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Cytolib install fails on github actions CI/CD for Ubuntu 22.04 (C++11?) #59

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FMKerckhof opened this issue Apr 30, 2024 · 1 comment
Open

Cytolib install fails on github actions CI/CD for Ubuntu 22.04 (C++11?) #59

FMKerckhof opened this issue Apr 30, 2024 · 1 comment

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@FMKerckhof
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Describe the bug

I am using github actions for CI/CD of a package that depends on cytolib. I am specifically specifying to use the github version (remotes::github::RGLab/cytolib) as a dependency in the DESCRIPTION file.

Windows and MacOS binary R CMD check succeed, but on Ubuntu 22.04 with R 4.3.3 I am observing a build error listed below.

2024-04-13T12:58:29.5751920Z * installing *source* package ‘cytolib’ ...
2024-04-13T12:58:29.5754222Z ** using staged installation
2024-04-13T12:58:29.9185594Z checking for a sed that does not truncate output... /usr/bin/sed
2024-04-13T12:58:30.0286921Z checking whether the C++ compiler works... yes
2024-04-13T12:58:30.0288306Z checking for C++ compiler default output file name... a.out
2024-04-13T12:58:30.0681681Z checking for suffix of executables... 
2024-04-13T12:58:30.1183968Z checking whether we are cross compiling... no
2024-04-13T12:58:30.1373322Z checking for suffix of object files... o
2024-04-13T12:58:30.1540567Z checking whether we are using the GNU C++ compiler... yes
2024-04-13T12:58:30.1699950Z checking whether g++ -std=gnu++17 accepts -g... yes
2024-04-13T12:58:30.1929642Z checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
2024-04-13T12:58:30.2354774Z checking whether we are using the GNU C++ compiler... (cached) yes
2024-04-13T12:58:30.2356448Z checking whether g++ -std=gnu++17 accepts -g... (cached) yes
2024-04-13T12:58:30.2357726Z configure: Parsing cytolib version info ...
2024-04-13T12:58:30.2389767Z configure: CYTOLIB_VERSION=2.12.1
2024-04-13T12:58:30.2562950Z configure: creating ./config.status
2024-04-13T12:58:30.3317539Z config.status: creating inst/include/cytolib/cytolibConfig.h
2024-04-13T12:58:30.3487525Z config.status: creating src/Makevars
2024-04-13T12:58:30.3909806Z ** libs
2024-04-13T12:58:30.4041392Z using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
2024-04-13T12:58:30.4042575Z using C++11
2024-04-13T12:58:30.4071008Z g++ -std=gnu++11 -I"/opt/R/4.3.3/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED  -I'/home/runner/work/_temp/Library/BH/include' -I'/home/runner/work/_temp/Library/RProtoBufLib/include' -I'/home/runner/work/_temp/Library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c dummy.cpp -o dummy.o
2024-04-13T12:58:30.4227164Z g++ -std=gnu++11 -I"/opt/R/4.3.3/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED  -I'/home/runner/work/_temp/Library/BH/include' -I'/home/runner/work/_temp/Library/RProtoBufLib/include' -I'/home/runner/work/_temp/Library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
2024-04-13T12:58:30.4566480Z g++ -std=gnu++11 -I"/opt/R/4.3.3/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED  -I'/home/runner/work/_temp/Library/BH/include' -I'/home/runner/work/_temp/Library/RProtoBufLib/include' -I'/home/runner/work/_temp/Library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
2024-04-13T12:58:30.8613720Z g++ -std=gnu++11 -I"/opt/R/4.3.3/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED  -I'/home/runner/work/_temp/Library/BH/include' -I'/home/runner/work/_temp/Library/RProtoBufLib/include' -I'/home/runner/work/_temp/Library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
2024-04-13T12:58:31.2679279Z boost/libs/filesystem/src/directory.cpp:100:13: error: no declaration matches ‘boost::filesystem::file_status boost::filesystem::directory_entry::get_status(boost::system::error_code*) const’
2024-04-13T12:58:31.2682355Z   100 | file_status directory_entry::get_status(system::error_code* ec) const
2024-04-13T12:58:31.2683488Z       |             ^~~~~~~~~~~~~~~
2024-04-13T12:58:31.2737103Z boost/libs/filesystem/src/directory.cpp:100:13: note: no functions named ‘boost::filesystem::file_status boost::filesystem::directory_entry::get_status(boost::system::error_code*) const’
2024-04-13T12:58:31.2739262Z In file included from boost/libs/filesystem/src/directory.cpp:18:
2024-04-13T12:58:31.2741706Z /home/runner/work/_temp/Library/BH/include/boost/filesystem/directory.hpp:65:7: note: ‘class boost::filesystem::directory_entry’ defined here
2024-04-13T12:58:31.2743369Z    65 | class directory_entry
2024-04-13T12:58:31.2743961Z       |       ^~~~~~~~~~~~~~~
2024-04-13T12:58:31.2746720Z boost/libs/filesystem/src/directory.cpp:127:13: error: no declaration matches ‘boost::filesystem::file_status boost::filesystem::directory_entry::get_symlink_status(boost::system::error_code*) const’
2024-04-13T12:58:31.2749194Z   127 | file_status directory_entry::get_symlink_status(system::error_code* ec) const
2024-04-13T12:58:31.2750206Z       |             ^~~~~~~~~~~~~~~
2024-04-13T12:58:31.2752728Z boost/libs/filesystem/src/directory.cpp:127:13: note: no functions named ‘boost::filesystem::file_status boost::filesystem::directory_entry::get_symlink_status(boost::system::error_code*) const’
2024-04-13T12:58:31.2754930Z In file included from boost/libs/filesystem/src/directory.cpp:18:
2024-04-13T12:58:31.2757342Z /home/runner/work/_temp/Library/BH/include/boost/filesystem/directory.hpp:65:7: note: ‘class boost::filesystem::directory_entry’ defined here
2024-04-13T12:58:31.2759011Z    65 | class directory_entry
2024-04-13T12:58:31.2759592Z       |       ^~~~~~~~~~~~~~~
2024-04-13T12:58:31.3245881Z make: *** [/opt/R/4.3.3/lib/R/etc/Makeconf:200: boost/libs/filesystem/src/directory.o] Error 1
2024-04-13T12:58:31.3252062Z ERROR: compilation failed for package ‘cytolib’

It appears that the error is the interface with boost (there are related issues, e.g. #49) Boost (BH) which is installed in by the github actions runner is 1.84.0-0, which should be compatible (887b8d8)

To Reproduce

I would assume any package depending on cytolib (like flowWorkspace etc.) should get a similar error with the same workflow?

Expected behavior

The build to pass on ubuntu 22.04, as it is LTS and I am using BH 1.84.0-0, which is also latest on CRAN?

SessionInfo:

cf. supra - as this is a github action I don't have an interactive session to run sessionInfo, but the necessary versions etc. should be provided
@FMKerckhof
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Maybe as additional context the runner is also installing:

  • RProtoBuflib 2.12.1
  • Rhd5lib 1.22.1

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@FMKerckhof