Back to Multiple platform build/check report for BioC 3.20: simplified long |
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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 264/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEfightR 1.26.0 (landing page) Malte Thodberg
| 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 CAGEfightR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEfightR.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: CAGEfightR |
Version: 1.26.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEfightR_1.26.0.tar.gz |
StartedAt: 2024-12-20 00:40:25 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 00:53:13 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 768.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CAGEfightR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEfightR_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAGEfightR.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 ‘CAGEfightR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAGEfightR’ version ‘1.26.0’ * 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 ‘CAGEfightR’ 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 whether startup messages can be suppressed ... 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 findLinks 8.924 1.242 9.553 calcShape 7.884 0.435 8.390 assignGeneID 6.636 0.198 7.151 trackCTSS 6.365 0.360 6.825 * 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
CAGEfightR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEfightR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘CAGEfightR’ ... ** 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 (CAGEfightR)
CAGEfightR.Rcheck/CAGEfightR-Ex.timings
name | user | system | elapsed | |
assignGeneID | 6.636 | 0.198 | 7.151 | |
assignMissingID | 2.074 | 0.060 | 2.157 | |
assignTxID | 1.807 | 0.043 | 1.867 | |
assignTxType | 0.001 | 0.002 | 0.002 | |
balanceBC | 0.001 | 0.000 | 0.004 | |
balanceD | 0.001 | 0.001 | 0.001 | |
bwCommonGenome | 0.083 | 0.011 | 0.104 | |
bwGenomeCompatibility | 0.039 | 0.007 | 0.047 | |
bwValid | 0.017 | 0.005 | 0.022 | |
calcBidirectionality | 0.925 | 0.018 | 0.951 | |
calcComposition | 2.857 | 0.053 | 2.928 | |
calcPooled | 0.207 | 0.007 | 0.215 | |
calcShape | 7.884 | 0.435 | 8.390 | |
calcSupport | 0.209 | 0.008 | 0.219 | |
calcTPM | 0.252 | 0.006 | 0.260 | |
calcTotalTags | 0.111 | 0.006 | 0.118 | |
checkCTSSs | 0.558 | 0.010 | 0.574 | |
checkPeaked | 0.127 | 0.007 | 0.133 | |
checkPooled | 0.119 | 0.006 | 0.127 | |
clusterBidirectionally | 0.000 | 0.001 | 0.001 | |
clusterUnidirectionally | 3.186 | 0.042 | 3.256 | |
combineClusters | 1.732 | 0.018 | 1.779 | |
convertBAM2BigWig | 0.000 | 0.001 | 0.000 | |
convertBED2BigWig | 0.000 | 0.002 | 0.002 | |
convertGRanges2GPos | 0.174 | 0.001 | 0.177 | |
exampleDesign | 0.009 | 0.017 | 0.027 | |
findLinks | 8.924 | 1.242 | 9.553 | |
findStretches | 0.959 | 0.160 | 1.232 | |
quantifyCTSSs | 0.001 | 0.002 | 0.002 | |
quantifyCTSSs2 | 0.000 | 0.001 | 0.002 | |
quantifyClusters | 0.850 | 0.116 | 0.971 | |
quantifyGenes | 2.595 | 0.264 | 2.936 | |
quickEnhancers | 0 | 0 | 0 | |
quickGenes | 0.000 | 0.001 | 0.001 | |
quickTSSs | 0.000 | 0.001 | 0.000 | |
shapeEntropy | 0.001 | 0.000 | 0.002 | |
shapeIQR | 0.001 | 0.001 | 0.002 | |
shapeMean | 0.001 | 0.001 | 0.002 | |
shapeMultimodality | 0.000 | 0.000 | 0.001 | |
subsetByBidirectionality | 0.964 | 0.070 | 1.129 | |
subsetByComposition | 2.634 | 0.070 | 2.827 | |
subsetBySupport | 0.177 | 0.014 | 0.192 | |
swapRanges | 0.343 | 0.016 | 0.361 | |
swapScores | 0.225 | 0.012 | 0.238 | |
trackBalance | 0.000 | 0.001 | 0.002 | |
trackCTSS | 6.365 | 0.360 | 6.825 | |
trackClusters | 3.775 | 0.045 | 3.860 | |
trackLinks | 2.258 | 0.594 | 2.577 | |
trimToPeak | 1.947 | 0.247 | 2.234 | |
trimToPercentiles | 4.785 | 0.088 | 4.942 | |
tuneTagClustering | 0.001 | 0.001 | 0.002 | |
utilsAggregateRows | 0.814 | 1.158 | 2.000 | |
utilsDeStrand | 0.272 | 0.007 | 0.281 | |
utilsScoreOverlaps | 0.155 | 0.002 | 0.162 | |
utilsSimplifyTxDb | 0.000 | 0.001 | 0.001 | |