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This page was generated on 2025-09-01 12:03 -0400 (Mon, 01 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 268/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.1  (landing page)
Charles Plessy
Snapshot Date: 2025-08-31 13:45 -0400 (Sun, 31 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 nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CAGEr_2.15.1.tar.gz
StartedAt: 2025-08-31 20:55:40 -0400 (Sun, 31 Aug 2025)
EndedAt: 2025-08-31 21:08:03 -0400 (Sun, 31 Aug 2025)
EllapsedTime: 743.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings CAGEr_2.15.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CAGEr.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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                43.718  0.266  43.984
exportToTrack          36.811  0.244  37.058
scoreShift             22.441  0.163  22.604
aggregateTagClusters   20.524  0.497  21.023
quantilePositions      12.364  0.024  12.389
annotateCTSS           12.029  0.172  12.204
distclu                 9.272  0.027   9.300
plotExpressionProfiles  6.922  0.122   7.044
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/CAGEr.Rcheck/00check.log’
for details.


Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-class3.2240.9344.168
CAGEr_Multicore3.5220.2973.818
CTSS-class0.2470.0000.247
CTSScoordinates0.0800.0020.082
CTSSnormalizedTpm0.6950.0740.770
CTSStagCount0.6120.1140.726
CTSStoGenes0.3770.0660.444
CustomConsensusClusters4.6520.1904.842
GeneExpDESeq20.4720.0090.481
GeneExpSE0.0030.0000.004
QuantileWidthFunctions0.1230.0060.129
TSSlogo2.4580.0662.528
aggregateTagClusters20.524 0.49721.023
annotateCTSS12.029 0.17212.204
byCtss0.0150.0010.016
consensusClusters0.1520.0000.151
consensusClustersDESeq22.0050.0072.012
consensusClustersTpm0.0050.0020.006
cumulativeCTSSdistribution3.6890.0543.743
distclu9.2720.0279.300
dot-ctss_summary_for_clusters0.8520.0020.854
exampleCAGEexp000
exportToTrack36.811 0.24437.058
expressionClasses1.9180.0011.920
filteredCTSSidx0.0100.0000.009
flagLowExpCTSS0.0360.0000.035
genomeName000
getCTSS1.0020.0141.016
getExpressionProfiles4.9480.0504.999
getShiftingPromoters1.8680.0101.879
hanabi0.2180.0110.229
hanabiPlot0.2940.0240.317
import.CAGEscanMolecule000
import.CTSS0.0750.0000.075
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData000
inputFiles0.0020.0000.001
inputFilesType0.0010.0000.001
librarySizes0.0010.0000.000
mapStats0.0470.0010.048
mergeCAGEsets2.0210.0402.061
mergeSamples0.4780.0090.487
moleculesGR2CTSS0.1280.0040.133
normalizeTagCount0.5230.0140.514
paraclu43.718 0.26643.984
parseCAGEscanBlocksToGrangeTSS0.0210.0000.021
plotAnnot2.1690.0092.178
plotCorrelation0.2360.0000.235
plotExpressionProfiles6.9220.1227.044
plotInterquantileWidth1.9590.0091.968
plotReverseCumulatives2.3400.0032.277
quantilePositions12.364 0.02412.389
quickEnhancers000
ranges2annot0.3230.0000.322
ranges2genes0.0560.0000.056
ranges2names0.0560.0000.055
resetCAGEexp0.3110.0010.312
rowSums.RleDataFrame0.0220.0000.022
rowsum.RleDataFrame0.0230.0010.024
sampleLabels0.0040.0000.004
scoreShift22.441 0.16322.604
seqNameTotalsSE0.0040.0000.004
setColors0.2890.0010.290
strandInvaders0.5880.0180.591
summariseChrExpr0.3850.0000.385
tagClusters0.3740.0000.374