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This page was generated on 2025-10-02 11:40 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4831
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4612
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4584
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: 2025-09-29 13:40 -0400 (Mon, 29 Sep 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: 2025-09-30 14:55:54 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 15:07:18 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 683.7 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_2.14.0.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                41.210  0.144  41.865
exportToTrack          35.802  0.261  36.687
aggregateTagClusters   20.739  0.151  21.241
scoreShift             18.936  0.237  19.282
quantilePositions      12.840  0.080  12.988
annotateCTSS           12.209  0.062  12.415
distclu                 9.614  0.049   9.755
plotExpressionProfiles  8.992  0.297   9.326
CAGEexp-class           5.560  0.720   6.351
getExpressionProfiles   5.776  0.045   5.943
* 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-class5.5600.7206.351
CAGEr_Multicore4.7310.0684.833
CTSS-class0.2750.0030.281
CTSScoordinates0.0860.0040.090
CTSSnormalizedTpm0.7780.0100.798
CTSStagCount0.7340.0510.792
CTSStoGenes0.5040.0350.544
CustomConsensusClusters4.7440.0904.900
GeneExpDESeq20.5410.0130.562
GeneExpSE0.0050.0000.008
QuantileWidthFunctions0.1470.0010.149
TSSlogo2.7900.0472.878
aggregateTagClusters20.739 0.15121.241
annotateCTSS12.209 0.06212.415
byCtss0.0190.0010.020
consensusClusters0.1780.0030.181
consensusClustersDESeq21.8990.0091.946
consensusClustersTpm0.0060.0000.006
cumulativeCTSSdistribution4.2260.0844.380
distclu9.6140.0499.755
dot-ctss_summary_for_clusters0.9510.0060.963
exampleCAGEexp0.0000.0010.000
exportToTrack35.802 0.26136.687
expressionClasses1.8710.0071.907
filteredCTSSidx0.0110.0010.012
flagLowExpCTSS0.0370.0010.040
genomeName000
getCTSS1.3240.0241.375
getExpressionProfiles5.7760.0455.943
getShiftingPromoters1.9480.0172.027
hanabi0.2500.0100.261
hanabiPlot0.2900.0180.310
import.CAGEscanMolecule000
import.CTSS0.0840.0010.085
import.bam0.0000.0000.001
import.bedCTSS0.0000.0010.000
import.bedScore000
import.bedmolecule0.0000.0010.000
importPublicData0.0000.0010.001
inputFiles0.0020.0000.002
inputFilesType0.0000.0000.001
librarySizes0.0010.0000.001
mapStats0.0500.0040.055
mergeCAGEsets2.5930.0422.658
mergeSamples0.7410.0100.756
moleculesGR2CTSS0.1320.0010.140
normalizeTagCount0.6150.0110.631
paraclu41.210 0.14441.865
parseCAGEscanBlocksToGrangeTSS0.0220.0010.022
plotAnnot3.4000.0273.471
plotCorrelation0.2500.0050.258
plotExpressionProfiles8.9920.2979.326
plotInterquantileWidth2.4390.0172.498
plotReverseCumulatives2.8530.0212.952
quantilePositions12.840 0.08012.988
quickEnhancers000
ranges2annot0.3520.0020.355
ranges2genes0.0670.0010.070
ranges2names0.0630.0010.065
resetCAGEexp0.3500.0020.362
rowSums.RleDataFrame0.0270.0000.028
rowsum.RleDataFrame0.0320.0010.034
sampleLabels0.0060.0000.007
scoreShift18.936 0.23719.282
seqNameTotalsSE0.0040.0000.003
setColors0.4660.0080.479
strandInvaders0.8330.0820.918
summariseChrExpr0.5710.0460.618
tagClusters0.4440.0280.472