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This page was generated on 2025-10-18 12:05 -0400 (Sat, 18 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: 2025-10-17 13:45 -0400 (Fri, 17 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: 2025-10-17 18:50:47 -0400 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 18:54:34 -0400 (Fri, 17 Oct 2025)
EllapsedTime: 226.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /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              12.373  0.021  12.508
exportToTrack        10.499  0.057  10.633
scoreShift            6.538  0.034   6.594
aggregateTagClusters  6.096  0.058   6.190
* 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-class1.7180.2742.046
CAGEr_Multicore1.6670.0051.684
CTSS-class0.0760.0000.077
CTSScoordinates0.0260.0010.027
CTSSnormalizedTpm0.2180.0040.224
CTSStagCount0.2060.0160.223
CTSStoGenes0.1670.0120.179
CustomConsensusClusters1.3700.0251.408
GeneExpDESeq20.1640.0040.174
GeneExpSE0.0020.0000.001
QuantileWidthFunctions0.0440.0000.045
TSSlogo0.8010.0140.820
aggregateTagClusters6.0960.0586.190
annotateCTSS3.5460.0103.639
byCtss0.0060.0000.006
consensusClusters0.0450.0010.045
consensusClustersDESeq20.5430.0010.549
consensusClustersTpm0.0020.0000.002
cumulativeCTSSdistribution1.1780.0231.257
distclu2.7110.0072.767
dot-ctss_summary_for_clusters0.2590.0020.261
exampleCAGEexp000
exportToTrack10.499 0.05710.633
expressionClasses0.5200.0000.533
filteredCTSSidx0.0030.0000.003
flagLowExpCTSS0.0110.0000.011
genomeName0.0000.0000.001
getCTSS0.3420.0070.351
getExpressionProfiles1.6150.0091.654
getShiftingPromoters0.5380.0020.541
hanabi0.0740.0040.078
hanabiPlot0.1060.0140.125
import.CAGEscanMolecule000
import.CTSS0.0250.0010.026
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
import.bigwig0.1330.0020.137
importPublicData000
inputFiles0.0000.0000.001
inputFilesType000
librarySizes0.0000.0000.001
mapStats0.0150.0010.017
mergeCAGEsets0.7320.0120.765
mergeSamples0.1810.0020.185
moleculesGR2CTSS0.0370.0000.041
normalizeTagCount0.1800.0030.184
paraclu12.373 0.02112.508
parseCAGEscanBlocksToGrangeTSS0.0060.0000.006
plotAnnot1.0260.0061.044
plotCorrelation0.0750.0020.077
plotExpressionProfiles2.6300.1022.750
plotInterquantileWidth1.4120.0291.462
plotReverseCumulatives0.8580.0220.893
quantilePositions3.6060.0223.645
quickEnhancers000
ranges2annot0.1090.0010.110
ranges2genes0.0170.0000.017
ranges2names0.0170.0000.017
resetCAGEexp0.0930.0010.093
rowSums.RleDataFrame0.0070.0000.007
rowsum.RleDataFrame0.0080.0010.008
sampleLabels0.0010.0000.002
scoreShift6.5380.0346.594
seqNameTotalsSE0.0010.0000.001
setColors0.1370.0010.139
strandInvaders0.2460.0270.277
summariseChrExpr0.1690.0120.183
tagClusters0.1240.0080.132