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This page was generated on 2025-10-01 12:07 -0400 (Wed, 01 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4575
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 302/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellbaseR 1.33.0  (landing page)
Mohammed OE Abdallah
Snapshot Date: 2025-09-30 13:45 -0400 (Tue, 30 Sep 2025)
git_url: https://git.bioconductor.org/packages/cellbaseR
git_branch: devel
git_last_commit: 551305d
git_last_commit_date: 2025-04-15 11:10:49 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for cellbaseR on taishan

To the developers/maintainers of the cellbaseR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellbaseR.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: cellbaseR
Version: 1.33.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cellbaseR_1.33.0.tar.gz
StartedAt: 2025-09-30 06:41:18 -0000 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 06:43:28 -0000 (Tue, 30 Sep 2025)
EllapsedTime: 130.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cellbaseR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cellbaseR_1.33.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cellbaseR.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 ‘cellbaseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellbaseR’ version ‘1.33.0’
* 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 ‘cellbaseR’ 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
AnnotateVcf-CellBaseR-method 4.242  0.893    6.36
* 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


Installation output

cellbaseR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL cellbaseR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘cellbaseR’ ...
** this is package ‘cellbaseR’ version ‘1.33.0’
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cellbaseR)

Tests output


Example timings

cellbaseR.Rcheck/cellbaseR-Ex.timings

nameusersystemelapsed
AnnotateVcf-CellBaseR-method4.2420.8936.360
CellBaseParam0.0030.0000.003
CellBaseR0.0260.0080.357
createGeneModel0.2840.0480.846
getCellBase-CellBaseR-method0.0720.0280.432
getCellBaseResourceHelp0.1550.0241.500
getChromosomeInfo-CellBaseR-method0.0410.0010.531
getClinical-CellBaseR-method0.5460.0120.920
getConservationByRegion0.0560.0000.393
getGene-CellBaseR-method0.2360.0360.781
getGeneInfo0.0710.0080.410
getMeta-CellBaseR-method0.0470.0000.373
getProtein-CellBaseR-method0.1220.0000.455
getProteinInfo0.1160.0040.452
getRegion-CellBaseR-method0.1750.0040.684
getRegulatoryByRegion0.0350.0040.367
getTranscript-CellBaseR-method0.0460.0000.378
getTranscriptByGene0.0430.0040.381
getVariant-CellBaseR-method0.0820.0040.428
getVariantAnnotation0.0820.0030.427
getXref-CellBaseR-method0.0340.0010.367