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This page was generated on 2026-05-07 11:36 -0400 (Thu, 07 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4990
kjohnson3macOS 13.7.7 Venturaarm644.6.0 Patched (2026-04-24 r89963) -- "Because it was There" 4723
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 276/2418HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.32.0  (landing page)
Malte Thodberg
Snapshot Date: 2026-05-06 13:40 -0400 (Wed, 06 May 2026)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_23
git_last_commit: e325147
git_last_commit_date: 2026-04-28 08:47:57 -0400 (Tue, 28 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  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
See other builds for CAGEfightR in R Universe.


CHECK results for CAGEfightR on kjohnson3

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: 1.32.0
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_1.32.0.tar.gz
StartedAt: 2026-05-06 19:14:04 -0400 (Wed, 06 May 2026)
EndedAt: 2026-05-06 19:16:43 -0400 (Wed, 06 May 2026)
EllapsedTime: 158.8 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_1.32.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.6.0 Patched (2026-04-24 r89963)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-06 23:14:04 UTC
* using option ‘--no-vignettes’
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.32.0’
* 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
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘CAGEfightR’ ...
** this is package ‘CAGEfightR’ version ‘1.32.0’
** 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
assignGeneID1.4080.0291.451
assignMissingID0.3510.0050.356
assignTxID0.3350.0060.344
assignTxType000
balanceBC0.0000.0000.001
balanceD000
bwCommonGenome0.0120.0020.015
bwGenomeCompatibility0.0050.0010.007
bwValid0.0020.0000.004
calcBidirectionality0.1280.0030.134
calcComposition0.4710.0100.481
calcPooled0.0290.0020.030
calcShape0.7750.0460.827
calcSupport0.0340.0010.036
calcTPM0.0390.0020.041
calcTotalTags0.0200.0010.022
checkCTSSs0.0740.0020.077
checkPeaked0.0330.0010.033
checkPooled0.0180.0010.018
clusterBidirectionally000
clusterUnidirectionally0.9430.0050.951
combineClusters0.2230.0030.227
convertBAM2BigWig000
convertBED2BigWig000
convertGRanges2GPos0.0230.0000.023
exampleDesign0.0010.0030.004
findLinks2.5440.5732.944
findStretches0.1280.0810.210
quantifyCTSSs000
quantifyCTSSs2000
quantifyClusters0.1440.0540.198
quantifyGenes0.4400.0840.531
quickEnhancers000
quickGenes000
quickTSSs000
shapeEntropy000
shapeIQR0.0000.0010.000
shapeMean000
shapeMultimodality000
subsetByBidirectionality0.1300.0390.127
subsetByComposition0.3940.0200.415
subsetBySupport0.0200.0010.022
swapRanges0.0740.0020.078
swapScores0.0290.0010.030
trackBalance000
trackCTSS1.1730.1011.275
trackClusters0.7780.0040.783
trackLinks0.3130.3820.599
trimToPeak0.2490.0550.305
trimToPercentiles0.5880.0100.597
tuneTagClustering000
utilsAggregateRows0.1270.1240.257
utilsDeStrand0.0330.0010.034
utilsScoreOverlaps0.0190.0000.019
utilsSimplifyTxDb0.0000.0000.001