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This page was generated on 2025-10-02 12:03 -0400 (Thu, 02 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4844
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4631
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4576
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 270/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.1  (landing page)
Charles Plessy
Snapshot Date: 2025-10-01 13:45 -0400 (Wed, 01 Oct 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: 2025-10-01 22:12:16 -0400 (Wed, 01 Oct 2025)
EndedAt: 2025-10-01 22:29:47 -0400 (Wed, 01 Oct 2025)
EllapsedTime: 1051.6 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 Patched (2025-08-23 r88802)
* 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                 54.826  3.472  61.540
exportToTrack           46.767  0.500  49.945
aggregateTagClusters    26.502  1.073  28.683
scoreShift              25.849  0.425  27.999
plotReverseCumulatives  19.753  0.108   5.329
annotateCTSS            16.391  0.391  17.275
quantilePositions       15.225  0.008  16.190
distclu                 11.145  0.158  11.524
plotExpressionProfiles  10.657  0.331  11.247
getExpressionProfiles    6.344  0.267   7.036
CustomConsensusClusters  5.654  0.432   6.522
normalizeTagCount        5.499  0.093   1.247
plotInterquantileWidth   4.906  0.371   5.337
* 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-class3.7430.3794.502
CAGEr_Multicore3.7130.6404.779
CTSS-class0.3180.0000.400
CTSScoordinates0.1180.0030.121
CTSSnormalizedTpm0.9940.0831.138
CTSStagCount0.9430.1431.150
CTSStoGenes0.4260.0790.563
CustomConsensusClusters5.6540.4326.522
GeneExpDESeq20.5750.0470.630
GeneExpSE0.0040.0010.005
QuantileWidthFunctions0.1570.0070.163
TSSlogo3.5920.2623.912
aggregateTagClusters26.502 1.07328.683
annotateCTSS16.391 0.39117.275
byCtss0.0250.0000.025
consensusClusters0.2310.0020.233
consensusClustersDESeq22.4650.0152.487
consensusClustersTpm0.0060.0000.006
cumulativeCTSSdistribution4.2670.0704.541
distclu11.145 0.15811.524
dot-ctss_summary_for_clusters1.0180.0041.085
exampleCAGEexp000
exportToTrack46.767 0.50049.945
expressionClasses2.4730.0022.639
filteredCTSSidx0.0140.0010.014
flagLowExpCTSS0.0520.0000.053
genomeName0.0000.0000.001
getCTSS1.1030.0101.216
getExpressionProfiles6.3440.2677.036
getShiftingPromoters2.7150.3083.144
hanabi0.3670.0430.414
hanabiPlot0.4400.0680.507
import.CAGEscanMolecule000
import.CTSS0.1390.0300.177
import.bam000
import.bedCTSS000
import.bedScore000
import.bedmolecule000
importPublicData0.0000.0000.001
inputFiles0.0010.0000.002
inputFilesType0.0010.0000.001
librarySizes0.0020.0000.001
mapStats0.0560.0060.063
mergeCAGEsets2.7930.3463.264
mergeSamples0.6810.0560.743
moleculesGR2CTSS0.1960.0150.212
normalizeTagCount5.4990.0931.247
paraclu54.826 3.47261.540
parseCAGEscanBlocksToGrangeTSS0.0240.0000.024
plotAnnot4.2370.0444.440
plotCorrelation0.3970.0170.418
plotExpressionProfiles10.657 0.33111.247
plotInterquantileWidth4.9060.3715.337
plotReverseCumulatives19.753 0.108 5.329
quantilePositions15.225 0.00816.190
quickEnhancers000
ranges2annot0.5690.0010.573
ranges2genes0.0890.0010.090
ranges2names0.0890.0000.089
resetCAGEexp0.4690.0000.480
rowSums.RleDataFrame0.0250.0000.024
rowsum.RleDataFrame0.0270.0000.027
sampleLabels0.0050.0000.004
scoreShift25.849 0.42527.999
seqNameTotalsSE0.0060.0000.006
setColors0.5170.0060.525
strandInvaders2.4300.0430.906
summariseChrExpr0.4810.0020.484
tagClusters0.4620.0050.486