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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 271/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.1  (landing page)
Charles Plessy
Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: devel
git_last_commit: b05b175
git_last_commit_date: 2025-06-22 03:10:05 -0400 (Sun, 22 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 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 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: 2.15.1
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_2.15.1.tar.gz
StartedAt: 2025-10-03 20:16:48 -0400 (Fri, 03 Oct 2025)
EndedAt: 2025-10-03 20:28:54 -0400 (Fri, 03 Oct 2025)
EllapsedTime: 725.3 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_2.15.1.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 ‘2.15.1’
* 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                 52.964  0.245  53.416
exportToTrack           47.381  0.289  47.951
scoreShift              26.793  0.274  27.216
aggregateTagClusters    26.404  0.178  26.680
quantilePositions       15.579  0.091  15.745
annotateCTSS            15.422  0.073  15.553
distclu                 11.395  0.070  11.528
plotExpressionProfiles  10.474  0.140  10.664
getExpressionProfiles    7.091  0.057   7.211
CAGEexp-class            5.396  1.115   6.572
CustomConsensusClusters  5.739  0.031   5.787
* 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-3.22-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-x86_64/Resources/library’
* installing *source* package ‘CAGEr’ ...
** this is package ‘CAGEr’ version ‘2.15.1’
** 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-class5.3961.1156.572
CAGEr_Multicore3.7080.0213.749
CTSS-class0.3270.0030.331
CTSScoordinates0.1010.0030.103
CTSSnormalizedTpm0.9090.0130.926
CTSStagCount0.8490.0780.933
CTSStoGenes0.6000.0520.658
CustomConsensusClusters5.7390.0315.787
GeneExpDESeq20.5940.0180.615
GeneExpSE0.0040.0010.004
QuantileWidthFunctions0.1660.0020.168
TSSlogo3.4200.0563.501
aggregateTagClusters26.404 0.17826.680
annotateCTSS15.422 0.07315.553
byCtss0.0120.0010.012
consensusClusters0.1740.0020.178
consensusClustersDESeq22.3010.0102.323
consensusClustersTpm0.0090.0000.009
cumulativeCTSSdistribution4.6780.0504.754
distclu11.395 0.07011.528
dot-ctss_summary_for_clusters1.1200.0101.138
exampleCAGEexp0.0000.0000.001
exportToTrack47.381 0.28947.951
expressionClasses2.4430.0172.480
filteredCTSSidx0.0110.0010.012
flagLowExpCTSS0.0430.0010.044
genomeName000
getCTSS1.3920.0241.430
getExpressionProfiles7.0910.0577.211
getShiftingPromoters2.3660.0172.400
hanabi0.2860.0070.295
hanabiPlot0.3760.0180.401
import.CAGEscanMolecule000
import.CTSS0.1020.0020.104
import.bam0.0000.0010.000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData0.0000.0000.001
inputFiles0.0020.0000.002
inputFilesType0.0020.0000.002
librarySizes0.0020.0000.002
mapStats0.0580.0050.064
mergeCAGEsets2.8320.0342.879
mergeSamples0.6640.0060.674
moleculesGR2CTSS0.1460.0010.148
normalizeTagCount0.6170.0050.625
paraclu52.964 0.24553.416
parseCAGEscanBlocksToGrangeTSS0.0280.0010.029
plotAnnot4.1350.0604.215
plotCorrelation0.3280.0040.333
plotExpressionProfiles10.474 0.14010.664
plotInterquantileWidth2.8580.0172.889
plotReverseCumulatives3.5060.0253.557
quantilePositions15.579 0.09115.745
quickEnhancers000
ranges2annot0.4120.0040.417
ranges2genes0.0590.0010.061
ranges2names0.0620.0010.063
resetCAGEexp0.3720.0020.375
rowSums.RleDataFrame0.0280.0000.029
rowsum.RleDataFrame0.0300.0010.030
sampleLabels0.0060.0010.006
scoreShift26.793 0.27427.216
seqNameTotalsSE0.0060.0010.006
setColors0.5610.0060.570
strandInvaders0.9690.0841.074
summariseChrExpr0.6550.0080.672
tagClusters0.5040.0140.521