[exp - 123amd64-default-build-as-user][science/cif-tools] Failed for cif-tools-1.0.3 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Fri, 18 Nov 2022 05:47:44 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/cif-tools-1.0.3.log
Build URL:      https://pkg-status.freebsd.org/package19/build.html?mastername=123amd64-default-build-as-user&build=36a871b3bb9d
Log:

=>> Building science/cif-tools
build started at Fri Nov 18 05:47:17 UTC 2022
port directory: /usr/ports/science/cif-tools
package name: cif-tools-1.0.3
building for: FreeBSD 123amd64-default-build-as-user-job-03 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    >============================
===>   cif-tools-1.0.3 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-03] Installing pkg-1.18.4...
[123amd64-default-build-as-user-job-03] 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_2.pkg
[123amd64-default-build-as-user-job-03] Installing cmake-core-3.24.3_2...
[123amd64-default-build-as-user-job-03] `-- Installing expat-2.5.0...
[123amd64-default-build-as-user-job-03] `-- Extracting expat-2.5.0: .......... done
[123amd64-default-build-as-user-job-03] `-- Installing jsoncpp-1.9.5...
[123amd64-default-build-as-user-job-03] `-- Extracting jsoncpp-1.9.5: .......... done
[123amd64-default-build-as-user-job-03] `-- Installing libuv-1.44.2...
[123amd64-default-build-as-user-job-03] `-- Extracting libuv-1.44.2: .......... done
[123amd64-default-build-as-user-job-03] `-- Installing rhash-1.4.3...
[123amd64-default-build-as-user-job-03] |   `-- Installing gettext-runtime-0.21...
[123amd64-default-build-as-user-job-03] |   | `-- Installing indexinfo-0.3.1...
[123amd64-default-build-as-user-job-03] |   | `-- Extracting indexinfo-0.3.1: .... done
[123amd64-default-build-as-user-job-03] |   `-- Extracting gettext-runtime-0.21: .......... done
[123amd64-default-build-as-user-job-03] `-- Extracting rhash-1.4.3: .......... done
[123amd64-default-build-as-user-job-03] Extracting cmake-core-3.24.3_2: .......... 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
[123amd64-default-build-as-user-job-03] Installing ninja-1.11.1,2...
[123amd64-default-build-as-user-job-03] `-- Installing python39-3.9.15_1...
[123amd64-default-build-as-user-job-03] |   `-- Installing libffi-3.4.3...
[123amd64-default-build-as-user-job-03] |   `-- Extracting libffi-3.4.3: .......... done
[123amd64-default-build-as-user-job-03] |   `-- Installing mpdecimal-2.5.1...
[123amd64-default-build-as-user-job-03] |   `-- Extracting mpdecimal-2.5.1: .......... done
[123amd64-default-build-as-user-job-03] |   `-- Installing readline-8.1.2...
[123amd64-default-build-as-user-job-03] |   `-- Extracting readline-8.1.2: .......... done
[123amd64-default-build-as-user-job-03] `-- Extracting python39-3.9.15_1: .......... done
[123amd64-default-build-as-user-job-03] 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
[123amd64-default-build-as-user-job-03] Installing boost-libs-1.80.0_1...
[123amd64-default-build-as-user-job-03] `-- Installing icu-72.1,1...
[123amd64-default-build-as-user-job-03] `-- Extracting icu-72.1,1: .......... done
[123amd64-default-build-as-user-job-03] 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
[123amd64-default-build-as-user-job-03] Installing libcifpp-5.0.3...
[123amd64-default-build-as-user-job-03] `-- Installing bash-5.2.9...
[123amd64-default-build-as-user-job-03] `-- Extracting bash-5.2.9: .......... done
[123amd64-default-build-as-user-job-03] 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 10.0.1
-- Detecting CXX compiler ABI info
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-- 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
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-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
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-- 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") 
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CMake Warning:
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-- 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