Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:05 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 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 262/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEfightR 1.24.0 (landing page) Malte Thodberg
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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: 1.24.0 |
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_1.24.0.tar.gz |
StartedAt: 2024-07-22 01:50:29 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 02:05:30 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 901.0 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CAGEfightR.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAGEfightR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAGEfightR’ version ‘1.24.0’ * 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 9.032 1.251 11.235 calcShape 6.862 0.432 8.836 assignGeneID 6.609 0.217 8.400 trackCTSS 6.382 0.368 8.064 trimToPercentiles 4.886 0.124 6.006 * 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 | 6.609 | 0.217 | 8.400 | |
assignMissingID | 2.103 | 0.053 | 2.593 | |
assignTxID | 1.863 | 0.051 | 2.623 | |
assignTxType | 0.001 | 0.001 | 0.002 | |
balanceBC | 0.001 | 0.001 | 0.002 | |
balanceD | 0.001 | 0.001 | 0.001 | |
bwCommonGenome | 0.080 | 0.009 | 0.121 | |
bwGenomeCompatibility | 0.038 | 0.005 | 0.056 | |
bwValid | 0.018 | 0.006 | 0.032 | |
calcBidirectionality | 0.994 | 0.031 | 1.529 | |
calcComposition | 2.876 | 0.060 | 3.659 | |
calcPooled | 0.229 | 0.021 | 0.306 | |
calcShape | 6.862 | 0.432 | 8.836 | |
calcSupport | 0.215 | 0.006 | 0.272 | |
calcTPM | 0.257 | 0.007 | 0.312 | |
calcTotalTags | 0.111 | 0.007 | 0.137 | |
checkCTSSs | 0.582 | 0.011 | 0.706 | |
checkPeaked | 0.136 | 0.007 | 0.172 | |
checkPooled | 0.171 | 0.013 | 0.225 | |
clusterBidirectionally | 0.000 | 0.000 | 0.001 | |
clusterUnidirectionally | 3.306 | 0.037 | 3.990 | |
combineClusters | 1.821 | 0.026 | 2.205 | |
convertBAM2BigWig | 0.000 | 0.001 | 0.000 | |
convertBED2BigWig | 0.001 | 0.001 | 0.002 | |
convertGRanges2GPos | 0.168 | 0.002 | 0.204 | |
exampleDesign | 0.010 | 0.017 | 0.032 | |
findLinks | 9.032 | 1.251 | 11.235 | |
findStretches | 0.96 | 0.16 | 1.34 | |
quantifyCTSSs | 0.000 | 0.002 | 0.003 | |
quantifyCTSSs2 | 0.001 | 0.002 | 0.001 | |
quantifyClusters | 0.865 | 0.118 | 1.171 | |
quantifyGenes | 2.634 | 0.251 | 3.446 | |
quickEnhancers | 0.000 | 0.001 | 0.000 | |
quickGenes | 0.001 | 0.001 | 0.001 | |
quickTSSs | 0.000 | 0.000 | 0.004 | |
shapeEntropy | 0.001 | 0.001 | 0.002 | |
shapeIQR | 0.001 | 0.000 | 0.002 | |
shapeMean | 0.002 | 0.001 | 0.004 | |
shapeMultimodality | 0 | 0 | 0 | |
subsetByBidirectionality | 0.968 | 0.049 | 1.221 | |
subsetByComposition | 2.586 | 0.056 | 3.142 | |
subsetBySupport | 0.191 | 0.025 | 0.252 | |
swapRanges | 0.333 | 0.014 | 0.413 | |
swapScores | 0.207 | 0.012 | 0.262 | |
trackBalance | 0.000 | 0.001 | 0.001 | |
trackCTSS | 6.382 | 0.368 | 8.064 | |
trackClusters | 3.802 | 0.052 | 4.754 | |
trackLinks | 2.260 | 0.618 | 3.061 | |
trimToPeak | 2.036 | 0.283 | 2.779 | |
trimToPercentiles | 4.886 | 0.124 | 6.006 | |
tuneTagClustering | 0.001 | 0.001 | 0.002 | |
utilsAggregateRows | 0.811 | 1.156 | 2.340 | |
utilsDeStrand | 0.273 | 0.008 | 0.325 | |
utilsScoreOverlaps | 0.154 | 0.003 | 0.193 | |
utilsSimplifyTxDb | 0.000 | 0.000 | 0.002 | |