Andrei-Florian Stoica
| Snapshot Date: 2025-11-11 13:45 -0500 (Tue, 11 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/CSOA |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9b11f08 |
| git_last_commit_date: 2025-10-29 11:37:44 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 486/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CSOA 1.0.0 (landing page) Andrei-Florian Stoica
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CSOA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CSOA.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. |
| Package: CSOA |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CSOA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CSOA_1.0.0.tar.gz |
| StartedAt: 2025-11-11 08:38:29 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 08:45:18 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 409.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CSOA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:CSOA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CSOA_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CSOA.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 ‘CSOA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CSOA’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘CSOA’ can be installed ... 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
scoreModules 10.240 0.140 10.406
runCSOA 7.637 0.164 7.822
scoreCells 7.716 0.016 7.752
featureWes 7.583 0.124 7.733
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
CSOA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL CSOA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘CSOA’ ... ** this is package ‘CSOA’ version ‘1.0.0’ ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CSOA)
CSOA.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(CSOA)
>
> test_check("CSOA")
Computing percentile sets...
Computing percentile sets...
Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
Also defined by 'alabaster.base'
Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
Also defined by 'alabaster.base'
Found more than one class "package_version" in cache; using the first, from namespace 'SeuratObject'
Also defined by 'alabaster.base'
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
194 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
194 overlaps have been selected for Jaccard-based filtering.
51 edges with low neighbor Jaccard scores have been removed.
27 edges with low neighbor Jaccard scores have been removed.
2 edges with low neighbor Jaccard scores have been removed.
114 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
194 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
159 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
113 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
194 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Saving pair scores file: pairsCSOA_acinar.qs...
Computing per-cell gene signature scores...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
105 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
248 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
258 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
244 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
Computing percentile sets...
Generating cell set overlaps...
38 overlaps will be used in the calculation of CSOA scores.
Computing percentile sets...
Generating cell set overlaps...
Processing overlaps...
7 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
5 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
9 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
5 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
11 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
3 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
9 overlaps will be used in the calculation of CSOA scores.
Normalizing expression matrix by rows...
Computing per-cell scores for gene pairs...
Computing per-cell gene signature scores...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
>
> proc.time()
user system elapsed
54.652 1.795 56.722
CSOA.Rcheck/CSOA-Ex.timings
| name | user | system | elapsed | |
| attachCellScores | 1.253 | 0.019 | 1.293 | |
| basicHeatmap | 0.495 | 0.008 | 0.507 | |
| breakWeakTies | 0.009 | 0.004 | 0.013 | |
| cellDistribution | 0.001 | 0.000 | 0.001 | |
| cellSetsOverlaps | 0.006 | 0.000 | 0.006 | |
| expMat | 0.939 | 0.052 | 0.994 | |
| featureWes | 7.583 | 0.124 | 7.733 | |
| geneRadialPlot | 0.837 | 0.055 | 0.900 | |
| generateOverlaps | 0.053 | 0.012 | 0.065 | |
| getPairs | 0 | 0 | 0 | |
| overlapCutoffPlot | 0.732 | 0.012 | 0.747 | |
| overlapGenes | 0.001 | 0.000 | 0.000 | |
| overlapNetworkPlot | 0.414 | 0.008 | 0.424 | |
| overlapPairs | 0.001 | 0.000 | 0.002 | |
| percentileSets | 0.014 | 0.002 | 0.016 | |
| processOverlaps | 0.016 | 0.001 | 0.018 | |
| qGrab | 0.020 | 0.004 | 0.031 | |
| runCSOA | 7.637 | 0.164 | 7.822 | |
| scoreCells | 7.716 | 0.016 | 7.752 | |
| scoreModules | 10.240 | 0.140 | 10.406 | |