Back to Multiple platform build/check report for BioC 3.22:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-16 12:07 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4867
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4655
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4600
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 269/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEfightR 1.29.1  (landing page)
Malte Thodberg
Snapshot Date: 2025-10-15 13:45 -0400 (Wed, 15 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 12.7.6 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: CAGEfightR
Version: 1.29.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CAGEfightR_1.29.1.tar.gz
StartedAt: 2025-10-14 06:22:25 -0000 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 06:30:30 -0000 (Tue, 14 Oct 2025)
EllapsedTime: 485.4 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEfightR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:CAGEfightR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CAGEfightR_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CAGEfightR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 loading without being on the library search path ... 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 6.614  1.196   7.078
* 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:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL CAGEfightR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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
assignGeneID4.3010.0724.410
assignMissingID1.3220.0041.329
assignTxID1.1010.0121.115
assignTxType0.0000.0000.001
balanceBC0.0000.0000.001
balanceD0.0000.0000.001
bwCommonGenome0.0510.0000.056
bwGenomeCompatibility0.0230.0000.022
bwValid0.010.000.01
calcBidirectionality0.6050.0040.611
calcComposition2.6150.1432.766
calcPooled0.1300.0200.151
calcShape3.2320.1163.355
calcSupport0.1270.0080.135
calcTPM0.1480.0120.160
calcTotalTags0.080.000.08
checkCTSSs0.3250.0160.345
checkPeaked0.0910.0000.091
checkPooled0.0800.0040.084
clusterBidirectionally000
clusterUnidirectionally2.1820.0162.205
combineClusters1.0880.0361.127
convertBAM2BigWig000
convertBED2BigWig0.0010.0000.001
convertGRanges2GPos0.1090.0000.109
exampleDesign0.0020.0030.005
findLinks6.6141.1967.078
findStretches0.4910.1190.613
quantifyCTSSs0.0000.0010.000
quantifyCTSSs2000
quantifyClusters0.4890.0970.587
quantifyGenes1.5700.2231.800
quickEnhancers000
quickGenes000
quickTSSs0.0000.0000.001
shapeEntropy0.0010.0000.001
shapeIQR000
shapeMean0.0010.0000.001
shapeMultimodality000
subsetByBidirectionality0.6290.0460.679
subsetByComposition1.5200.1521.678
subsetBySupport0.0980.0160.114
swapRanges0.2580.0390.298
swapScores0.1290.0040.134
trackBalance000
trackCTSS3.9450.5434.502
trackClusters2.6220.1552.785
trackLinks1.1970.5601.437
trimToPeak1.1700.1551.329
trimToPercentiles2.9750.1083.092
tuneTagClustering000
utilsAggregateRows0.3380.0840.423
utilsDeStrand0.1740.0040.179
utilsScoreOverlaps0.0950.0000.095
utilsSimplifyTxDb000