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This page was generated on 2025-08-21 12:06 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4819
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4597
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4539
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 267/2318HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.1  (landing page)
Charles Plessy
Snapshot Date: 2025-08-20 13:45 -0400 (Wed, 20 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 24.04.3 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 kjohnson3

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: 2025-08-20 18:28:56 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 18:32:33 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 216.6 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 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 13.7.7
* 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              12.171  0.047  12.288
exportToTrack        10.437  0.073  10.549
scoreShift            6.957  0.078   7.091
aggregateTagClusters  6.036  0.065   6.138
* 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-arm64/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-class1.7640.2492.067
CAGEr_Multicore1.6690.0171.691
CTSS-class0.0740.0010.076
CTSScoordinates0.0230.0010.025
CTSSnormalizedTpm0.2160.0050.222
CTSStagCount0.2060.0160.222
CTSStoGenes0.1620.0070.170
CustomConsensusClusters1.3570.0061.364
GeneExpDESeq20.1660.0040.171
GeneExpSE0.0020.0010.001
QuantileWidthFunctions0.0590.0010.060
TSSlogo0.7510.0120.779
aggregateTagClusters6.0360.0656.138
annotateCTSS3.5190.0093.572
byCtss0.0070.0010.007
consensusClusters0.0450.0010.046
consensusClustersDESeq20.5450.0010.551
consensusClustersTpm0.0010.0000.002
cumulativeCTSSdistribution1.1770.0251.211
distclu2.6730.0082.683
dot-ctss_summary_for_clusters0.2610.0010.266
exampleCAGEexp000
exportToTrack10.437 0.07310.549
expressionClasses0.5190.0010.523
filteredCTSSidx0.0030.0000.003
flagLowExpCTSS0.010.000.01
genomeName0.0000.0000.001
getCTSS0.3620.0080.373
getExpressionProfiles1.6190.0091.644
getShiftingPromoters0.5410.0010.542
hanabi0.0760.0020.081
hanabiPlot0.0860.0060.092
import.CAGEscanMolecule000
import.CTSS0.0250.0010.026
import.bam000
import.bedCTSS0.0010.0000.000
import.bedScore000
import.bedmolecule000
importPublicData0.0000.0000.001
inputFiles000
inputFilesType000
librarySizes000
mapStats0.0170.0010.017
mergeCAGEsets0.7250.0120.740
mergeSamples0.1930.0020.195
moleculesGR2CTSS0.0370.0000.042
normalizeTagCount0.2060.0040.217
paraclu12.171 0.04712.288
parseCAGEscanBlocksToGrangeTSS0.0060.0000.006
plotAnnot0.6870.0040.698
plotCorrelation0.0710.0010.071
plotExpressionProfiles2.1930.0712.282
plotInterquantileWidth0.6550.0040.660
plotReverseCumulatives0.7520.0100.765
quantilePositions3.6670.0203.698
quickEnhancers0.0000.0010.000
ranges2annot0.1150.0010.116
ranges2genes0.0190.0000.020
ranges2names0.0180.0010.018
resetCAGEexp0.0930.0000.092
rowSums.RleDataFrame0.0070.0000.007
rowsum.RleDataFrame0.0070.0010.007
sampleLabels0.0010.0000.002
scoreShift6.9570.0787.091
seqNameTotalsSE0.0010.0000.001
setColors0.1360.0020.139
strandInvaders0.2540.0300.287
summariseChrExpr0.1730.0160.190
tagClusters0.1230.0050.130