[exp - 142amd64-default-build-as-user][science/votca] Failed for votca-2025_4 in configure
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Thu, 25 Sep 2025 06:37:28 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/package19/data/142amd64-default-build-as-user/666d543a7f23/logs/votca-2025_4.log
Build URL: https://pkg-status.freebsd.org/package19/build.html?mastername=142amd64-default-build-as-user&build=666d543a7f23
Log:
=>> Building science/votca
build started at Thu Sep 25 06:35:16 -00 2025
port directory: /usr/ports/science/votca
package name: votca-2025_4
building for: FreeBSD 142amd64-default-build-as-user-job-05 14.2-RELEASE-p5 FreeBSD 14.2-RELEASE-p5 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 2499 Sep 21 00:03 /usr/ports/science/votca/Makefile
Ports top last git commit: 666d543a7f
Ports top unclean checkout: no
Port dir last git commit: a6233e5a2f
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.3
Host OSVERSION: 1600000
Jail OSVERSION: 1402000
Job Id: 05
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1402000
UNAME_v=FreeBSD 14.2-RELEASE-p5
UNAME_r=14.2-RELEASE-p5
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=3.4.3
MASTERMNT=/poudriere/data/.m/142amd64-default-build-as-user/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
GID=0
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
UID=0
PWD=/poudriere/data/.m/142amd64-default-build-as-user/05/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=142amd64-default-build-as-user
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/poudriere/data/.m/142amd64-default-build-as-user/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.3
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 votca-2025_4:
APPS=on: Build applications
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.11" XDG_DATA_HOME=/wrkdirs/usr/ports/science/votca/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/votca/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/votca/work/.cache HOME=/wrkdirs/usr/ports/science/votca/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/votca/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/votca/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] " PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/science/votca/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/votca/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/votca/work/.cache HOME=/wrkdirs/usr/ports/science/votca/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/votca/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/votca/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/science/votca/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DBOOST_TIMER_ENABLE_DEPRECATED " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="i
nstall -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--
APPS="" NO_APPS="@comment " CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=14.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/votca" EXAMPLESDIR="share/examples/votca" DATADIR="share/votca" WWWDIR="www/votca" ETCDIR="etc/votca"
--End PLIST_SUB--
--SUB_LIST--
APPS="" NO_APPS="@comment " PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/votca DOCSDIR=/usr/local/share/doc/votca EXAMPLESDIR=/usr/local/share/examples/votca WWWDIR=/usr/local/www/votca ETCDIR=/usr/local/etc/votca
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
FORCE_PACKAGE=yes
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
---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
pipebuf (-y) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534
===> License APACHE20 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> votca-2025_4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.3.1.pkg
[142amd64-default-build-as-user-job-05] Installing pkg-2.3.1...
[142amd64-default-build-as-user-job-05] Extracting pkg-2.3.1: .......... done
===> votca-2025_4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of votca-2025_4
===========================================================================
=======================<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 votca-2025_4 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 votca-2025_4 for building
=> SHA256 Checksum OK for votca-votca-v2025_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=nobody UID=65534 GID=65534
===> License APACHE20 accepted by the user
===> Fetching all distfiles required by votca-2025_4 for building
===> Extracting for votca-2025_4
=> SHA256 Checksum OK for votca-votca-v2025_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=nobody UID=65534 GID=65534
===> Patching for votca-2025_4
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> votca-2025_4 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.3.3_1.pkg
[142amd64-default-build-as-user-job-05] Installing bash-5.3.3_1...
[142amd64-default-build-as-user-job-05] `-- Installing gettext-runtime-0.23.1...
[142amd64-default-build-as-user-job-05] | `-- Installing indexinfo-0.3.1_1...
[142amd64-default-build-as-user-job-05] | `-- Extracting indexinfo-0.3.1_1: .... done
[142amd64-default-build-as-user-job-05] `-- Extracting gettext-runtime-0.23.1: .......... done
[142amd64-default-build-as-user-job-05] Extracting bash-5.3.3_1: .......... done
===> votca-2025_4 depends on executable: bash - found
===> Returning to build of votca-2025_4
===> votca-2025_4 depends on executable: lmp - not found
===> Installing existing package /packages/All/lammps-20241119_2.pkg
[142amd64-default-build-as-user-job-05] Installing lammps-20241119_2...
[142amd64-default-build-as-user-job-05] `-- Installing curl-8.15.0...
[142amd64-default-build-as-user-job-05] | `-- Installing brotli-1.1.0,1...
[142amd64-default-build-as-user-job-05] | `-- Extracting brotli-1.1.0,1: .......... done
[142amd64-default-build-as-user-job-05] | `-- Installing libidn2-2.3.8...
[142amd64-default-build-as-user-job-05] | | `-- Installing libunistring-1.3...
[142amd64-default-build-as-user-job-05] | | `-- Extracting libunistring-1.3: .......... done
[142amd64-default-build-as-user-job-05] | `-- Extracting libidn2-2.3.8: .......... done
[142amd64-default-build-as-user-job-05] | `-- Installing libnghttp2-1.67.0...
[142amd64-default-build-as-user-job-05] | `-- Extracting libnghttp2-1.67.0: .......... done
[142amd64-default-build-as-user-job-05] | `-- Installing libpsl-0.21.5_2...
[142amd64-default-build-as-user-job-05] | `-- Extracting libpsl-0.21.5_2: .......... done
[142amd64-default-build-as-user-job-05] | `-- Installing libssh2-1.11.1,3...
