[package - 131amd64-default][science/cif-tools] Failed for cif-tools-1.0.3 in build
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Date: Wed, 16 Nov 2022 04:02:32 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/beefy16/data/131amd64-default/387f99b7180f/logs/cif-tools-1.0.3.log
Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=131amd64-default&build=387f99b7180f
Log:
=>> Building science/cif-tools
build started at Wed Nov 16 04:02:09 UTC 2022
port directory: /usr/ports/science/cif-tools
package name: cif-tools-1.0.3
building for: FreeBSD 131amd64-default-job-05 13.1-RELEASE-p3 FreeBSD 13.1-RELEASE-p3 amd64
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> cif-tools-1.0.3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[131amd64-default-job-05] Installing pkg-1.18.4...
[131amd64-default-job-05] Extracting pkg-1.18.4: .......... done
===> cif-tools-1.0.3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of cif-tools-1.0.3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by cif-tools-1.0.3 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by cif-tools-1.0.3 for building
=> SHA256 Checksum OK for PDB-REDO-cif-tools-v1.0.3_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by cif-tools-1.0.3 for building
===> Extracting for cif-tools-1.0.3
=> SHA256 Checksum OK for PDB-REDO-cif-tools-v1.0.3_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for cif-tools-1.0.3
===> Applying FreeBSD patches for cif-tools-1.0.3 from /usr/ports/science/cif-tools/files
===========================================================================
=======================<phase: build-depends >============================
===> cif-tools-1.0.3 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.24.3_1.pkg
[131amd64-default-job-05] Installing cmake-core-3.24.3_1...
[131amd64-default-job-05] `-- Installing expat-2.5.0...
[131amd64-default-job-05] `-- Extracting expat-2.5.0: .......... done
[131amd64-default-job-05] `-- Installing jsoncpp-1.9.5...
[131amd64-default-job-05] `-- Extracting jsoncpp-1.9.5: .......... done
[131amd64-default-job-05] `-- Installing libuv-1.44.2...
[131amd64-default-job-05] `-- Extracting libuv-1.44.2: .......... done
[131amd64-default-job-05] `-- Installing rhash-1.4.3...
[131amd64-default-job-05] | `-- Installing gettext-runtime-0.21...
[131amd64-default-job-05] | | `-- Installing indexinfo-0.3.1...
[131amd64-default-job-05] | | `-- Extracting indexinfo-0.3.1: .... done
[131amd64-default-job-05] | `-- Extracting gettext-runtime-0.21: .......... done
[131amd64-default-job-05] `-- Extracting rhash-1.4.3: .......... done
[131amd64-default-job-05] Extracting cmake-core-3.24.3_1: .......... done
===> cif-tools-1.0.3 depends on file: /usr/local/bin/cmake - found
===> Returning to build of cif-tools-1.0.3
===> cif-tools-1.0.3 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.11.1,2.pkg
[131amd64-default-job-05] Installing ninja-1.11.1,2...
[131amd64-default-job-05] `-- Installing python39-3.9.15_1...
[131amd64-default-job-05] | `-- Installing libffi-3.4.3...
[131amd64-default-job-05] | `-- Extracting libffi-3.4.3: .......... done
[131amd64-default-job-05] | `-- Installing mpdecimal-2.5.1...
[131amd64-default-job-05] | `-- Extracting mpdecimal-2.5.1: .......... done
[131amd64-default-job-05] | `-- Installing readline-8.1.2...
[131amd64-default-job-05] | `-- Extracting readline-8.1.2: .......... done
[131amd64-default-job-05] `-- Extracting python39-3.9.15_1: .......... done
[131amd64-default-job-05] Extracting ninja-1.11.1,2: ........ done
=====
Message from python39-3.9.15_1:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> cif-tools-1.0.3 depends on executable: ninja - found
===> Returning to build of cif-tools-1.0.3
===========================================================================
=======================<phase: lib-depends >============================
===> cif-tools-1.0.3 depends on shared library: libboost_iostreams.so - not found
===> Installing existing package /packages/All/boost-libs-1.80.0_1.pkg
[131amd64-default-job-05] Installing boost-libs-1.80.0_1...
[131amd64-default-job-05] `-- Installing icu-72.1,1...
[131amd64-default-job-05] `-- Extracting icu-72.1,1: .......... done
[131amd64-default-job-05] Extracting boost-libs-1.80.0_1: .......... done
=====
Message from boost-libs-1.80.0_1:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> cif-tools-1.0.3 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so)
===> Returning to build of cif-tools-1.0.3
===> cif-tools-1.0.3 depends on shared library: libcifpp.so - not found
===> Installing existing package /packages/All/libcifpp-5.0.3.pkg
[131amd64-default-job-05] Installing libcifpp-5.0.3...
[131amd64-default-job-05] `-- Installing bash-5.2.9...
