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This page was generated on 2025-01-09 12:10 -0500 (Thu, 09 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4358
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 194/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSingular 1.22.0  (landing page)
Aaron Lun
Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025)
git_url: https://git.bioconductor.org/packages/BiocSingular
git_branch: RELEASE_3_20
git_last_commit: aa0f642
git_last_commit_date: 2024-10-29 10:34:47 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

INSTALL results for BiocSingular on taishan

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: 1.22.0
Command: /home/biocbuild/R/R/bin/R CMD INSTALL BiocSingular
StartedAt: 2025-01-08 20:49:47 -0000 (Wed, 08 Jan 2025)
EndedAt: 2025-01-08 20:50:25 -0000 (Wed, 08 Jan 2025)
EllapsedTime: 37.5 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-4.4.2/site-library’
* installing *source* package ‘BiocSingular’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.2/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c compute_scale.cpp -o compute_scale.o
In file included from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6,
                 from /home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
                 from compute_scale.cpp:2:
/home/biocbuild/R/R-4.4.2/site-library/assorthead/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:112:66:   required from here
  112 |                     auto paired = tatami_stats::variances::direct(range.value, range.number, NR, false);
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.2/site-library/assorthead/include/tatami_stats/variances.hpp:95:29: 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
   95 | std::pair<Output_, Output_> direct(const Value_* value, Index_ num_nonzero, Index_ num_all, bool skip_nan) {
      |                             ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o BiocSingular.so RcppExports.o compute_scale.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.4.2/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)