrkdirs/usr/ports/science/code_saturne/work/code_saturne-8.0.0/build-aux/petsc-variables.makefile:7: getlinklibs] Error 1
checking for PETSc library... configure: WARNING: no PETSc support
no
checking for HYPRE... yes
checking for pdflatex... /usr/local/bin/pdflatex
checking for bibtex... /usr/local/bin/bibtex
checking for makeindex... /usr/local/bin/makeindex
checking for doxygen... /usr/local/bin/doxygen
checking for dot... /usr/local/bin/dot
checking for sphinx-build... /wrkdirs/usr/ports/science/code_saturne/work/.bin/sphinx-build
checking for PyQt5 version >= 5.0... ld-elf.so.1: Shared object "libpython3.9.so.1.0" not found, required by "python3.9"
no
checking for PyQt4 version >= 4.5... ld-elf.so.1: Shared object "libpython3.9.so.1.0" not found, required by "python3.9"
no
configure: error: in `/wrkdirs/usr/ports/science/code_saturne/work/code_saturne-8.0.0':
configure: error: cannot find PyQt5 support (>= 5.0) or PyQt4 support (>= 4.5), Graphical User Interface cannot be installed
See `config.log' for more details
===> Script "configure" failed unexpectedly.
Please report the problem to thierry@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/science/code_saturne/work/code_saturne-8.0.0/config.log"
including the output of the failure of your make command. Also, it might be
a good idea to provide an overview of all packages installed on your system
(e.g. a /usr/local/sbin/pkg-static info -g -Ea).
*** Error code 1
Stop.
make: stopped in /usr/ports/science/code_saturne