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This page was generated on 2025-08-22 12:06 -0400 (Fri, 22 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4599
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4541
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 268/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.1  (landing page)
Charles Plessy
Snapshot Date: 2025-08-21 13:45 -0400 (Thu, 21 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: 2025-08-21 18:28:41 -0400 (Thu, 21 Aug 2025)
EndedAt: 2025-08-21 18:32:15 -0400 (Thu, 21 Aug 2025)
EllapsedTime: 214.6 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              12.211  0.050  12.318
exportToTrack        10.449  0.070  10.549
scoreShift            6.311  0.049   6.417
aggregateTagClusters  6.097  0.049   6.171
* 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-class1.7130.2581.992
CAGEr_Multicore1.5900.0061.602
CTSS-class0.0760.0010.085
CTSScoordinates0.0250.0010.026
CTSSnormalizedTpm0.2120.0050.218
CTSStagCount0.2030.0150.221
CTSStoGenes0.1600.0080.168
CustomConsensusClusters1.3470.0061.360
GeneExpDESeq20.1650.0050.171
GeneExpSE0.0010.0000.001
QuantileWidthFunctions0.0560.0010.057
TSSlogo0.7510.0120.781
aggregateTagClusters6.0970.0496.171
annotateCTSS3.4970.0103.515
byCtss0.0060.0010.007
consensusClusters0.0450.0010.045
consensusClustersDESeq20.5550.0010.556
consensusClustersTpm0.0020.0000.002
cumulativeCTSSdistribution1.1750.0231.200
distclu2.6760.0082.698
dot-ctss_summary_for_clusters0.2520.0030.254
exampleCAGEexp0.0000.0000.001
exportToTrack10.449 0.07010.549
expressionClasses0.5130.0010.515
filteredCTSSidx0.0030.0000.003
flagLowExpCTSS0.0110.0000.011
genomeName000
getCTSS0.3670.0060.373
getExpressionProfiles1.6230.0061.641
getShiftingPromoters0.5480.0010.561
hanabi0.0770.0040.081
hanabiPlot0.0920.0070.105
import.CAGEscanMolecule000
import.CTSS0.0250.0010.026
import.bam000
import.bedCTSS000
import.bedScore0.0000.0010.000
import.bedmolecule000
importPublicData000
inputFiles0.0000.0000.001
inputFilesType0.0010.0000.000
librarySizes0.0000.0000.001
mapStats0.0170.0020.018
mergeCAGEsets0.7570.0130.784
mergeSamples0.1940.0030.197
moleculesGR2CTSS0.0390.0000.039
normalizeTagCount0.2210.0040.225
paraclu12.211 0.05012.318
parseCAGEscanBlocksToGrangeTSS0.0050.0010.006
plotAnnot0.6810.0050.687
plotCorrelation0.0690.0010.071
plotExpressionProfiles2.1830.0682.264
plotInterquantileWidth0.6460.0020.652
plotReverseCumulatives1.3120.0281.350
quantilePositions3.5720.0343.612
quickEnhancers000
ranges2annot0.0970.0000.097
ranges2genes0.0170.0000.017
ranges2names0.0170.0000.017
resetCAGEexp0.0910.0000.092
rowSums.RleDataFrame0.0070.0000.007
rowsum.RleDataFrame0.0070.0010.008
sampleLabels0.0010.0000.001
scoreShift6.3110.0496.417
seqNameTotalsSE0.0010.0000.001
setColors0.1330.0020.135
strandInvaders0.2470.0310.278
summariseChrExpr0.1770.0130.194
tagClusters0.1340.0100.144