Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-18 12:05 -0400 (Sat, 18 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4632 |
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 272/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CAGEr 2.15.2 (landing page) Charles Plessy
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 2.15.2 |
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_2.15.2.tar.gz |
StartedAt: 2025-10-17 18:50:47 -0400 (Fri, 17 Oct 2025) |
EndedAt: 2025-10-17 18:54:34 -0400 (Fri, 17 Oct 2025) |
EllapsedTime: 226.7 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_2.15.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CAGEr.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CAGEr/DESCRIPTION’ ... OK * this is package ‘CAGEr’ version ‘2.15.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 30 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 12.373 0.021 12.508 exportToTrack 10.499 0.057 10.633 scoreShift 6.538 0.034 6.594 aggregateTagClusters 6.096 0.058 6.190 * 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/4.5-arm64/Resources/library’ * installing *source* package ‘CAGEr’ ... ** this is package ‘CAGEr’ version ‘2.15.2’ ** 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 | 1.718 | 0.274 | 2.046 | |
CAGEr_Multicore | 1.667 | 0.005 | 1.684 | |
CTSS-class | 0.076 | 0.000 | 0.077 | |
CTSScoordinates | 0.026 | 0.001 | 0.027 | |
CTSSnormalizedTpm | 0.218 | 0.004 | 0.224 | |
CTSStagCount | 0.206 | 0.016 | 0.223 | |
CTSStoGenes | 0.167 | 0.012 | 0.179 | |
CustomConsensusClusters | 1.370 | 0.025 | 1.408 | |
GeneExpDESeq2 | 0.164 | 0.004 | 0.174 | |
GeneExpSE | 0.002 | 0.000 | 0.001 | |
QuantileWidthFunctions | 0.044 | 0.000 | 0.045 | |
TSSlogo | 0.801 | 0.014 | 0.820 | |
aggregateTagClusters | 6.096 | 0.058 | 6.190 | |
annotateCTSS | 3.546 | 0.010 | 3.639 | |
byCtss | 0.006 | 0.000 | 0.006 | |
consensusClusters | 0.045 | 0.001 | 0.045 | |
consensusClustersDESeq2 | 0.543 | 0.001 | 0.549 | |
consensusClustersTpm | 0.002 | 0.000 | 0.002 | |
cumulativeCTSSdistribution | 1.178 | 0.023 | 1.257 | |
distclu | 2.711 | 0.007 | 2.767 | |
dot-ctss_summary_for_clusters | 0.259 | 0.002 | 0.261 | |
exampleCAGEexp | 0 | 0 | 0 | |
exportToTrack | 10.499 | 0.057 | 10.633 | |
expressionClasses | 0.520 | 0.000 | 0.533 | |
filteredCTSSidx | 0.003 | 0.000 | 0.003 | |
flagLowExpCTSS | 0.011 | 0.000 | 0.011 | |
genomeName | 0.000 | 0.000 | 0.001 | |
getCTSS | 0.342 | 0.007 | 0.351 | |
getExpressionProfiles | 1.615 | 0.009 | 1.654 | |
getShiftingPromoters | 0.538 | 0.002 | 0.541 | |
hanabi | 0.074 | 0.004 | 0.078 | |
hanabiPlot | 0.106 | 0.014 | 0.125 | |
import.CAGEscanMolecule | 0 | 0 | 0 | |
import.CTSS | 0.025 | 0.001 | 0.026 | |
import.bam | 0 | 0 | 0 | |
import.bedCTSS | 0 | 0 | 0 | |
import.bedScore | 0 | 0 | 0 | |
import.bedmolecule | 0 | 0 | 0 | |
import.bigwig | 0.133 | 0.002 | 0.137 | |
importPublicData | 0 | 0 | 0 | |
inputFiles | 0.000 | 0.000 | 0.001 | |
inputFilesType | 0 | 0 | 0 | |
librarySizes | 0.000 | 0.000 | 0.001 | |
mapStats | 0.015 | 0.001 | 0.017 | |
mergeCAGEsets | 0.732 | 0.012 | 0.765 | |
mergeSamples | 0.181 | 0.002 | 0.185 | |
moleculesGR2CTSS | 0.037 | 0.000 | 0.041 | |
normalizeTagCount | 0.180 | 0.003 | 0.184 | |
paraclu | 12.373 | 0.021 | 12.508 | |
parseCAGEscanBlocksToGrangeTSS | 0.006 | 0.000 | 0.006 | |
plotAnnot | 1.026 | 0.006 | 1.044 | |
plotCorrelation | 0.075 | 0.002 | 0.077 | |
plotExpressionProfiles | 2.630 | 0.102 | 2.750 | |
plotInterquantileWidth | 1.412 | 0.029 | 1.462 | |
plotReverseCumulatives | 0.858 | 0.022 | 0.893 | |
quantilePositions | 3.606 | 0.022 | 3.645 | |
quickEnhancers | 0 | 0 | 0 | |
ranges2annot | 0.109 | 0.001 | 0.110 | |
ranges2genes | 0.017 | 0.000 | 0.017 | |
ranges2names | 0.017 | 0.000 | 0.017 | |
resetCAGEexp | 0.093 | 0.001 | 0.093 | |
rowSums.RleDataFrame | 0.007 | 0.000 | 0.007 | |
rowsum.RleDataFrame | 0.008 | 0.001 | 0.008 | |
sampleLabels | 0.001 | 0.000 | 0.002 | |
scoreShift | 6.538 | 0.034 | 6.594 | |
seqNameTotalsSE | 0.001 | 0.000 | 0.001 | |
setColors | 0.137 | 0.001 | 0.139 | |
strandInvaders | 0.246 | 0.027 | 0.277 | |
summariseChrExpr | 0.169 | 0.012 | 0.183 | |
tagClusters | 0.124 | 0.008 | 0.132 | |