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This page was generated on 2025-10-20 12:06 -0400 (Mon, 20 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 272/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.2  (landing page)
Charles Plessy
Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 2025)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: devel
git_last_commit: 679bef9
git_last_commit_date: 2025-10-14 05:35:27 -0400 (Tue, 14 Oct 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    ERROR  


CHECK results for CAGEr on kjohnson3

To the developers/maintainers of the CAGEr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CAGEr.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: CAGEr
Version: 2.15.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.15.2.tar.gz
StartedAt: 2025-10-19 18:45:47 -0400 (Sun, 19 Oct 2025)
EndedAt: 2025-10-19 18:49:27 -0400 (Sun, 19 Oct 2025)
EllapsedTime: 220.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CAGEr_2.15.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CAGEr.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.15.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘CAGEr’ 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 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
paraclu              12.107  0.020  12.143
exportToTrack        10.390  0.059  10.474
scoreShift            6.418  0.032   6.458
aggregateTagClusters  6.002  0.060   6.065
* 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

CAGEr.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘CAGEr’ ...
** this is package ‘CAGEr’ version ‘2.15.2’
** 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 (CAGEr)

Tests output


Example timings

CAGEr.Rcheck/CAGEr-Ex.timings

nameusersystemelapsed
CAGEexp-class1.7300.2411.986
CAGEr_Multicore1.7280.0031.736
CTSS-class0.0750.0000.077
CTSScoordinates0.0240.0020.025
CTSSnormalizedTpm0.2160.0040.220
CTSStagCount0.2030.0150.219
CTSStoGenes0.1640.0100.175
CustomConsensusClusters1.3710.0071.389
GeneExpDESeq20.1640.0050.169
GeneExpSE0.0010.0000.001
QuantileWidthFunctions0.0470.0010.047
TSSlogo0.8040.0130.825
aggregateTagClusters6.0020.0606.065
annotateCTSS3.4650.0113.476
byCtss0.0070.0000.006
consensusClusters0.0450.0010.047
consensusClustersDESeq20.5490.0010.550
consensusClustersTpm0.0020.0000.002
cumulativeCTSSdistribution1.1990.0211.221
distclu2.6950.0112.709
dot-ctss_summary_for_clusters0.2570.0010.258
exampleCAGEexp000
exportToTrack10.390 0.05910.474
expressionClasses0.5030.0000.503
filteredCTSSidx0.0030.0000.003
flagLowExpCTSS0.0100.0000.011
genomeName000
getCTSS0.3330.0070.340
getExpressionProfiles1.5750.0071.584
getShiftingPromoters0.5120.0010.513
hanabi0.0760.0040.081
hanabiPlot0.1110.0100.120
import.CAGEscanMolecule0.0010.0000.000
import.CTSS0.0230.0000.024
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
import.bigwig0.1160.0020.118
importPublicData000
inputFiles0.0000.0000.001
inputFilesType0.0010.0000.001
librarySizes000
mapStats0.0160.0010.017
mergeCAGEsets0.7480.0120.761
mergeSamples0.1860.0020.189
moleculesGR2CTSS0.0390.0000.040
normalizeTagCount0.1880.0020.191
paraclu12.107 0.02012.143
parseCAGEscanBlocksToGrangeTSS0.0070.0000.006
plotAnnot1.0370.0051.053
plotCorrelation0.0740.0010.075
plotExpressionProfiles2.6250.0932.728
plotInterquantileWidth1.3630.0241.392
plotReverseCumulatives0.8610.0260.898
quantilePositions3.6100.0183.634
quickEnhancers000
ranges2annot0.1140.0010.115
ranges2genes0.0170.0010.018
ranges2names0.0180.0000.018
resetCAGEexp0.0930.0010.094
rowSums.RleDataFrame0.0070.0000.007
rowsum.RleDataFrame0.0070.0010.007
sampleLabels0.0010.0000.001
scoreShift6.4180.0326.458
seqNameTotalsSE0.0020.0000.001
setColors0.1390.0020.141
strandInvaders0.2570.0310.289
summariseChrExpr0.1800.0130.193
tagClusters0.1250.0090.134