[131amd64-default-job-05] `-- Extracting bash-5.2.9: .......... done
[131amd64-default-job-05] Extracting libcifpp-5.0.3: .......... done
===> cif-tools-1.0.3 depends on shared library: libcifpp.so - found (/usr/local/lib/libcifpp.so)
===> Returning to build of cif-tools-1.0.3
===========================================================================
=======================<phase: configure >============================
===> Configuring for cif-tools-1.0.3
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/cif-tools/work/.build
-- The CXX compiler identification is Clang 13.0.0
-- 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
-- Looking for C++ include filesystem
-- Looking for C++ include filesystem - found
-- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED
-- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED - Success
CMake Warning at CMakeLists.txt:112 (find_package):
By not providing "FindMrc.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "Mrc", but
CMake did not find one.
Could not find a package configuration file provided by "Mrc" with any of
the following names:
MrcConfig.cmake
mrc-config.cmake
Add the installation prefix of "Mrc" to CMAKE_PREFIX_PATH or set "Mrc_DIR"
to a directory containing one of the above files. If "Mrc" provides a
separate development package or SDK, be sure it has been installed.
CMake Warning at CMakeLists.txt:117 (message):
Not using resources since mrc was not found
-- Found Boost: /usr/local/include (found suitable version "1.80.0", minimum required is "1.70.0") found components: program_options
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.12")
-- Looking for lzma_auto_decoder in /usr/lib/liblzma.so
-- Looking for lzma_auto_decoder in /usr/lib/liblzma.so - found
-- Looking for lzma_easy_encoder in /usr/lib/liblzma.so
-- Looking for lzma_easy_encoder in /usr/lib/liblzma.so - found
-- Looking for lzma_lzma_preset in /usr/lib/liblzma.so
-- Looking for lzma_lzma_preset in /usr/lib/liblzma.so - found
-- Found LibLZMA: /usr/lib/liblzma.so (found version "5.2.5")
-- Configuring done
-- Generating done
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
-- Build files have been written to: /wrkdirs/usr/ports/science/cif-tools/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for cif-tools-1.0.3
[ 4% 2/24] /usr/bin/c++ -DCACHE_DIR=\"/usr/local/var/cache/libcifpp\" -DDATA_DIR=\"/usr/local/share/libcifpp\" -I/wrkdirs/usr/ports/science/cif-tools/work/.build -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/PRIVATE -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/cifpp::cifpp -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -std=gnu++17 -MD -MT CMakeFiles/pdb2cif.dir/src/pr-main.cpp.o -MF CMakeFiles/pdb2cif.dir/src/pr-main.cpp.o.d -o CMakeFiles/pdb2cif.dir/src/pr-main.cpp.o -c /wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/src/pr-main.cpp
FAILED: CMakeFiles/pdb2cif.dir/src/pr-main.cpp.o
/usr/bin/c++ -DCACHE_DIR=\"/usr/local/var/cache/libcifpp\" -DDATA_DIR=\"/usr/local/share/libcifpp\" -I/wrkdirs/usr/ports/science/cif-tools/work/.build -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/PRIVATE -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/cifpp::cifpp -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -std=gnu++17 -MD -MT CMakeFiles/pdb2cif.dir/src/pr-main.cpp.o -MF CMakeFiles/pdb2cif.dir/src/pr-main.cpp.o.d -o CMakeFiles/pdb2cif.dir/src/pr-main.cpp.o -c /wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/src/pr-main.cpp
/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/src/pr-main.cpp:39:10: fatal error: 'cif++/Cif++.hpp' file not found
#include "cif++/Cif++.hpp"
^~~~~~~~~~~~~~~~~
1 error generated.
[ 8% 2/24] /usr/bin/c++ -DCACHE_DIR=\"/usr/local/var/cache/libcifpp\" -DDATA_DIR=\"/usr/local/share/libcifpp\" -I/wrkdirs/usr/ports/science/cif-tools/work/.build -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/PRIVATE -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/cifpp::cifpp -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -std=gnu++17 -MD -MT CMakeFiles/pdb2cif.dir/src/pdb2cif.cpp.o -MF CMakeFiles/pdb2cif.dir/src/pdb2cif.cpp.o.d -o CMakeFiles/pdb2cif.dir/src/pdb2cif.cpp.o -c /wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/src/pdb2cif.cpp
FAILED: CMakeFiles/pdb2cif.dir/src/pdb2cif.cpp.o
/usr/bin/c++ -DCACHE_DIR=\"/usr/local/var/cache/libcifpp\" -DDATA_DIR=\"/usr/local/share/libcifpp\" -I/wrkdirs/usr/ports/science/cif-tools/work/.build -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/PRIVATE -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/cifpp::cifpp -I/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/include -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -std=gnu++17 -MD -MT CMakeFiles/pdb2cif.dir/src/pdb2cif.cpp.o -MF CMakeFiles/pdb2cif.dir/src/pdb2cif.cpp.o.d -o CMakeFiles/pdb2cif.dir/src/pdb2cif.cpp.o -c /wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/src/pdb2cif.cpp
/wrkdirs/usr/ports/science/cif-tools/work/cif-tools-1.0.3/src/pdb2cif.cpp:41:10: fatal error: 'cif++/Cif++.hpp' file not found
#include "cif++/Cif++.hpp"
^~~~~~~~~~~~~~~~~
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 in /usr/ports/science/cif-tools