Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-09-29 11:37 -0400 (Mon, 29 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4580
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 268/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.14.0  (landing page)
Charles Plessy
Snapshot Date: 2025-09-25 13:40 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/CAGEr
git_branch: RELEASE_3_21
git_last_commit: 446e1ca
git_last_commit_date: 2025-04-15 10:18:00 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for CAGEr on nebbiolo1

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: 2.14.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CAGEr_2.14.0.tar.gz
StartedAt: 2025-09-28 21:37:11 -0400 (Sun, 28 Sep 2025)
EndedAt: 2025-09-28 21:49:49 -0400 (Sun, 28 Sep 2025)
EllapsedTime: 758.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CAGEr.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CAGEr_2.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-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 ‘2.14.0’
* 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                43.881  0.212  44.112
exportToTrack          35.683  0.020  35.704
aggregateTagClusters   20.060  0.127  20.188
scoreShift             18.049  0.298  18.347
quantilePositions      12.488  0.129  12.616
annotateCTSS           11.995  0.142  12.137
distclu                 9.020  0.012   9.033
plotExpressionProfiles  8.173  0.055   8.228
* 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-3.21-bioc/meat/CAGEr.Rcheck/00check.log’
for details.


Installation output

CAGEr.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CAGEr’ ...
** this is package ‘CAGEr’ version ‘2.14.0’
** 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-class2.8820.1343.020
CAGEr_Multicore3.6000.1103.717
CTSS-class0.2620.0020.265
CTSScoordinates0.0760.0020.079
CTSSnormalizedTpm0.6830.0160.699
CTSStagCount0.6190.1100.731
CTSStoGenes0.3520.0580.411
CustomConsensusClusters4.6950.1114.808
GeneExpDESeq20.4870.0320.519
GeneExpSE0.0030.0010.004
QuantileWidthFunctions0.1510.0110.162
TSSlogo2.6880.0572.745
aggregateTagClusters20.060 0.12720.188
annotateCTSS11.995 0.14212.137
byCtss0.0150.0000.015
consensusClusters0.1490.0010.150
consensusClustersDESeq21.9490.0011.950
consensusClustersTpm0.0050.0000.006
cumulativeCTSSdistribution3.5310.0393.571
distclu9.0200.0129.033
dot-ctss_summary_for_clusters0.8010.0010.803
exampleCAGEexp0.0000.0010.000
exportToTrack35.683 0.02035.704
expressionClasses1.930.001.93
filteredCTSSidx0.0080.0010.009
flagLowExpCTSS0.0330.0000.034
genomeName0.0010.0000.001
getCTSS0.9390.0030.942
getExpressionProfiles4.9320.0034.935
getShiftingPromoters1.9360.0011.937
hanabi0.2390.0060.245
hanabiPlot0.2820.0280.310
import.CAGEscanMolecule000
import.CTSS0.0760.0010.077
import.bam000
import.bedCTSS0.0000.0000.001
import.bedScore000
import.bedmolecule000
importPublicData0.0000.0000.001
inputFiles0.0010.0000.001
inputFilesType0.0020.0000.002
librarySizes0.0000.0010.001
mapStats0.0520.0000.052
mergeCAGEsets2.0480.0062.054
mergeSamples0.5000.0040.504
moleculesGR2CTSS0.1310.0010.131
normalizeTagCount0.4730.0020.454
paraclu43.881 0.21244.112
parseCAGEscanBlocksToGrangeTSS0.0220.0000.023
plotAnnot3.1860.0313.218
plotCorrelation0.2270.0030.230
plotExpressionProfiles8.1730.0558.228
plotInterquantileWidth2.2850.0182.303
plotReverseCumulatives2.7980.0062.742
quantilePositions12.488 0.12912.616
quickEnhancers000
ranges2annot0.3740.0000.374
ranges2genes0.0580.0000.059
ranges2names0.0530.0000.053
resetCAGEexp0.2980.0000.297
rowSums.RleDataFrame0.0210.0000.021
rowsum.RleDataFrame0.0220.0010.023
sampleLabels0.0040.0000.004
scoreShift18.049 0.29818.347
seqNameTotalsSE0.0040.0000.005
setColors0.2980.0170.315
strandInvaders0.6150.0980.698
summariseChrExpr0.3950.0010.396
tagClusters0.3930.0060.399