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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 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
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 173/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BindingSiteFinder 2.7.1  (landing page)
Mirko Brüggemann
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 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 24.04.2 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


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: 2025-08-08 19:31:16 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 19:52:28 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 1272.9 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 (2025-06-13)
* 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
processingStepsFlowChart   37.099  4.998  54.649
quickFigure                41.148  0.557  42.286
BSFind                     32.779  0.589  33.617
bindingSiteDefinednessPlot 31.213  0.877  52.793
estimateBsWidth            13.178 10.859 166.282
calculateBsFoldChange      17.324  0.555  29.591
plotBsMA                   14.603  0.255  15.401
plotBsVolcano              13.467  0.638  37.058
geneRegulationPlot         11.814  0.415  14.458
bindingSiteCoveragePlot    10.433  0.419  10.938
estimateBsWidthPlot         9.085  0.615  15.662
rangeCoveragePlot           7.813  0.201   8.124
plotBsBackgroundFilter      6.206  0.281   6.899
supportRatioPlot            5.785  0.106   5.948
calculateBsBackground       5.571  0.219  11.828
mergeSummaryPlot            5.034  0.130   5.270
filterBsBackground          4.400  0.256   8.237
geneOverlapsPlot            2.739  0.212   6.825
* 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 (2025-06-13) -- "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 
331.428   4.695 338.056 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.2410.0190.264
BSFind32.779 0.58933.617
add-BSFDataSet2.3990.0492.461
annotateWithScore1.6160.0171.642
assignToGenes2.3570.0242.395
assignToTranscriptRegions2.6730.0712.756
bindingSiteCoveragePlot10.433 0.41910.938
bindingSiteDefinednessPlot31.213 0.87752.793
calculateBsBackground 5.571 0.21911.828
calculateBsFoldChange17.324 0.55529.591
calculateSignalToFlankScore1.6890.0793.694
clipCoverage1.9040.1034.219
collapseReplicates0.2140.0350.580
combineBSF3.0220.1264.933
coverageOverRanges1.0090.0431.546
duplicatedSitesPlot0.8290.0791.744
estimateBsWidth 13.178 10.859166.282
estimateBsWidthPlot 9.085 0.61515.662
exportTargetGenes0.0360.0050.143
exportToBED0.0350.0050.106
filterBsBackground4.4000.2568.237
geneOverlapsPlot2.7390.2126.825
geneRegulationPlot11.814 0.41514.458
getMeta0.0420.0030.050
getName0.0420.0030.046
getRanges0.0730.0120.098
getSignal0.1010.0060.113
getSummary1.4310.0351.525
globalScorePlot1.4750.0661.797
imputeBsDifferencesForTestdata2.5800.0822.866
makeBindingSites3.1450.0693.274
makeBsSummaryPlot1.5850.0301.646
mergeCrosslinkDiagnosticsPlot1.7210.0431.806
mergeSummaryPlot5.0340.1305.270
plotBsBackgroundFilter6.2060.2816.899
plotBsMA14.603 0.25515.401
plotBsVolcano13.467 0.63837.058
processingStepsFlowChart37.099 4.99854.649
processingStepsTable0.0900.0070.098
pureClipGeneWiseFilter0.4970.0130.518
pureClipGlobalFilter0.0890.0060.096
pureClipGlobalFilterPlot0.3610.0100.471
quickFigure41.148 0.55742.286
rangeCoveragePlot7.8130.2018.124
reproducibilityCutoffPlot3.4220.0663.526
reproducibilityFilter2.1460.0362.206
reproducibilityFilterPlot2.7720.0412.840
reproducibilitySamplesPlot2.2320.0332.293
reproducibilityScatterPlot4.6120.0974.741
setMeta0.0440.0050.048
setName0.0410.0050.047
setRanges0.0760.0050.081
setSignal0.0720.0050.077
setSummary0.0390.0040.044
show0.0370.0040.040
subset-BSFDataSet0.0540.0040.057
summary0.0650.0050.070
supportRatio4.2480.0514.330
supportRatioPlot5.7850.1065.948
targetGeneSpectrumPlot2.7400.0422.802
transcriptRegionOverlapsPlot3.0040.0413.071
transcriptRegionSpectrumPlot3.0970.0413.155