Multiple platform build/check report for BioC 3.20 - INSTALL results for cytolib on nebbiolo2

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*

INSTALL results for cytolib on nebbiolo2

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.

raw results

Summary

Package: cytolib

Version: 2.18.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cytolib

StartedAt: 2024-12-19 15:08:16 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 15:08:26 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 10.0 seconds

RetCode: 1

Status: ERROR

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cytolib
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* 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/R/site-library/cytolib’
* restoring previous ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/cytolib’