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This page was generated on 2025-09-29 11:39 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4580
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 266/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.28.0  (landing page)
Malte Thodberg
Snapshot Date: 2025-09-25 13:40 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/CAGEfightR
git_branch: RELEASE_3_21
git_last_commit: f30b594
git_last_commit_date: 2025-04-15 11:33:34 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CAGEfightR on kjohnson1

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: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2025-09-26 14:44:22 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 14:51:58 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 455.7 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEfightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAGEfightR’ version ‘1.28.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
findLinks 7.69   1.07   8.347
* 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-arm64/Resources/library’
* installing *source* package ‘CAGEfightR’ ...
** this is package ‘CAGEfightR’ version ‘1.28.0’
** 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
assignGeneID4.4900.1194.654
assignMissingID1.1970.0391.250
assignTxID1.0980.0351.137
assignTxType0.0000.0000.001
balanceBC0.0010.0010.001
balanceD0.0010.0000.001
bwCommonGenome0.0380.0060.046
bwGenomeCompatibility0.0180.0030.021
bwValid0.0090.0030.013
calcBidirectionality0.5150.0250.544
calcComposition2.7870.0572.852
calcPooled0.1010.0130.114
calcShape2.3740.2042.590
calcSupport0.1350.0090.147
calcTPM0.1470.0090.155
calcTotalTags0.0770.0070.083
checkCTSSs0.2420.0120.254
checkPeaked0.0850.0060.092
checkPooled0.0650.0110.077
clusterBidirectionally0.0000.0000.001
clusterUnidirectionally1.5530.0471.629
combineClusters0.8600.0350.898
convertBAM2BigWig000
convertBED2BigWig0.0000.0010.001
convertGRanges2GPos0.0790.0010.082
exampleDesign0.0030.0120.015
findLinks7.6901.0708.347
findStretches0.3870.2010.590
quantifyCTSSs0.0010.0010.000
quantifyCTSSs20.0000.0000.001
quantifyClusters0.4360.1740.612
quantifyGenes1.3930.2901.688
quickEnhancers0.0000.0000.001
quickGenes000
quickTSSs0.0000.0000.001
shapeEntropy0.0000.0000.001
shapeIQR000
shapeMean0.0010.0010.001
shapeMultimodality000
subsetByBidirectionality0.4290.0520.487
subsetByComposition1.2660.0961.368
subsetBySupport0.0680.0190.087
swapRanges0.2270.0180.248
swapScores0.0870.0060.095
trackBalance000
trackCTSS3.6890.4674.180
trackClusters2.5120.0472.576
trackLinks0.9700.5961.368
trimToPeak0.8680.2951.170
trimToPercentiles2.0240.0902.141
tuneTagClustering0.0000.0010.001
utilsAggregateRows0.3880.4150.805
utilsDeStrand0.1310.0050.136
utilsScoreOverlaps0.0600.0010.060
utilsSimplifyTxDb0.0000.0000.001