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This page was generated on 2025-10-23 12:03 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 272/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.2  (landing page)
Charles Plessy
Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 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    OK  


CHECK results for CAGEr on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CAGEr_2.15.2.tar.gz
StartedAt: 2025-10-22 21:48:19 -0400 (Wed, 22 Oct 2025)
EndedAt: 2025-10-22 22:00:34 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 734.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CAGEr_2.15.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CAGEr.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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                42.623  0.125  42.748
exportToTrack          35.992  0.062  36.058
scoreShift             21.861  0.230  22.091
aggregateTagClusters   19.986  0.149  20.136
quantilePositions      12.068  0.061  12.130
annotateCTSS           11.819  0.070  11.889
distclu                 9.270  0.009   9.280
plotExpressionProfiles  7.970  0.052   8.022
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-class2.7510.0912.844
CAGEr_Multicore3.2710.0013.272
CTSS-class0.2390.0000.238
CTSScoordinates0.0750.0020.076
CTSSnormalizedTpm0.6630.0110.674
CTSStagCount0.6140.1200.734
CTSStoGenes0.3530.0600.414
CustomConsensusClusters4.4760.0174.494
GeneExpDESeq20.4530.0060.460
GeneExpSE0.0030.0000.004
QuantileWidthFunctions0.1240.0000.124
TSSlogo2.5690.0222.594
aggregateTagClusters19.986 0.14920.136
annotateCTSS11.819 0.07011.889
byCtss0.0160.0000.016
consensusClusters0.1650.0020.167
consensusClustersDESeq21.9970.0742.071
consensusClustersTpm0.0050.0000.006
cumulativeCTSSdistribution3.5670.0673.634
distclu9.2700.0099.280
dot-ctss_summary_for_clusters0.8760.0010.878
exampleCAGEexp0.0010.0000.000
exportToTrack35.992 0.06236.058
expressionClasses1.8580.0341.892
filteredCTSSidx0.0110.0000.011
flagLowExpCTSS0.0330.0010.034
genomeName000
getCTSS0.8860.0070.893
getExpressionProfiles4.8340.0084.842
getShiftingPromoters1.8550.0441.899
hanabi0.2150.0030.218
hanabiPlot0.2680.0280.297
import.CAGEscanMolecule000
import.CTSS0.0740.0040.077
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule0.0010.0000.000
import.bigwig0.3220.0030.326
importPublicData000
inputFiles0.0010.0000.001
inputFilesType0.0010.0000.001
librarySizes0.0010.0000.001
mapStats0.0490.0000.049
mergeCAGEsets1.9560.0241.979
mergeSamples0.4230.0010.424
moleculesGR2CTSS0.1170.0010.118
normalizeTagCount0.5270.0010.507
paraclu42.623 0.12542.748
parseCAGEscanBlocksToGrangeTSS0.0190.0010.020
plotAnnot3.1570.0123.169
plotCorrelation0.2330.0020.235
plotExpressionProfiles7.9700.0528.022
plotInterquantileWidth2.2300.0152.244
plotReverseCumulatives2.6140.0342.589
quantilePositions12.068 0.06112.130
quickEnhancers0.0010.0000.000
ranges2annot0.3220.0000.322
ranges2genes0.0540.0000.054
ranges2names0.0530.0000.053
resetCAGEexp0.3080.0000.308
rowSums.RleDataFrame0.0210.0010.022
rowsum.RleDataFrame0.0260.0000.026
sampleLabels0.0030.0010.004
scoreShift21.861 0.23022.091
seqNameTotalsSE0.0040.0000.004
setColors0.2820.0010.283
strandInvaders0.5620.0230.569
summariseChrExpr0.3810.0000.380
tagClusters0.3710.0000.371