Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -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 266/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEr 2.12.0 (landing page) Charles Plessy
| 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 CAGEr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.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: CAGEr |
Version: 2.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.12.0.tar.gz |
StartedAt: 2024-12-20 00:41:37 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:04:06 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1349.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CAGEr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAGEr.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAGEr/DESCRIPTION’ ... OK * this is package ‘CAGEr’ version ‘2.12.0’ * 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 ‘CAGEr’ 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 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed paraclu 123.504 0.403 126.873 exportToTrack 103.219 0.439 104.982 aggregateTagClusters 57.231 0.379 58.692 scoreShift 45.469 0.409 46.585 quantilePositions 35.782 0.099 36.240 annotateCTSS 35.240 0.178 36.109 distclu 26.243 0.082 26.476 plotExpressionProfiles 18.415 0.162 18.934 getExpressionProfiles 15.074 0.069 15.374 CustomConsensusClusters 13.502 0.072 13.777 CAGEexp-class 8.998 1.332 10.465 cumulativeCTSSdistribution 9.523 0.070 9.751 TSSlogo 6.911 0.086 7.178 plotReverseCumulatives 5.937 0.046 6.002 consensusClustersDESeq2 5.917 0.026 6.014 plotAnnot 5.742 0.082 6.103 mergeCAGEsets 5.743 0.048 5.892 getShiftingPromoters 5.483 0.022 5.606 expressionClasses 5.455 0.016 5.502 plotInterquantileWidth 5.237 0.024 5.288 * 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
CAGEr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘CAGEr’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (CAGEr)
CAGEr.Rcheck/CAGEr-Ex.timings
name | user | system | elapsed | |
CAGEexp-class | 8.998 | 1.332 | 10.465 | |
CAGEr_Multicore | 4.235 | 0.016 | 4.260 | |
CTSS-class | 0.642 | 0.004 | 0.647 | |
CTSScoordinates | 0.196 | 0.007 | 0.204 | |
CTSSnormalizedTpm | 1.829 | 0.047 | 1.884 | |
CTSStagCount | 1.818 | 0.214 | 2.045 | |
CTSStoGenes | 1.123 | 0.106 | 1.240 | |
CustomConsensusClusters | 13.502 | 0.072 | 13.777 | |
GeneExpDESeq2 | 1.204 | 0.022 | 1.236 | |
GeneExpSE | 0.009 | 0.001 | 0.010 | |
QuantileWidthFunctions | 0.386 | 0.003 | 0.392 | |
TSSlogo | 6.911 | 0.086 | 7.178 | |
aggregateTagClusters | 57.231 | 0.379 | 58.692 | |
annotateCTSS | 35.240 | 0.178 | 36.109 | |
byCtss | 0.028 | 0.001 | 0.031 | |
consensusClusters | 0.382 | 0.008 | 0.395 | |
consensusClustersDESeq2 | 5.917 | 0.026 | 6.014 | |
consensusClustersTpm | 0.014 | 0.001 | 0.015 | |
cumulativeCTSSdistribution | 9.523 | 0.070 | 9.751 | |
distclu | 26.243 | 0.082 | 26.476 | |
dot-ctss_summary_for_clusters | 2.134 | 0.014 | 2.151 | |
exampleCAGEexp | 0.000 | 0.002 | 0.003 | |
exportToTrack | 103.219 | 0.439 | 104.982 | |
expressionClasses | 5.455 | 0.016 | 5.502 | |
filteredCTSSidx | 0.024 | 0.000 | 0.025 | |
flagLowExpCTSS | 0.087 | 0.001 | 0.089 | |
genomeName | 0.000 | 0.000 | 0.002 | |
getCTSS | 2.534 | 0.028 | 2.584 | |
getExpressionProfiles | 15.074 | 0.069 | 15.374 | |
getShiftingPromoters | 5.483 | 0.022 | 5.606 | |
hanabi | 0.530 | 0.006 | 0.581 | |
hanabiPlot | 0.658 | 0.022 | 0.683 | |
import.CAGEscanMolecule | 0.000 | 0.001 | 0.001 | |
import.CTSS | 0.196 | 0.003 | 0.201 | |
import.bam | 0.000 | 0.001 | 0.000 | |
import.bedCTSS | 0.000 | 0.000 | 0.001 | |
import.bedScore | 0.000 | 0.001 | 0.001 | |
import.bedmolecule | 0 | 0 | 0 | |
importPublicData | 0.001 | 0.002 | 0.003 | |
inputFiles | 0.003 | 0.001 | 0.003 | |
inputFilesType | 0.002 | 0.000 | 0.003 | |
librarySizes | 0.003 | 0.001 | 0.003 | |
mapStats | 0.131 | 0.010 | 0.142 | |
mergeCAGEsets | 5.743 | 0.048 | 5.892 | |
mergeSamples | 1.417 | 0.012 | 1.442 | |
moleculesGR2CTSS | 0.323 | 0.002 | 0.326 | |
normalizeTagCount | 1.399 | 0.015 | 1.423 | |
paraclu | 123.504 | 0.403 | 126.873 | |
parseCAGEscanBlocksToGrangeTSS | 0.056 | 0.001 | 0.058 | |
plotAnnot | 5.742 | 0.082 | 6.103 | |
plotCorrelation | 0.681 | 0.012 | 0.716 | |
plotExpressionProfiles | 18.415 | 0.162 | 18.934 | |
plotInterquantileWidth | 5.237 | 0.024 | 5.288 | |
plotReverseCumulatives | 5.937 | 0.046 | 6.002 | |
quantilePositions | 35.782 | 0.099 | 36.240 | |
quickEnhancers | 0.000 | 0.001 | 0.001 | |
ranges2annot | 0.902 | 0.005 | 0.913 | |
ranges2genes | 0.138 | 0.001 | 0.139 | |
ranges2names | 0.139 | 0.002 | 0.142 | |
resetCAGEexp | 0.878 | 0.005 | 0.886 | |
rowSums.RleDataFrame | 0.052 | 0.001 | 0.054 | |
rowsum.RleDataFrame | 0.059 | 0.004 | 0.062 | |
sampleLabels | 0.009 | 0.001 | 0.010 | |
scoreShift | 45.469 | 0.409 | 46.585 | |
seqNameTotalsSE | 0.008 | 0.000 | 0.010 | |
setColors | 0.972 | 0.008 | 0.985 | |
strandInvaders | 1.671 | 0.144 | 1.850 | |
summariseChrExpr | 1.198 | 0.008 | 1.214 | |
tagClusters | 1.041 | 0.016 | 1.064 | |