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This page was generated on 2025-08-12 12:05 -0400 (Tue, 12 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
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-11 13:45 -0400 (Mon, 11 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
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: 2025-08-11 23:27:01 -0400 (Mon, 11 Aug 2025)
EndedAt: 2025-08-11 23:39:17 -0400 (Mon, 11 Aug 2025)
EllapsedTime: 735.8 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 24.04.2 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                43.302  0.295  43.598
exportToTrack          36.108  0.028  36.142
scoreShift             22.237  0.193  22.430
aggregateTagClusters   20.489  0.307  20.798
annotateCTSS           12.208  0.062  12.272
quantilePositions      12.130  0.004  12.135
distclu                 9.395  0.008   9.407
plotExpressionProfiles  6.875  0.101   6.976
* 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-class2.9070.0852.993
CAGEr_Multicore3.4450.0643.508
CTSS-class0.2410.0000.241
CTSScoordinates0.0760.0020.077
CTSSnormalizedTpm0.6860.0570.744
CTSStagCount0.6190.1150.735
CTSStoGenes0.3610.0580.419
CustomConsensusClusters4.5940.0634.656
GeneExpDESeq20.4600.0150.476
GeneExpSE0.0030.0000.004
QuantileWidthFunctions0.1290.0010.131
TSSlogo2.5210.0772.601
aggregateTagClusters20.489 0.30720.798
annotateCTSS12.208 0.06212.272
byCtss0.0160.0010.017
consensusClusters0.1540.0000.154
consensusClustersDESeq21.9730.0011.974
consensusClustersTpm0.0070.0000.006
cumulativeCTSSdistribution3.6440.0413.685
distclu9.3950.0089.407
dot-ctss_summary_for_clusters0.8120.0000.813
exampleCAGEexp000
exportToTrack36.108 0.02836.142
expressionClasses1.8110.0031.814
filteredCTSSidx0.0090.0000.009
flagLowExpCTSS0.0340.0000.033
genomeName000
getCTSS0.9290.0060.935
getExpressionProfiles4.7780.0354.813
getShiftingPromoters1.8680.0041.872
hanabi0.2320.0080.240
hanabiPlot0.2880.0220.310
import.CAGEscanMolecule000
import.CTSS0.0970.0000.097
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData000
inputFiles0.0010.0000.001
inputFilesType0.0010.0000.001
librarySizes0.0010.0000.001
mapStats0.0490.0000.049
mergeCAGEsets1.9130.0241.937
mergeSamples0.4270.0080.435
moleculesGR2CTSS0.1200.0050.125
normalizeTagCount0.4680.0000.448
paraclu43.302 0.29543.598
parseCAGEscanBlocksToGrangeTSS0.0180.0020.020
plotAnnot2.1340.0212.156
plotCorrelation0.2250.0000.226
plotExpressionProfiles6.8750.1016.976
plotInterquantileWidth1.9300.0041.934
plotReverseCumulatives2.2410.0042.187
quantilePositions12.130 0.00412.135
quickEnhancers000
ranges2annot0.3330.0000.333
ranges2genes0.0550.0010.057
ranges2names0.0830.0000.083
resetCAGEexp0.3080.0000.308
rowSums.RleDataFrame0.020.000.02
rowsum.RleDataFrame0.0220.0000.022
sampleLabels0.0030.0000.003
scoreShift22.237 0.19322.430
seqNameTotalsSE0.0030.0000.003
setColors0.2920.0000.292
strandInvaders0.5860.0260.597
summariseChrExpr0.3860.0010.386
tagClusters0.3820.0010.383