Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-21 13:22 -0400 (Fri, 21 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 261/2242 | 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 | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 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: 2.11.3 |
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: 2024-06-20 19:35:45 -0400 (Thu, 20 Jun 2024) |
EndedAt: 2024-06-20 19:39:02 -0400 (Thu, 20 Jun 2024) |
EllapsedTime: 196.1 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 RC (2024-06-06 r86719) * 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 11.427 0.019 11.446 exportToTrack 8.905 0.013 8.918 aggregateTagClusters 5.053 0.013 5.067 * 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 | 0.992 | 0.210 | 1.208 | |
CAGEr_Multicore | 1.446 | 0.002 | 1.449 | |
CTSS-class | 0.065 | 0.000 | 0.065 | |
CTSScoordinates | 0.023 | 0.001 | 0.024 | |
CTSSnormalizedTpm | 0.183 | 0.004 | 0.187 | |
CTSStagCount | 0.168 | 0.005 | 0.173 | |
CTSStoGenes | 0.118 | 0.001 | 0.119 | |
CustomConsensusClusters | 1.223 | 0.003 | 1.226 | |
GeneExpDESeq2 | 0.159 | 0.003 | 0.162 | |
GeneExpSE | 0.001 | 0.000 | 0.001 | |
QuantileWidthFunctions | 0.037 | 0.000 | 0.037 | |
TSSlogo | 0.664 | 0.010 | 0.677 | |
aggregateTagClusters | 5.053 | 0.013 | 5.067 | |
annotateCTSS | 3.899 | 0.009 | 3.909 | |
byCtss | 0.006 | 0.001 | 0.007 | |
consensusClusters | 0.046 | 0.001 | 0.047 | |
consensusClustersDESeq2 | 0.504 | 0.001 | 0.505 | |
consensusClustersTpm | 0.002 | 0.000 | 0.002 | |
cumulativeCTSSdistribution | 1.044 | 0.020 | 1.063 | |
distclu | 2.384 | 0.005 | 2.390 | |
dot-ctss_summary_for_clusters | 0.222 | 0.005 | 0.228 | |
exampleCAGEexp | 0 | 0 | 0 | |
exportToTrack | 8.905 | 0.013 | 8.918 | |
expressionClasses | 0.470 | 0.001 | 0.471 | |
flagLowExpCTSS | 0.008 | 0.000 | 0.009 | |
genomeName | 0 | 0 | 0 | |
getCTSS | 0.325 | 0.007 | 0.331 | |
getExpressionProfiles | 1.553 | 0.015 | 1.568 | |
getShiftingPromoters | 0.517 | 0.001 | 0.518 | |
hanabi | 0.068 | 0.003 | 0.071 | |
hanabiPlot | 0.079 | 0.005 | 0.083 | |
import.CAGEscanMolecule | 0 | 0 | 0 | |
import.CTSS | 0.020 | 0.000 | 0.021 | |
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 | 0.001 | 0.000 | 0.000 | |
inputFilesType | 0.000 | 0.000 | 0.001 | |
librarySizes | 0 | 0 | 0 | |
mapStats | 0.014 | 0.001 | 0.015 | |
mergeCAGEsets | 0.626 | 0.011 | 0.638 | |
mergeSamples | 0.158 | 0.001 | 0.159 | |
moleculesGR2CTSS | 0.044 | 0.001 | 0.045 | |
normalizeTagCount | 0.163 | 0.001 | 0.164 | |
paraclu | 11.427 | 0.019 | 11.446 | |
parseCAGEscanBlocksToGrangeTSS | 0.005 | 0.000 | 0.006 | |
plotAnnot | 0.617 | 0.004 | 0.623 | |
plotCorrelation | 0.062 | 0.000 | 0.063 | |
plotExpressionProfiles | 2.468 | 0.042 | 2.510 | |
plotInterquantileWidth | 0.564 | 0.006 | 0.571 | |
plotReverseCumulatives | 0.627 | 0.012 | 0.640 | |
quantilePositions | 3.279 | 0.015 | 3.295 | |
quickEnhancers | 0 | 0 | 0 | |
ranges2annot | 0.093 | 0.001 | 0.094 | |
ranges2genes | 0.015 | 0.000 | 0.015 | |
ranges2names | 0.015 | 0.000 | 0.015 | |
resetCAGEexp | 0.079 | 0.000 | 0.080 | |
rowSums.RleDataFrame | 0.007 | 0.000 | 0.006 | |
rowsum.RleDataFrame | 0.006 | 0.000 | 0.006 | |
sampleLabels | 0.001 | 0.000 | 0.002 | |
scoreShift | 4.680 | 0.032 | 4.711 | |
seqNameTotalsSE | 0.001 | 0.000 | 0.001 | |
setColors | 0.117 | 0.002 | 0.119 | |
strandInvaders | 0.206 | 0.028 | 0.234 | |
summariseChrExpr | 0.142 | 0.002 | 0.144 | |
tagClusters | 0.094 | 0.001 | 0.095 | |