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This page was generated on 2025-04-22 13:15 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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: 2025-04-21 13:40 -0400 (Mon, 21 Apr 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 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (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: 1.28.0
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: 2025-04-21 19:32:18 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 19:39:19 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 420.5 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 4.5.0 RC (2025-04-04 r88126)
* 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 ‘1.28.0’
* 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 6.137  0.829    6.47
* 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 ‘1.28.0’
** 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
assignGeneID3.7930.1283.976
assignMissingID1.1130.0361.155
assignTxID1.0250.0271.059
assignTxType0.0000.0000.001
balanceBC0.0000.0000.001
balanceD0.0010.0010.001
bwCommonGenome0.0460.0070.055
bwGenomeCompatibility0.0240.0040.028
bwValid0.0110.0040.015
calcBidirectionality0.5470.0160.566
calcComposition1.5650.0421.620
calcPooled0.1410.0120.154
calcShape2.5380.1422.695
calcSupport0.1150.0070.122
calcTPM0.1370.0050.143
calcTotalTags0.0640.0030.068
checkCTSSs0.2830.0060.292
checkPeaked0.0990.0120.113
checkPooled0.0590.0050.063
clusterBidirectionally000
clusterUnidirectionally1.7520.0271.796
combineClusters2.0670.0542.134
convertBAM2BigWig0.0000.0000.001
convertBED2BigWig0.0000.0000.001
convertGRanges2GPos0.0720.0010.073
exampleDesign0.0040.0070.012
findLinks6.1370.8296.470
findStretches0.4650.0660.537
quantifyCTSSs0.0000.0000.001
quantifyCTSSs20.0000.0000.001
quantifyClusters0.4460.0620.514
quantifyGenes1.4010.1111.520
quickEnhancers0.0000.0000.001
quickGenes0.0000.0010.000
quickTSSs000
shapeEntropy0.0010.0000.001
shapeIQR0.0000.0010.001
shapeMean0.0000.0000.001
shapeMultimodality0.0000.0010.000
subsetByBidirectionality0.4640.0330.499
subsetByComposition1.2950.0431.346
subsetBySupport0.0770.0070.084
swapRanges0.1900.0090.200
swapScores0.1090.0050.115
trackBalance0.0000.0010.001
trackCTSS3.5410.2263.782
trackClusters2.2650.0412.317
trackLinks1.0800.3851.268
trimToPeak0.9850.1061.094
trimToPercentiles2.3010.0422.355
tuneTagClustering0.0000.0010.001
utilsAggregateRows0.3780.4150.807
utilsDeStrand0.1370.0040.141
utilsScoreOverlaps0.0810.0010.083
utilsSimplifyTxDb0.0000.0010.000