Multiple platform build/check report for BioC 3.21 - INSTALL results for cytolib on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4372
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 kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: cytolib

Version: 2.19.0

Command: /home/biocbuild/R/R/bin/R CMD INSTALL cytolib

StartedAt: 2024-12-22 19:48:18 -0000 (Sun, 22 Dec 2024)

EndedAt: 2024-12-22 19:48:42 -0000 (Sun, 22 Dec 2024)

EllapsedTime: 23.9 seconds

RetCode: 1

Status: ERROR

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL cytolib
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 accepts -g... (cached) yes
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.19.0
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/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/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c dummy.cpp -o dummy.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/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/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/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/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/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/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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/R/R/etc/Makeconf:204: boost/libs/filesystem/src/directory.o] Error 1
ERROR: compilation failed for package ‘cytolib’
* removing ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib’
* restoring previous ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib’