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This page was generated on 2025-10-08 12:51 -0400 (Wed, 08 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" 4641
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4586
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: 2025-10-07 13:45 -0400 (Tue, 07 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  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
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: 2025-10-07 20:23:19 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 20:30:57 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 458.2 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 6.613  0.971   7.063
* 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
assignGeneID4.1800.1284.375
assignMissingID1.2170.0451.271
assignTxID1.0080.0301.045
assignTxType0.0010.0000.001
balanceBC0.0010.0000.001
balanceD0.0000.0000.001
bwCommonGenome0.0400.0060.048
bwGenomeCompatibility0.0220.0030.025
bwValid0.0110.0040.014
calcBidirectionality0.4640.0160.481
calcComposition2.5860.0532.651
calcPooled0.1110.0140.127
calcShape2.7540.1702.951
calcSupport0.1200.0050.125
calcTPM0.1520.0070.161
calcTotalTags0.0760.0040.082
checkCTSSs0.2780.0060.287
checkPeaked0.0720.0030.074
checkPooled0.0640.0030.067
clusterBidirectionally000
clusterUnidirectionally1.7330.0311.777
combineClusters0.9450.0200.972
convertBAM2BigWig000
convertBED2BigWig0.0000.0000.001
convertGRanges2GPos0.0860.0010.088
exampleDesign0.0040.0090.014
findLinks6.6130.9717.063
findStretches0.4500.0660.519
quantifyCTSSs0.0000.0010.001
quantifyCTSSs2000
quantifyClusters0.4450.0610.508
quantifyGenes1.4620.1231.593
quickEnhancers000
quickGenes0.0000.0000.001
quickTSSs000
shapeEntropy0.0000.0000.001
shapeIQR0.0000.0000.001
shapeMean0.0010.0010.002
shapeMultimodality0.0000.0000.001
subsetByBidirectionality0.5060.0290.539
subsetByComposition1.4430.0501.504
subsetBySupport0.0900.0080.098
swapRanges0.2390.0160.256
swapScores0.1100.0050.116
trackBalance000
trackCTSS3.7470.2263.994
trackClusters2.4010.0322.447
trackLinks1.1660.4131.383
trimToPeak1.0700.1321.220
trimToPercentiles2.3760.0412.430
tuneTagClustering0.0010.0000.001
utilsAggregateRows0.3710.4090.790
utilsDeStrand0.1480.0030.152
utilsScoreOverlaps0.0710.0000.073
utilsSimplifyTxDb000