Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 298/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cellbaseR 1.30.0 (landing page) Mohammed OE Abdallah
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
Package: cellbaseR |
Version: 1.30.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cellbaseR_1.30.0.tar.gz |
StartedAt: 2024-12-19 21:10:34 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 21:16:19 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 345.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cellbaseR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cellbaseR_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cellbaseR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘cellbaseR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cellbaseR’ version ‘1.30.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 3.476 0.809 5.879 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
cellbaseR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cellbaseR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘cellbaseR’ ... ** 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)
cellbaseR.Rcheck/cellbaseR-Ex.timings
name | user | system | elapsed | |
AnnotateVcf-CellBaseR-method | 3.476 | 0.809 | 5.879 | |
CellBaseParam | 0.002 | 0.000 | 0.002 | |
CellBaseR | 0.026 | 0.006 | 0.186 | |
createGeneModel | 0.244 | 0.014 | 0.509 | |
getCellBase-CellBaseR-method | 0.068 | 0.002 | 0.232 | |
getCellBaseResourceHelp | 0.226 | 0.007 | 1.577 | |
getChromosomeInfo-CellBaseR-method | 0.042 | 0.001 | 0.277 | |
getClinical-CellBaseR-method | 0.409 | 0.023 | 0.634 | |
getConservationByRegion | 0.055 | 0.001 | 0.228 | |
getGene-CellBaseR-method | 0.216 | 0.000 | 0.471 | |
getGeneInfo | 0.055 | 0.003 | 0.219 | |
getMeta-CellBaseR-method | 0.066 | 0.001 | 0.224 | |
getProtein-CellBaseR-method | 0.146 | 0.004 | 0.326 | |
getProteinInfo | 0.107 | 0.014 | 0.283 | |
getRegion-CellBaseR-method | 0.150 | 0.018 | 0.342 | |
getRegulatoryByRegion | 0.026 | 0.002 | 0.187 | |
getTranscript-CellBaseR-method | 0.047 | 0.002 | 0.210 | |
getTranscriptByGene | 0.067 | 0.002 | 0.232 | |
getVariant-CellBaseR-method | 0.083 | 0.003 | 0.258 | |
getVariantAnnotation | 0.070 | 0.002 | 0.244 | |
getXref-CellBaseR-method | 0.034 | 0.001 | 0.197 | |