[exp - 123amd64-default-build-as-user][science/dssp] Failed for dssp-4.0.5 in build
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Date: Sat, 19 Nov 2022 03:02:49 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/package19/data/123amd64-default-build-as-user/36a871b3bb9d/logs/dssp-4.0.5.log
Build URL: https://pkg-status.freebsd.org/package19/build.html?mastername=123amd64-default-build-as-user&build=36a871b3bb9d
Log:
=>> Building science/dssp
build started at Sat Nov 19 03:02:27 UTC 2022
port directory: /usr/ports/science/dssp
package name: dssp-4.0.5
building for: FreeBSD 123amd64-default-build-as-user-job-13 12.3-RELEASE-p8 FreeBSD 12.3-RELEASE-p8 amd64
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> dssp-4.0.5 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[123amd64-default-build-as-user-job-13] Installing pkg-1.18.4...
[123amd64-default-build-as-user-job-13] Extracting pkg-1.18.4: .......... done
===> dssp-4.0.5 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of dssp-4.0.5
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.0.5 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.0.5 for building
=> SHA256 Checksum OK for PDB-REDO-dssp-v4.0.5_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.0.5 for building
===> Extracting for dssp-4.0.5
=> SHA256 Checksum OK for PDB-REDO-dssp-v4.0.5_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for dssp-4.0.5
===========================================================================
=======================<phase: build-depends >============================
===> dssp-4.0.5 depends on executable: mrc - not found
===> Installing existing package /packages/All/mrc-1.3.4.7.pkg
[123amd64-default-build-as-user-job-13] Installing mrc-1.3.4.7...
[123amd64-default-build-as-user-job-13] `-- Installing boost-libs-1.80.0_1...
[123amd64-default-build-as-user-job-13] | `-- Installing icu-72.1,1...
[123amd64-default-build-as-user-job-13] | `-- Extracting icu-72.1,1: .......... done
[123amd64-default-build-as-user-job-13] `-- Extracting boost-libs-1.80.0_1: .......... done
[123amd64-default-build-as-user-job-13] Extracting mrc-1.3.4.7: ......... 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.
===> dssp-4.0.5 depends on executable: mrc - found
===> Returning to build of dssp-4.0.5
===> dssp-4.0.5 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.24.3_2.pkg
[123amd64-default-build-as-user-job-13] Installing cmake-core-3.24.3_2...
[123amd64-default-build-as-user-job-13] `-- Installing expat-2.5.0...
[123amd64-default-build-as-user-job-13] `-- Extracting expat-2.5.0: .......... done
[123amd64-default-build-as-user-job-13] `-- Installing jsoncpp-1.9.5...
[123amd64-default-build-as-user-job-13] `-- Extracting jsoncpp-1.9.5: .......... done
[123amd64-default-build-as-user-job-13] `-- Installing libuv-1.44.2...
[123amd64-default-build-as-user-job-13] `-- Extracting libuv-1.44.2: .......... done
[123amd64-default-build-as-user-job-13] `-- Installing rhash-1.4.3...
[123amd64-default-build-as-user-job-13] | `-- Installing gettext-runtime-0.21...
[123amd64-default-build-as-user-job-13] | | `-- Installing indexinfo-0.3.1...
[123amd64-default-build-as-user-job-13] | | `-- Extracting indexinfo-0.3.1: .... done
[123amd64-default-build-as-user-job-13] | `-- Extracting gettext-runtime-0.21: .......... done
[123amd64-default-build-as-user-job-13] `-- Extracting rhash-1.4.3: .......... done
[123amd64-default-build-as-user-job-13] Extracting cmake-core-3.24.3_2: .......... done
===> dssp-4.0.5 depends on file: /usr/local/bin/cmake - found
===> Returning to build of dssp-4.0.5
===========================================================================
=======================<phase: lib-depends >============================
===> dssp-4.0.5 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so)
===> dssp-4.0.5 depends on shared library: libcifpp.so - not found
===> Installing existing package /packages/All/libcifpp-5.0.3.pkg
[123amd64-default-build-as-user-job-13] Installing libcifpp-5.0.3...
[123amd64-default-build-as-user-job-13] `-- Installing bash-5.2.9...
[123amd64-default-build-as-user-job-13] `-- Extracting bash-5.2.9: .......... done
[123amd64-default-build-as-user-job-13] Extracting libcifpp-5.0.3: .......... done
===> dssp-4.0.5 depends on shared library: libcifpp.so - found (/usr/local/lib/libcifpp.so)
===> Returning to build of dssp-4.0.5
===========================================================================
=======================<phase: configure >============================
===> Configuring for dssp-4.0.5
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/dssp/work/.build
-- The CXX compiler identification is Clang 10.0.1
-- 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
-- Found Mrc: /usr/local/bin/mrc (found version "1.3.5")
Using resources compiled with
-- 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 "1.2.11")
-- 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")
-- Found Boost: /usr/local/include (found version "1.80.0") found components: date_time program_options
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_C_COMPILER
CMAKE_C_FLAGS
CMAKE_C_FLAGS_DEBUG
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /wrkdirs/usr/ports/science/dssp/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for dssp-4.0.5
/usr/local/bin/cmake -S/wrkdirs/usr/ports/science/dssp/work/dssp-4.0.5 -B/wrkdirs/usr/ports/science/dssp/work/.build --check-build-system CMakeFiles/Makefile.cmake 0
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/usr/bin/make -f CMakeFiles/Makefile2 all
--- CMakeFiles/mkdssp.dir/all ---
--- CMakeFiles/unit-test.dir/all ---
--- CMakeFiles/mkdssp.dir/all ---
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--- unit-test_rsrc.obj ---
--- CMakeFiles/mkdssp.dir/all ---
--- mkdssp_rsrc.obj ---
--- CMakeFiles/unit-test.dir/all ---
[ 12%] Generating unit-test_rsrc.obj, ALL
--- CMakeFiles/mkdssp.dir/all ---
[ 25%] Generating mkdssp_rsrc.obj, ALL
--- CMakeFiles/unit-test.dir/all ---
/usr/local/bin/mrc -o /wrkdirs/usr/ports/science/dssp/work/.build/unit-test_rsrc.obj /mmcif_pdbx_v50.dic
--- CMakeFiles/mkdssp.dir/all ---
/usr/local/bin/mrc -o /wrkdirs/usr/ports/science/dssp/work/.build/mkdssp_rsrc.obj /mmcif_pdbx_v50.dic
--- CMakeFiles/unit-test.dir/all ---
Error executing mrc: Could not open data file
--- CMakeFiles/mkdssp.dir/all ---
Error executing mrc: Could not open data file
*** [mkdssp_rsrc.obj] Error code 1
make[3]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
1 error
make[3]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
--- CMakeFiles/unit-test.dir/all ---
*** [unit-test_rsrc.obj] Error code 1
make[3]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
1 error
make[3]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
*** [CMakeFiles/unit-test.dir/all] Error code 2
make[2]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
--- CMakeFiles/mkdssp.dir/all ---
*** [CMakeFiles/mkdssp.dir/all] Error code 2
make[2]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
2 errors
make[2]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
*** [all] Error code 2
make[1]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
1 error
make[1]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
===> 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/dssp