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This page was generated on 2025-10-09 12:04 -0400 (Thu, 09 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4854
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4642
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4587
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4584
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 269/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.29.1  (landing page)
Malte Thodberg
Snapshot Date: 2025-10-08 14:17 -0400 (Wed, 08 Oct 2025)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: devel
git_last_commit: 6331b70
git_last_commit_date: 2025-06-21 20:25:57 -0400 (Sat, 21 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CAGEfightR on lconway

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.

raw results


Summary

Package: CAGEfightR
Version: 1.29.1
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_1.29.1.tar.gz
StartedAt: 2025-10-08 20:36:55 -0400 (Wed, 08 Oct 2025)
EndedAt: 2025-10-08 20:44:24 -0400 (Wed, 08 Oct 2025)
EllapsedTime: 448.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.29.1’
* 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 6.418  0.834   6.767
* 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


Installation output

CAGEfightR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘CAGEfightR’ ...
** this is package ‘CAGEfightR’ version ‘1.29.1’
** 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)

Tests output


Example timings

CAGEfightR.Rcheck/CAGEfightR-Ex.timings

nameusersystemelapsed
assignGeneID4.1090.1284.307
assignMissingID1.2970.0511.358
assignTxID1.0970.0291.138
assignTxType0.0000.0010.001
balanceBC0.0010.0000.001
balanceD0.0000.0000.001
bwCommonGenome0.0370.0050.044
bwGenomeCompatibility0.0200.0030.024
bwValid0.0100.0030.013
calcBidirectionality0.4790.0150.497
calcComposition2.5450.0472.606
calcPooled0.1110.0120.125
calcShape2.5910.1562.760
calcSupport0.1200.0040.126
calcTPM0.1450.0060.152
calcTotalTags0.0650.0040.070
checkCTSSs0.2660.0070.274
checkPeaked0.0750.0040.080
checkPooled0.0680.0040.073
clusterBidirectionally0.0000.0010.001
clusterUnidirectionally1.7130.0301.751
combineClusters0.8930.0190.917
convertBAM2BigWig000
convertBED2BigWig0.0000.0010.000
convertGRanges2GPos0.0760.0010.077
exampleDesign0.0040.0070.011
findLinks6.4180.8346.767
findStretches0.4140.0580.474
quantifyCTSSs0.0000.0010.001
quantifyCTSSs2000
quantifyClusters0.4380.0640.509
quantifyGenes1.3830.1241.518
quickEnhancers000
quickGenes0.0000.0000.001
quickTSSs0.0000.0000.001
shapeEntropy0.0010.0010.001
shapeIQR0.0010.0000.000
shapeMean0.0010.0010.001
shapeMultimodality0.0000.0010.000
subsetByBidirectionality0.4580.0250.484
subsetByComposition1.3550.0441.406
subsetBySupport0.0840.0070.092
swapRanges0.2250.0180.245
swapScores0.1050.0040.110
trackBalance000
trackCTSS3.6120.2303.868
trackClusters2.3260.0332.376
trackLinks1.1000.4971.425
trimToPeak0.9980.1321.155
trimToPercentiles2.4720.0482.542
tuneTagClustering000
utilsAggregateRows0.3920.4110.824
utilsDeStrand0.1390.0040.143
utilsScoreOverlaps0.0810.0010.083
utilsSimplifyTxDb0.0000.0000.001