Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-06 11:42 -0400 (Sat, 06 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4391 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 3833 |
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 261/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEr 2.11.3 (landing page) Charles Plessy
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 2.11.3 |
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_2.11.3.tar.gz |
StartedAt: 2024-07-05 22:15:58 -0400 (Fri, 05 Jul 2024) |
EndedAt: 2024-07-05 22:21:02 -0400 (Fri, 05 Jul 2024) |
EllapsedTime: 303.9 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_2.11.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CAGEr.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAGEr/DESCRIPTION’ ... OK * this is package ‘CAGEr’ version ‘2.11.3’ * 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 14.789 0.070 17.569 exportToTrack 12.299 0.052 14.743 aggregateTagClusters 7.440 0.060 8.899 scoreShift 6.237 0.046 7.472 quantilePositions 5.438 0.061 6.547 annotateCTSS 4.211 0.014 5.045 * 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-arm64/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 | 2.136 | 0.250 | 2.881 | |
CAGEr_Multicore | 2.056 | 0.004 | 2.518 | |
CTSS-class | 0.083 | 0.001 | 0.109 | |
CTSScoordinates | 0.028 | 0.001 | 0.031 | |
CTSSnormalizedTpm | 0.264 | 0.009 | 0.331 | |
CTSStagCount | 0.233 | 0.020 | 0.311 | |
CTSStoGenes | 0.166 | 0.011 | 0.204 | |
CustomConsensusClusters | 1.639 | 0.033 | 2.023 | |
GeneExpDESeq2 | 0.194 | 0.005 | 0.235 | |
GeneExpSE | 0.001 | 0.000 | 0.002 | |
QuantileWidthFunctions | 0.055 | 0.000 | 0.071 | |
TSSlogo | 0.875 | 0.016 | 1.025 | |
aggregateTagClusters | 7.440 | 0.060 | 8.899 | |
annotateCTSS | 4.211 | 0.014 | 5.045 | |
byCtss | 0.007 | 0.000 | 0.007 | |
consensusClusters | 0.045 | 0.001 | 0.045 | |
consensusClustersDESeq2 | 0.660 | 0.001 | 0.797 | |
consensusClustersTpm | 0.002 | 0.000 | 0.006 | |
cumulativeCTSSdistribution | 1.401 | 0.029 | 1.688 | |
distclu | 3.219 | 0.010 | 3.886 | |
dot-ctss_summary_for_clusters | 0.312 | 0.002 | 0.368 | |
exampleCAGEexp | 0 | 0 | 0 | |
exportToTrack | 12.299 | 0.052 | 14.743 | |
expressionClasses | 0.638 | 0.001 | 0.737 | |
flagLowExpCTSS | 0.016 | 0.000 | 0.017 | |
genomeName | 0 | 0 | 0 | |
getCTSS | 0.434 | 0.009 | 0.524 | |
getExpressionProfiles | 2.057 | 0.013 | 2.460 | |
getShiftingPromoters | 0.612 | 0.002 | 0.719 | |
hanabi | 0.085 | 0.003 | 0.106 | |
hanabiPlot | 0.110 | 0.007 | 0.142 | |
import.CAGEscanMolecule | 0 | 0 | 0 | |
import.CTSS | 0.026 | 0.001 | 0.030 | |
import.bam | 0 | 0 | 0 | |
import.bedCTSS | 0 | 0 | 0 | |
import.bedScore | 0 | 0 | 0 | |
import.bedmolecule | 0 | 0 | 0 | |
importPublicData | 0 | 0 | 0 | |
inputFiles | 0 | 0 | 0 | |
inputFilesType | 0.000 | 0.000 | 0.001 | |
librarySizes | 0 | 0 | 0 | |
mapStats | 0.017 | 0.001 | 0.018 | |
mergeCAGEsets | 0.872 | 0.014 | 1.058 | |
mergeSamples | 0.227 | 0.002 | 0.267 | |
moleculesGR2CTSS | 0.043 | 0.000 | 0.045 | |
normalizeTagCount | 0.253 | 0.004 | 0.304 | |
paraclu | 14.789 | 0.070 | 17.569 | |
parseCAGEscanBlocksToGrangeTSS | 0.007 | 0.000 | 0.008 | |
plotAnnot | 0.821 | 0.008 | 0.984 | |
plotCorrelation | 0.090 | 0.001 | 0.116 | |
plotExpressionProfiles | 2.623 | 0.071 | 3.218 | |
plotInterquantileWidth | 0.777 | 0.007 | 0.946 | |
plotReverseCumulatives | 0.893 | 0.007 | 1.056 | |
quantilePositions | 5.438 | 0.061 | 6.547 | |
quickEnhancers | 0 | 0 | 0 | |
ranges2annot | 0.135 | 0.002 | 0.168 | |
ranges2genes | 0.022 | 0.002 | 0.025 | |
ranges2names | 0.019 | 0.000 | 0.023 | |
resetCAGEexp | 0.104 | 0.001 | 0.120 | |
rowSums.RleDataFrame | 0.007 | 0.000 | 0.007 | |
rowsum.RleDataFrame | 0.008 | 0.001 | 0.014 | |
sampleLabels | 0.001 | 0.000 | 0.001 | |
scoreShift | 6.237 | 0.046 | 7.472 | |
seqNameTotalsSE | 0.003 | 0.000 | 0.003 | |
setColors | 0.154 | 0.003 | 0.189 | |
strandInvaders | 0.314 | 0.038 | 0.418 | |
summariseChrExpr | 0.197 | 0.008 | 0.246 | |
tagClusters | 0.143 | 0.007 | 0.189 | |