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This page was generated on 2025-10-25 12:04 -0400 (Sat, 25 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4658
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 273/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.2  (landing page)
Charles Plessy
Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 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    NA    NA  


CHECK results for CAGEr on lconway

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: 2025-10-24 19:59:00 -0400 (Fri, 24 Oct 2025)
EndedAt: 2025-10-24 20:10:32 -0400 (Fri, 24 Oct 2025)
EllapsedTime: 692.8 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: 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 ‘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                 50.602  0.269  51.122
exportToTrack           43.534  0.269  44.219
scoreShift              24.627  0.218  24.999
aggregateTagClusters    24.454  0.162  24.700
quantilePositions       14.243  0.098  14.403
annotateCTSS            14.057  0.072  14.191
distclu                 10.912  0.061  11.021
plotExpressionProfiles   9.668  0.152   9.869
getExpressionProfiles    6.534  0.049   6.628
CAGEexp-class            5.081  1.057   6.205
CustomConsensusClusters  5.828  0.038   5.888
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/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-class5.0811.0576.205
CAGEr_Multicore3.6320.0203.668
CTSS-class0.2980.0030.302
CTSScoordinates0.0900.0030.094
CTSSnormalizedTpm0.8530.0170.873
CTSStagCount0.8450.0730.923
CTSStoGenes0.5820.0470.633
CustomConsensusClusters5.8280.0385.888
GeneExpDESeq20.5490.0180.571
GeneExpSE0.0030.0010.005
QuantileWidthFunctions0.1530.0020.155
TSSlogo3.1560.0543.237
aggregateTagClusters24.454 0.16224.700
annotateCTSS14.057 0.07214.191
byCtss0.0170.0000.018
consensusClusters0.1600.0020.162
consensusClustersDESeq22.3430.0122.365
consensusClustersTpm0.0070.0010.007
cumulativeCTSSdistribution4.3800.0454.443
distclu10.912 0.06111.021
dot-ctss_summary_for_clusters1.0630.0101.078
exampleCAGEexp0.0000.0010.000
exportToTrack43.534 0.26944.219
expressionClasses2.3200.0122.349
filteredCTSSidx0.0160.0010.016
flagLowExpCTSS0.050.000.05
genomeName0.0010.0000.001
getCTSS1.2480.0231.281
getExpressionProfiles6.5340.0496.628
getShiftingPromoters2.2070.0152.239
hanabi0.2620.0080.274
hanabiPlot0.3500.0160.370
import.CAGEscanMolecule000
import.CTSS0.0920.0030.094
import.bam0.0000.0010.000
import.bedCTSS0.0000.0010.001
import.bedScore000
import.bedmolecule000
import.bigwig0.4230.0060.435
importPublicData0.0000.0010.002
inputFiles0.0010.0000.002
inputFilesType0.0020.0010.001
librarySizes0.0020.0010.002
mapStats0.0590.0060.065
mergeCAGEsets2.6380.0372.699
mergeSamples0.6730.0060.683
moleculesGR2CTSS0.1430.0020.150
normalizeTagCount0.6210.0060.633
paraclu50.602 0.26951.122
parseCAGEscanBlocksToGrangeTSS0.0290.0010.030
plotAnnot3.7760.0243.819
plotCorrelation0.3010.0040.306
plotExpressionProfiles9.6680.1529.869
plotInterquantileWidth2.6910.0152.716
plotReverseCumulatives4.4450.0714.536
quantilePositions14.243 0.09814.403
quickEnhancers0.0000.0010.001
ranges2annot0.4560.0080.467
ranges2genes0.0740.0030.077
ranges2names0.0720.0020.074
resetCAGEexp0.4040.0050.415
rowSums.RleDataFrame0.0200.0000.021
rowsum.RleDataFrame0.0290.0020.030
sampleLabels0.0050.0010.005
scoreShift24.627 0.21824.999
seqNameTotalsSE0.0040.0000.005
setColors0.4880.0070.498
strandInvaders0.8450.0690.920
summariseChrExpr0.6000.0060.609
tagClusters0.4570.0110.470