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This page was generated on 2025-08-21 11:40 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 268/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.14.0  (landing page)
Charles Plessy
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_21
git_last_commit: 446e1ca
git_last_commit_date: 2025-04-15 10:18:00 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CAGEr on kjohnson1

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: 2.14.0
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_2.14.0.tar.gz
StartedAt: 2025-08-19 15:09:58 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 15:21:07 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 668.4 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_2.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/CAGEr.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CAGEr/DESCRIPTION’ ... OK
* this is package ‘CAGEr’ version ‘2.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CAGEexp-class.Rd: MultiAssayExperiment, DataFrame, Rle
  CAGEr-class.Rd: MultiAssayExperiment
  CTSStagCount.Rd: DataFrame, Rle, RangedSummarizedExperiment
  CTSStoGenes.Rd: SummarizedExperiment
  CustomConsensusClusters.Rd: GRanges, RangedSummarizedExperiment
  TSSlogo.Rd: BSgenome
  aggregateTagClusters.Rd: RangedSummarizedExperiment
  annotateCTSS.Rd: GRanges, TxDb
  bam2CTSS.Rd: GRanges
  byCtss.Rd: data.table
  consensusClusters.Rd: GRanges, SummarizedExperiment
  distclu.Rd: GRangesList
  dot-ctss_summary_for_clusters.Rd: GRanges
  expressionClasses.Rd: Rle
  flagLowExpCTSS.Rd: Rle
  getCTSS.Rd: RangedSummarizedExperiment
  import.CAGEscanMolecule.Rd: GRanges
  import.CTSS.Rd: GPos
  loadFileIntoGPos.Rd: GPos
  moleculesGR2CTSS.Rd: GRanges
  paraclu.Rd: RangedSummarizedExperiment, GRangesList
  plotCorrelation.Rd: SummarizedExperiment, DataFrame
  quantilePositions.Rd: RangedSummarizedExperiment
  ranges2annot.Rd: rowRanges, Rle
  ranges2names.Rd: Rle
  strandInvaders.Rd: Rle
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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                42.191  0.199  43.250
exportToTrack          36.569  0.241  37.293
aggregateTagClusters   20.971  0.147  21.341
scoreShift             17.557  0.146  18.006
quantilePositions      12.455  0.093  12.639
annotateCTSS           12.116  0.060  12.481
distclu                 9.534  0.049   9.719
plotExpressionProfiles  7.538  0.218   7.917
CAGEexp-class           5.525  0.726   6.385
getExpressionProfiles   5.552  0.041   5.765
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/CAGEr.Rcheck/00check.log’
for details.


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-arm64/Resources/library’
* installing *source* package ‘CAGEr’ ...
** this is package ‘CAGEr’ version ‘2.14.0’
** 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-class5.5250.7266.385
CAGEr_Multicore4.5790.0404.652
CTSS-class0.2810.0030.286
CTSScoordinates0.0880.0030.092
CTSSnormalizedTpm0.8180.0140.841
CTSStagCount0.7450.0550.849
CTSStoGenes0.5450.0360.588
CustomConsensusClusters4.7790.0614.944
GeneExpDESeq20.5590.0150.592
GeneExpSE0.0040.0000.004
QuantileWidthFunctions0.1530.0020.159
TSSlogo2.6400.0442.770
aggregateTagClusters20.971 0.14721.341
annotateCTSS12.116 0.06012.481
byCtss0.0190.0010.020
consensusClusters0.1500.0020.153
consensusClustersDESeq21.7840.0081.812
consensusClustersTpm0.0070.0000.007
cumulativeCTSSdistribution4.1360.0844.320
distclu9.5340.0499.719
dot-ctss_summary_for_clusters0.9780.0080.991
exampleCAGEexp0.0000.0010.001
exportToTrack36.569 0.24137.293
expressionClasses1.7960.0071.832
filteredCTSSidx0.0090.0000.009
flagLowExpCTSS0.0350.0000.037
genomeName0.0010.0000.000
getCTSS1.2480.0201.298
getExpressionProfiles5.5520.0415.765
getShiftingPromoters1.8490.0081.892
hanabi0.2510.0110.264
hanabiPlot0.3050.0150.325
import.CAGEscanMolecule000
import.CTSS0.0830.0020.086
import.bam000
import.bedCTSS0.0000.0010.000
import.bedScore000
import.bedmolecule000
importPublicData0.0000.0010.001
inputFiles0.0020.0000.002
inputFilesType0.0020.0000.001
librarySizes0.0010.0000.001
mapStats0.0520.0040.057
mergeCAGEsets2.6030.0472.692
mergeSamples0.6190.0050.627
moleculesGR2CTSS0.1280.0010.129
normalizeTagCount0.6680.0140.701
paraclu42.191 0.19943.250
parseCAGEscanBlocksToGrangeTSS0.0240.0010.025
plotAnnot2.3520.0572.433
plotCorrelation0.2510.0050.259
plotExpressionProfiles7.5380.2187.917
plotInterquantileWidth3.8090.0523.876
plotReverseCumulatives2.3510.0832.450
quantilePositions12.455 0.09312.639
quickEnhancers0.0000.0010.000
ranges2annot0.4140.0070.424
ranges2genes0.0640.0020.067
ranges2names0.0630.0010.064
resetCAGEexp0.3520.0020.367
rowSums.RleDataFrame0.0220.0000.023
rowsum.RleDataFrame0.0250.0010.026
sampleLabels0.0060.0010.006
scoreShift17.557 0.14618.006
seqNameTotalsSE0.0040.0000.003
setColors0.4550.0060.461
strandInvaders0.8210.0940.928
summariseChrExpr0.5940.0150.633
tagClusters0.4100.0130.426