Multiple platform build/check report for BioC 3.21 - BUILD results for scGPS 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"	4749
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4461
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4411
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4366
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4276
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*

BUILD results for scGPS on kunpeng2

To the developers/maintainers of the scGPS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scGPS.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: scGPS

Version: 1.21.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data scGPS

StartedAt: 2024-12-09 21:05:13 -0000 (Mon, 09 Dec 2024)

EndedAt: 2024-12-09 21:06:08 -0000 (Mon, 09 Dec 2024)

EllapsedTime: 54.1 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data scGPS
###
##############################################################################
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* checking for file ‘scGPS/DESCRIPTION’ ... OK
* preparing ‘scGPS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘scGPS’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c dist_mat_cpp.cpp -o dist_mat_cpp.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c dist_parallel_cpp.cpp -o dist_parallel_cpp.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c utils_rcpp.cpp -o utils_rcpp.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o scGPS.so RcppExports.o dist_mat_cpp.o dist_parallel_cpp.o utils_rcpp.o -lopenblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/tmp/RtmpMjZCUF/Rinst8d4c620f42979/00LOCK-scGPS/00new/scGPS/libs
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so':
  /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/libs/Rcpp.so)
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘scGPS’
* removing ‘/home/biocbuild/tmp/RtmpMjZCUF/Rinst8d4c620f42979/scGPS’
      -----------------------------------
ERROR: package installation failed