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This page was generated on 2025-08-21 12:07 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4819
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4539
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 197/2318HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocSingular 1.25.0  (landing page)
Aaron Lun
Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 Aug 2025)
git_url: https://git.bioconductor.org/packages/BiocSingular
git_branch: devel
git_last_commit: 8400644
git_last_commit_date: 2025-04-15 11:41:16 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK 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: 1.25.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BiocSingular.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocSingular_1.25.0.tar.gz
StartedAt: 2025-08-19 05:17:17 -0000 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 06:03:13 -0000 (Tue, 19 Aug 2025)
EllapsedTime: 2756.3 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: BiocSingular.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BiocSingular.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocSingular_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocSingular.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocSingular/DESCRIPTION’ ... OK
* this is package ‘BiocSingular’ version ‘1.25.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BiocSingular’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'options.Rd':
  ‘blockGrid’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BiocSingularParam.Rd: DelayedMatrix-class, bpparam
  DeferredMatrix.Rd: ScaledMatrix-class
  LowRankMatrix.Rd: DelayedMatrix-class, DelayedArray
  options.Rd: irlba, rsvd, ScaledMatrix-class, blockGrid
  runExactSVD.Rd: BiocParallelParam-class
  runIrlbaSVD.Rd: irlba, BiocParallelParam-class
  runRandomSVD.Rd: rsvd, BiocParallelParam-class
  runSVD.Rd: BiocParallelParam-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ...

Installation output

BiocSingular.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BiocSingular
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BiocSingular’ ...
** this is package ‘BiocSingular’ version ‘1.25.0’
** 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-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/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-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/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-4.5.0/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:5,
                 from /home/biocbuild/R/R-4.5.0/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
                 from compute_scale.cpp:2:
/home/biocbuild/R/R-4.5.0/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-4.5.0/site-library/assorthead/include/tatami_stats/variances.hpp:98:29: 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
   98 | 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-4.5.0/lib -L/usr/local/lib -o BiocSingular.so RcppExports.o compute_scale.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)

Tests output


Example timings

BiocSingular.Rcheck/BiocSingular-Ex.timings

nameusersystemelapsed
BiocSingularParam0.0430.0560.160
LowRankMatrix0.1671.5208.157
runExactSVD0.0330.0060.197
runIrlbaSVD0.0240.0040.116
runPCA0.0920.0060.435
runRandomSVD0.1520.0070.402