Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 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: 2024-06-24 13:27:20 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 13:34:54 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 454.2 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 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAGEfightR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CAGEfightR’ version ‘1.24.0’ * 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 8.077 0.781 8.43 * 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-arm64/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 | 3.605 | 0.095 | 3.745 | |
assignMissingID | 1.192 | 0.054 | 1.247 | |
assignTxID | 1.142 | 0.038 | 1.180 | |
assignTxType | 0.000 | 0.000 | 0.001 | |
balanceBC | 0.000 | 0.000 | 0.001 | |
balanceD | 0.000 | 0.000 | 0.001 | |
bwCommonGenome | 0.039 | 0.006 | 0.047 | |
bwGenomeCompatibility | 0.019 | 0.004 | 0.023 | |
bwValid | 0.009 | 0.004 | 0.013 | |
calcBidirectionality | 0.488 | 0.017 | 0.505 | |
calcComposition | 1.610 | 0.047 | 1.657 | |
calcPooled | 0.105 | 0.012 | 0.117 | |
calcShape | 2.467 | 0.138 | 2.624 | |
calcSupport | 0.139 | 0.005 | 0.147 | |
calcTPM | 0.148 | 0.006 | 0.155 | |
calcTotalTags | 0.090 | 0.005 | 0.095 | |
checkCTSSs | 0.272 | 0.008 | 0.286 | |
checkPeaked | 0.087 | 0.005 | 0.091 | |
checkPooled | 0.104 | 0.010 | 0.115 | |
clusterBidirectionally | 0.000 | 0.001 | 0.001 | |
clusterUnidirectionally | 1.384 | 0.028 | 1.432 | |
combineClusters | 0.749 | 0.018 | 0.779 | |
convertBAM2BigWig | 0 | 0 | 0 | |
convertBED2BigWig | 0.001 | 0.001 | 0.000 | |
convertGRanges2GPos | 0.077 | 0.000 | 0.078 | |
exampleDesign | 0.004 | 0.013 | 0.018 | |
findLinks | 8.077 | 0.781 | 8.430 | |
findStretches | 0.389 | 0.108 | 0.498 | |
quantifyCTSSs | 0.000 | 0.000 | 0.001 | |
quantifyCTSSs2 | 0 | 0 | 0 | |
quantifyClusters | 0.473 | 0.135 | 0.609 | |
quantifyGenes | 1.453 | 0.179 | 1.633 | |
quickEnhancers | 0 | 0 | 0 | |
quickGenes | 0 | 0 | 0 | |
quickTSSs | 0.001 | 0.000 | 0.000 | |
shapeEntropy | 0.000 | 0.001 | 0.000 | |
shapeIQR | 0.000 | 0.000 | 0.001 | |
shapeMean | 0.001 | 0.000 | 0.001 | |
shapeMultimodality | 0 | 0 | 0 | |
subsetByBidirectionality | 0.449 | 0.043 | 0.493 | |
subsetByComposition | 1.350 | 0.054 | 1.406 | |
subsetBySupport | 0.067 | 0.011 | 0.079 | |
swapRanges | 0.227 | 0.014 | 0.242 | |
swapScores | 0.096 | 0.010 | 0.106 | |
trackBalance | 0.000 | 0.000 | 0.001 | |
trackCTSS | 3.925 | 0.290 | 4.215 | |
trackClusters | 2.565 | 0.043 | 2.608 | |
trackLinks | 0.964 | 0.437 | 1.183 | |
trimToPeak | 0.707 | 0.161 | 0.869 | |
trimToPercentiles | 1.723 | 0.077 | 1.799 | |
tuneTagClustering | 0.000 | 0.000 | 0.001 | |
utilsAggregateRows | 0.419 | 0.376 | 0.797 | |
utilsDeStrand | 0.115 | 0.004 | 0.119 | |
utilsScoreOverlaps | 0.061 | 0.001 | 0.063 | |
utilsSimplifyTxDb | 0 | 0 | 0 | |