Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-01 11:35:48 -0400 (Wed, 01 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
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 297/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cellbaseR 1.28.0 (landing page) Mohammed OE Abdallah
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.28.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cellbaseR_1.28.0.tar.gz |
StartedAt: 2024-05-01 03:47:46 -0400 (Wed, 01 May 2024) |
EndedAt: 2024-05-01 03:50:10 -0400 (Wed, 01 May 2024) |
EllapsedTime: 143.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cellbaseR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cellbaseR_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cellbaseR.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘cellbaseR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘cellbaseR’ version ‘1.28.0’ * 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 4.11 0.951 6.623 * 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-3.19-bioc/R/bin/R CMD INSTALL cellbaseR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 | 4.110 | 0.951 | 6.623 | |
CellBaseParam | 0.002 | 0.001 | 0.002 | |
CellBaseR | 0.024 | 0.000 | 0.177 | |
createGeneModel | 0.195 | 0.028 | 0.474 | |
getCellBase-CellBaseR-method | 0.050 | 0.004 | 0.215 | |
getCellBaseResourceHelp | 0.213 | 0.020 | 1.541 | |
getChromosomeInfo-CellBaseR-method | 0.040 | 0.008 | 0.306 | |
getClinical-CellBaseR-method | 0.413 | 0.044 | 0.665 | |
getConservationByRegion | 0.058 | 0.000 | 0.235 | |
getGene-CellBaseR-method | 0.221 | 0.009 | 0.475 | |
getGeneInfo | 0.056 | 0.000 | 0.218 | |
getMeta-CellBaseR-method | 0.047 | 0.000 | 0.202 | |
getProtein-CellBaseR-method | 0.145 | 0.008 | 0.319 | |
getProteinInfo | 0.095 | 0.008 | 0.264 | |
getRegion-CellBaseR-method | 0.137 | 0.011 | 0.332 | |
getRegulatoryByRegion | 0.036 | 0.000 | 0.192 | |
getTranscript-CellBaseR-method | 0.060 | 0.004 | 0.223 | |
getTranscriptByGene | 0.056 | 0.000 | 0.216 | |
getVariant-CellBaseR-method | 0.124 | 0.000 | 0.294 | |
getVariantAnnotation | 0.104 | 0.008 | 0.280 | |
getXref-CellBaseR-method | 0.040 | 0.000 | 0.205 | |