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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 267/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.1  (landing page)
Charles Plessy
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2025-08-08 19:48:07 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 19:59:54 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 707.6 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 (2025-06-13)
* 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                 53.002  0.285  53.498
exportToTrack           46.553  0.310  47.179
scoreShift              26.990  0.264  27.386
aggregateTagClusters    25.695  0.197  26.026
quantilePositions       15.947  0.095  16.139
annotateCTSS            15.168  0.077  15.310
distclu                 11.219  0.068  11.349
plotExpressionProfiles   8.626  0.131   8.811
getExpressionProfiles    6.596  0.038   6.659
CAGEexp-class            5.234  1.063   6.365
CustomConsensusClusters  5.983  0.038   6.052
* 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-class5.2341.0636.365
CAGEr_Multicore3.7690.0193.801
CTSS-class0.3080.0030.312
CTSScoordinates0.1010.0030.105
CTSSnormalizedTpm0.8410.0130.857
CTSStagCount0.8370.0580.898
CTSStoGenes0.5990.0390.642
CustomConsensusClusters5.9830.0386.052
GeneExpDESeq20.6130.0190.635
GeneExpSE0.0040.0010.005
QuantileWidthFunctions0.1880.0020.192
TSSlogo3.0850.0503.156
aggregateTagClusters25.695 0.19726.026
annotateCTSS15.168 0.07715.310
byCtss0.0200.0050.025
consensusClusters0.1820.0040.188
consensusClustersDESeq22.4270.0122.450
consensusClustersTpm0.0080.0000.009
cumulativeCTSSdistribution4.5690.0464.635
distclu11.219 0.06811.349
dot-ctss_summary_for_clusters1.0140.0071.026
exampleCAGEexp0.0000.0010.000
exportToTrack46.553 0.31047.179
expressionClasses2.2050.0122.229
filteredCTSSidx0.0110.0000.011
flagLowExpCTSS0.0360.0000.037
genomeName0.0000.0000.001
getCTSS1.2670.0241.299
getExpressionProfiles6.5960.0386.659
getShiftingPromoters2.2730.0082.288
hanabi0.2720.0090.283
hanabiPlot0.3120.0160.331
import.CAGEscanMolecule000
import.CTSS0.0880.0020.091
import.bam000
import.bedCTSS0.0000.0000.001
import.bedScore000
import.bedmolecule000
importPublicData0.0000.0000.001
inputFiles0.0020.0000.002
inputFilesType0.0020.0010.002
librarySizes0.0020.0000.002
mapStats0.0570.0030.060
mergeCAGEsets2.7630.0362.805
mergeSamples0.7690.0090.782
moleculesGR2CTSS0.1520.0020.154
normalizeTagCount0.6430.0070.653
paraclu53.002 0.28553.498
parseCAGEscanBlocksToGrangeTSS0.0280.0010.029
plotAnnot2.7760.0262.829
plotCorrelation0.3040.0050.311
plotExpressionProfiles8.6260.1318.811
plotInterquantileWidth2.4820.0182.518
plotReverseCumulatives2.8810.0232.921
quantilePositions15.947 0.09516.139
quickEnhancers000
ranges2annot0.4260.0030.431
ranges2genes0.1260.0030.130
ranges2names0.0680.0010.069
resetCAGEexp0.4050.0030.409
rowSums.RleDataFrame0.0220.0010.022
rowsum.RleDataFrame0.0250.0010.027
sampleLabels0.0030.0000.003
scoreShift26.990 0.26427.386
seqNameTotalsSE0.0050.0010.005
setColors0.4880.0050.496
strandInvaders0.8740.0971.008
summariseChrExpr0.6230.0060.633
tagClusters0.4950.0100.507