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This page was generated on 2025-09-25 12:05 -0400 (Thu, 25 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 174/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BindingSiteFinder 2.7.1  (landing page)
Mirko Brüggemann
Snapshot Date: 2025-09-24 13:45 -0400 (Wed, 24 Sep 2025)
git_url: https://git.bioconductor.org/packages/BindingSiteFinder
git_branch: devel
git_last_commit: c9c0024
git_last_commit_date: 2025-06-21 19:17:25 -0400 (Sat, 21 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    TIMEOUT  


CHECK results for BindingSiteFinder on lconway

To the developers/maintainers of the BindingSiteFinder package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BindingSiteFinder.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: BindingSiteFinder
Version: 2.7.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BindingSiteFinder_2.7.1.tar.gz
StartedAt: 2025-09-24 19:36:45 -0400 (Wed, 24 Sep 2025)
EndedAt: 2025-09-24 19:57:14 -0400 (Wed, 24 Sep 2025)
EllapsedTime: 1228.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BindingSiteFinder.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BindingSiteFinder_2.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/BindingSiteFinder.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 ‘BindingSiteFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BindingSiteFinder’ version ‘2.7.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘BindingSiteFinder’ 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:
  BSFind.Rd: GenomicRanges, CompressedGRangesList
  annotateWithScore.Rd: GenomicRanges
  assignToGenes.Rd: GenomicRanges, overlaps
  assignToTranscriptRegions.Rd: CompressedGRangesList, overlaps
  bindingSiteDefinednessPlot.Rd: ggplot
  calculateBsBackground.Rd: GenomicRanges
  duplicatedSitesPlot.Rd: ggplot
  estimateBsWidth.Rd: GenomicRanges
  estimateBsWidthPlot.Rd: ggplot
  geneOverlapsPlot.Rd: ggplot
  geneRegulationPlot.Rd: GenomicRanges
  globalScorePlot.Rd: ggplot
  makeBsSummaryPlot.Rd: ggplot
  mergeCrosslinkDiagnosticsPlot.Rd: ggplot
  plotBsBackgroundFilter.Rd: ggplot
  plotBsMA.Rd: ggplot
  plotBsVolcano.Rd: ggplot
  processingStepsFlowChart.Rd: ggplot
  pureClipGeneWiseFilter.Rd: GenomicRanges, overlaps
  pureClipGlobalFilter.Rd: GenomicRanges
  pureClipGlobalFilterPlot.Rd: ggplot
  reproducibilityFilterPlot.Rd: ggplot
  reproducibilitySamplesPlot.Rd: ggplot
  targetGeneSpectrumPlot.Rd: ggplot
  transcriptRegionOverlapsPlot.Rd: ggplot
  transcriptRegionSpectrumPlot.Rd: ggplot
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
quickFigure                44.117  1.405  45.960
processingStepsFlowChart   35.872  1.279  51.119
BSFind                     35.966  0.589  36.868
bindingSiteDefinednessPlot 33.662  0.618  45.371
calculateBsFoldChange      19.412  0.526  30.840
plotBsMA                   14.554  0.268  15.321
plotBsVolcano              13.272  0.264  14.173
filterBsBackground          5.665  6.300  71.990
bindingSiteCoveragePlot    11.301  0.472  11.897
geneRegulationPlot         11.090  0.233  13.218
estimateBsWidth            10.455  0.759  32.250
estimateBsWidthPlot         9.782  0.660  20.475
rangeCoveragePlot           8.166  0.173   8.436
combineBSF                  4.578  3.061  41.177
reproducibilityScatterPlot  7.031  0.091   7.208
plotBsBackgroundFilter      5.581  0.274  10.596
calculateBsBackground       4.368  0.080   5.928
geneOverlapsPlot            3.200  0.184   6.257
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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/BindingSiteFinder.Rcheck/00check.log’
for details.


Installation output

BindingSiteFinder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BindingSiteFinder’ ...
** this is package ‘BindingSiteFinder’ version ‘2.7.1’
** using staged installation
** R
** 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 (BindingSiteFinder)

Tests output

BindingSiteFinder.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("BindingSiteFinder")
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
> test_check("BindingSiteFinder")
[1] "make bs"
[1] "calc ratio"
[1] "make bs"
[1] "calc ratio"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 240 ]
> 
> proc.time()
   user  system elapsed 
332.229   4.483 338.470 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.2280.0070.239
BSFind35.966 0.58936.868
add-BSFDataSet2.6610.0532.751
annotateWithScore1.8760.0241.918
assignToGenes2.6600.0302.726
assignToTranscriptRegions2.8910.0412.957
bindingSiteCoveragePlot11.301 0.47211.897
bindingSiteDefinednessPlot33.662 0.61845.371
calculateBsBackground4.3680.0805.928
calculateBsFoldChange19.412 0.52630.840
calculateSignalToFlankScore1.4770.1264.527
clipCoverage2.2620.0642.374
collapseReplicates0.2240.0120.453
combineBSF 4.578 3.06141.177
coverageOverRanges1.0380.1204.966
duplicatedSitesPlot0.6820.0753.981
estimateBsWidth10.455 0.75932.250
estimateBsWidthPlot 9.782 0.66020.475
exportTargetGenes0.0370.0040.138
exportToBED0.0350.0030.113
filterBsBackground 5.665 6.30071.990
geneOverlapsPlot3.2000.1846.257
geneRegulationPlot11.090 0.23313.218
getMeta0.0400.0070.213
getName0.0390.0060.075
getRanges0.0640.0100.175
getSignal0.1190.0130.151
getSummary1.3490.0291.424
globalScorePlot1.9160.0512.079
imputeBsDifferencesForTestdata2.6850.0512.875
makeBindingSites2.9180.0583.107
makeBsSummaryPlot1.6070.0361.797
mergeCrosslinkDiagnosticsPlot1.4110.0411.681
mergeSummaryPlot3.8900.0954.466
plotBsBackgroundFilter 5.581 0.27410.596
plotBsMA14.554 0.26815.321
plotBsVolcano13.272 0.26414.173
processingStepsFlowChart35.872 1.27951.119
processingStepsTable0.0960.0040.103
pureClipGeneWiseFilter0.5280.0180.551
pureClipGlobalFilter0.0900.0020.093
pureClipGlobalFilterPlot0.5620.0060.573
quickFigure44.117 1.40545.960
rangeCoveragePlot8.1660.1738.436
reproducibilityCutoffPlot4.4350.1034.594
reproducibilityFilter2.2360.0442.314
reproducibilityFilterPlot2.8510.0502.939
reproducibilitySamplesPlot2.1670.0332.227
reproducibilityScatterPlot7.0310.0917.208
setMeta0.0420.0010.044
setName0.0480.0010.050
setRanges0.0770.0030.082
setSignal0.0780.0040.088
setSummary0.0410.0020.043
show0.0420.0020.044
subset-BSFDataSet0.0710.0020.074
summary0.0740.0020.077
supportRatio4.3670.0574.453
supportRatioPlot4.6760.0594.761
targetGeneSpectrumPlot2.7630.0282.805
transcriptRegionOverlapsPlot3.1680.0283.213
transcriptRegionSpectrumPlot3.3540.0353.406