[142amd64-default-build-as-user-job-05] | `-- Extracting libssh2-1.11.1,3: .......... done
[142amd64-default-build-as-user-job-05] | `-- Installing zstd-1.5.7...
<snip>
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Found EXPAT: /usr/local/lib/libexpat.so (found version "2.7.1")
-- Found GMX: /usr/local/bin/gmx_d
-- Found UnixCommands: /usr/local/bin/bash
-- Looking for C++ include algorithm
-- Looking for C++ include algorithm - found
-- Looking for C++ include iomanip
-- Looking for C++ include iomanip - found
-- Looking for C++ include numeric
-- Looking for C++ include numeric - found
-- Looking for C++ include cstdlib
-- Looking for C++ include cstdlib - found
-- Found HDF5: hdf5_cpp-shared (found version "1.12.2") found components: CXX
-- Found LMP: /usr/local/bin/lmp
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pytest'
-- Checking for module 'libint2'
-- Found libint2, version 2.11.0
-- Found libint2: /usr/local/include (found suitable version "2.11.0", minimum required is "2.6")
-- Found libecpint: /usr/local/lib/cmake/ecpint
-- Found python module lxml
-- Found python module h5py
-- Found python module rdkit
-- Found Python: /usr/local/include/python3.11 (found suitable version "3.11.13", minimum required is "3.5") found components: Development Development.Module Development.Embed
CMake Warning at xtp/src/pyxtp/CMakeLists.txt:3 (find_package):
By not providing "Findpybind11.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "pybind11",
but CMake did not find one.
Could not find a package configuration file provided by "pybind11" with any
of the following names:
pybind11Config.cmake
pybind11-config.cmake
Add the installation prefix of "pybind11" to CMAKE_PREFIX_PATH or set
"pybind11_DIR" to a directory containing one of the above files. If
"pybind11" provides a separate development package or SDK, be sure it has
been installed.
-- Found python module ase
-- Found python module xmltodict
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pytest'
-- Skipping xtp python bindings
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Could NOT find CLANG_FORMAT: Found unsuitable version "0.0", but required is at least "11" (found CLANG_FORMAT_EXECUTABLE-NOTFOUND)
-- The following features have been enabled:
* BUILD_XTP, Build xtp module
* BUILD_TESTING, Enable unit tests
* INSTALL_RC_FILES, Install votca rc files (VOTCARC.bash etc.)
* BUILD_MANPAGES, Build manpages (disable for cross-compile)
* INSTALL_CSGAPPS, Install extra app using csg
-- The following RECOMMENDED packages have been found:
* GROMACS (required version >= 2019.6)
Used to read/write gromacs data files
* FFTW3
Enables FFT functionality
* PkgConfig
Used to detect fftw package
Used to detect libint2 package
-- The following REQUIRED packages have been found:
* Boost (required version >= 1.71.0)
Extended C++ libraries
* Eigen3 (required version >= 3.3.0)
C++ vector data structures
* Threads
Used for thread parallelization
* OpenMP (required version >= 4.5)
Used for thread parallelization in tools
* EXPAT
Used for XML parsing
* UnixCommands
Used in testing
* Libxc
Provides exchange-correclation functionals
* libint2 (required version >= 2.6)
Calculates Gaussian integrals
* ecpint
Calculates Gaussian integrals over pseudo potentials
* HDF5
Used to read h5md data files
Used to read/write HDF5 data files
* Python (required version >= 3.5)
Used in csg scripts and docu
Used to build xtp python bindings
-- The following features have been disabled:
* ENABLE_RPATH_INJECT, Inject rpath into executables
* INJECT_MARCH_NATIVE, Add -march=native to CXX flags
* BUILD_OWN_GROMACS, Build an internal version of gromacs
* BUILD_OWN_LIBINT, Build an internal version of libint
* ENABLE_VALGRIND_TESTING, Run unit tests through valgrind, too
* ENABLE_REGRESSION_TESTING, Enable regression tests
* USE_CUDA, Use CUDA for GPU acceleration
-- The following OPTIONAL packages have not been found:
* MKL
Enables accelerated performance with MKL
* Doxygen
Needed to build API documentation
* CLANG_FORMAT (required version >= 11)
-- The following RECOMMENDED packages have not been found:
* pybind11
Used to build xtp python bindings
-- Configuring done (74.7s)
CMake Error at tools/src/libtools/CMakeLists.txt:28 (target_link_libraries):
Target "votca_tools" links to:
Boost::system
but the target was not found. Possible reasons include:
* There is a typo in the target name.
* A find_package call is missing for an IMPORTED target.
* An ALIAS target is missing.
CMake Error at csg/src/libcsg/CMakeLists.txt:39 (target_link_libraries):
Target "votca_csg" links to:
Boost::system
but the target was not found. Possible reasons include:
* There is a typo in the target name.
* A find_package call is missing for an IMPORTED target.
* An ALIAS target is missing.
CMake Error at xtp/src/libxtp/CMakeLists.txt:13 (target_link_libraries):
Target "votca_xtp" links to:
Boost::system
but the target was not found. Possible reasons include:
* There is a typo in the target name.
* A find_package call is missing for an IMPORTED target.
* An ALIAS target is missing.
-- Generating done (1.3s)
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_VERBOSE_MAKEFILE
FETCHCONTENT_FULLY_DISCONNECTED
LOCALBASE
Python3_EXECUTABLE
Python_ADDITIONAL_VERSIONS
CMake Generate step failed. Build files cannot be regenerated correctly.
*** Error code 1
Stop.
make: stopped in /usr/ports/science/votca