Back to Multiple platform build/check report for BioC 3.22:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-06 12:04 -0400 (Mon, 06 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4853
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4640
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4585
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 271/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 2.15.1  (landing page)
Charles Plessy
Snapshot Date: 2025-10-05 13:45 -0400 (Sun, 05 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 lconway

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: 2025-10-05 20:14:44 -0400 (Sun, 05 Oct 2025)
EndedAt: 2025-10-05 20:26:50 -0400 (Sun, 05 Oct 2025)
EllapsedTime: 725.9 seconds
RetCode: 0
Status:   OK  
CheckDir: CAGEr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/CAGEr.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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                 54.030  0.235  54.462
exportToTrack           47.424  0.331  48.074
scoreShift              25.538  0.204  25.869
aggregateTagClusters    25.262  0.176  25.547
quantilePositions       16.945  0.162  17.203
annotateCTSS            15.378  0.087  15.552
distclu                 11.699  0.062  11.813
plotExpressionProfiles  10.051  0.125  10.228
getExpressionProfiles    6.644  0.047   6.726
CAGEexp-class            5.286  1.115   6.456
CustomConsensusClusters  6.194  0.036   6.249
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CAGEr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/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-class5.2861.1156.456
CAGEr_Multicore3.6440.0163.673
CTSS-class0.3210.0020.324
CTSScoordinates0.1190.0030.123
CTSSnormalizedTpm0.8570.0130.874
CTSStagCount0.8590.0720.933
CTSStoGenes0.5990.0510.652
CustomConsensusClusters6.1940.0366.249
GeneExpDESeq20.6180.0180.638
GeneExpSE0.0060.0010.006
QuantileWidthFunctions0.1680.0010.170
TSSlogo3.5600.0563.639
aggregateTagClusters25.262 0.17625.547
annotateCTSS15.378 0.08715.552
byCtss0.0150.0010.015
consensusClusters0.1950.0040.199
consensusClustersDESeq22.4910.0152.520
consensusClustersTpm0.0090.0010.009
cumulativeCTSSdistribution4.6670.0484.739
distclu11.699 0.06211.813
dot-ctss_summary_for_clusters1.1290.0091.145
exampleCAGEexp0.0000.0010.001
exportToTrack47.424 0.33148.074
expressionClasses2.2300.0102.252
filteredCTSSidx0.0110.0000.011
flagLowExpCTSS0.0360.0000.036
genomeName0.0000.0000.001
getCTSS1.1850.0191.210
getExpressionProfiles6.6440.0476.726
getShiftingPromoters2.2180.0122.238
hanabi0.2620.0050.268
hanabiPlot0.3470.0160.365
import.CAGEscanMolecule0.0000.0000.001
import.CTSS0.0990.0030.101
import.bam0.0010.0000.001
import.bedCTSS0.0000.0010.001
import.bedScore0.0010.0000.000
import.bedmolecule000
importPublicData0.0000.0010.001
inputFiles0.0010.0010.001
inputFilesType0.0020.0010.002
librarySizes0.0010.0000.002
mapStats0.0540.0060.061
mergeCAGEsets2.6880.0352.737
mergeSamples0.6370.0060.645
moleculesGR2CTSS0.1510.0020.153
normalizeTagCount0.6870.0080.699
paraclu54.030 0.23554.462
parseCAGEscanBlocksToGrangeTSS0.0310.0010.033
plotAnnot4.0170.0504.088
plotCorrelation0.2980.0040.305
plotExpressionProfiles10.051 0.12510.228
plotInterquantileWidth3.0020.0213.045
plotReverseCumulatives3.3710.0233.415
quantilePositions16.945 0.16217.203
quickEnhancers0.0000.0010.000
ranges2annot0.4340.0040.439
ranges2genes0.0870.0030.091
ranges2names0.0620.0000.063
resetCAGEexp0.3780.0020.382
rowSums.RleDataFrame0.0260.0000.027
rowsum.RleDataFrame0.0320.0010.034
sampleLabels0.0050.0010.005
scoreShift25.538 0.20425.869
seqNameTotalsSE0.0040.0000.005
setColors0.4880.0050.494
strandInvaders0.9000.1011.015
summariseChrExpr0.6240.0040.629
tagClusters0.4660.0110.478