Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 490/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cytolib 2.18.0 (landing page) Mike Jiang
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
To the developers/maintainers of the cytolib package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cytolib.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: cytolib |
Version: 2.18.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 cytolib |
StartedAt: 2024-12-19 16:47:59 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 16:48:03 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 4.0 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 cytolib ### ############################################################################## ############################################################################## * checking for file ‘cytolib/DESCRIPTION’ ... OK * preparing ‘cytolib’: * checking DESCRIPTION meta-information ... OK * cleaning src * running ‘cleanup’ * installing the package to build vignettes ----------------------------------- * installing *source* package ‘cytolib’ ... ** using staged installation checking for a sed that does not truncate output... /usr/bin/sed checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++17 accepts -g... yes checking how to run the C++ preprocessor... g++ -std=gnu++17 -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ -std=gnu++17 accepts -g... (cached) yes configure: Parsing cytolib version info ... configure: CYTOLIB_VERSION=2.18.0 configure: creating ./config.status config.status: creating inst/include/cytolib/cytolibConfig.h config.status: creating src/Makevars ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c dummy.cpp -o dummy.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DROUT -I../inst/include -w -Wfatal-errors -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RProtoBufLib/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o boost/libs/filesystem/src/directory.cpp: In function ‘void boost::filesystem::detail::directory_iterator_construct(boost::filesystem::directory_iterator&, const boost::filesystem::path&, unsigned int, directory_iterator_params*, boost::system::error_code*)’: boost/libs/filesystem/src/directory.cpp:1055:17: error: ‘void boost::filesystem::directory_entry::assign_with_status(boost::filesystem::path&&, boost::filesystem::file_status, boost::filesystem::file_status)’ is private within this context 1054 | imp->dir_entry.assign_with_status | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1055 | ( | ^ 1056 | #if !defined(BOOST_NO_CXX11_RVALUE_REFERENCES) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1057 | static_cast< path&& >(full_path), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1058 | #else | ~~~~~ 1059 | full_path, | ~~~~~~~~~~ 1060 | #endif | ~~~~~~ 1061 | file_stat, | ~~~~~~~~~~ 1062 | symlink_file_stat | ~~~~~~~~~~~~~~~~~ 1063 | ); | ~ compilation terminated due to -Wfatal-errors. make: *** [/home/biocbuild/bbs-3.20-bioc/R/etc/Makeconf:202: boost/libs/filesystem/src/directory.o] Error 1 ERROR: compilation failed for package ‘cytolib’ * removing ‘/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpxbX1Kn/Rinst24b8987521bbf2/cytolib’ ----------------------------------- ERROR: package installation failed