Multiple platform build/check report for BioC 3.20 - INSTALL results for BiocSingular on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4693
palomino6	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4409
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"	4407
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"	4356
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.0 (2024-04-24) -- "Puppy Cup"	4407
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 BiocSingular on kunpeng2

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

Version: 1.21.1

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

StartedAt: 2024-06-30 20:02:20 -0000 (Sun, 30 Jun 2024)

EndedAt: 2024-06-30 20:03:08 -0000 (Sun, 30 Jun 2024)

EllapsedTime: 47.5 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL BiocSingular
###
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* installing to library ‘/home/biocbuild/R/R-4.4.0/site-library’
* installing *source* package ‘BiocSingular’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.0/site-library/beachmat/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c compute_scale.cpp -o compute_scale.o
compute_scale.cpp: In function ‘Rcpp::List compute_center_and_scale(Rcpp::RObject, int)’:
compute_scale.cpp:45:21: warning: unused variable ‘iptr’ [-Wunused-variable]
   45 |             double* iptr;
      |                     ^~~~
In file included from /home/biocbuild/R/R-4.4.0/site-library/beachmat/include/tatami_stats/tatami_stats.hpp:11,
                 from compute_scale.cpp:2:
/home/biocbuild/R/R-4.4.0/site-library/beachmat/include/tatami_stats/variances.hpp: In instantiation of ‘std::pair<_FIter, _FIter> tatami_stats::variances::direct(const Value_*, Index_, Index_, bool) [with Output_ = double; Value_ = double; Index_ = int]’:
compute_scale.cpp:113:103:   required from here
/home/biocbuild/R/R-4.4.0/site-library/beachmat/include/tatami_stats/variances.hpp:86:29: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
   86 | std::pair<Output_, Output_> direct(const Value_* value, Index_ num_nonzero, Index_ num_all, bool skip_nan) {
      |                             ^~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.0/lib -L/usr/local/lib -o BiocSingular.so RcppExports.o compute_scale.o -L/home/biocbuild/R/R-4.4.0/lib -lR
installing to /home/biocbuild/R/R-4.4.0/site-library/00LOCK-BiocSingular/00new/BiocSingular/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocSingular)