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This page was generated on 2025-09-27 12:04 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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: 2025-09-26 13:45 -0400 (Fri, 26 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: 2025-09-26 19:39:44 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 20:00:49 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 1265.1 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                43.587  0.661  44.810
processingStepsFlowChart   34.819  3.663  81.275
BSFind                     36.171  0.604  37.134
bindingSiteDefinednessPlot 35.452  0.601  46.599
estimateBsWidth            12.751 11.824 150.572
calculateBsFoldChange      17.897  0.585  31.457
plotBsMA                   12.773  0.253  13.851
geneRegulationPlot         12.088  0.295  14.253
plotBsVolcano              12.004  0.364  14.553
bindingSiteCoveragePlot    11.216  0.499  11.850
estimateBsWidthPlot        10.800  0.826  16.989
rangeCoveragePlot           8.276  0.173   8.552
reproducibilityScatterPlot  6.666  0.084   6.801
plotBsBackgroundFilter      5.557  0.255   9.141
reproducibilityCutoffPlot   5.584  0.135   5.781
mergeSummaryPlot            4.998  0.096   5.478
calculateBsBackground       4.279  0.071   6.329
filterBsBackground          3.977  0.155   6.339
geneOverlapsPlot            2.746  0.168   6.146
* 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 
330.491   4.440 336.698 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.2110.0080.285
BSFind36.171 0.60437.134
add-BSFDataSet2.8160.0582.901
annotateWithScore1.9150.0221.957
assignToGenes2.6180.0322.672
assignToTranscriptRegions3.0820.0553.171
bindingSiteCoveragePlot11.216 0.49911.850
bindingSiteDefinednessPlot35.452 0.60146.599
calculateBsBackground4.2790.0716.329
calculateBsFoldChange17.897 0.58531.457
calculateSignalToFlankScore1.4060.1102.859
clipCoverage2.4520.2353.930
collapseReplicates0.1920.0160.278
combineBSF3.1860.1473.902
coverageOverRanges1.1630.0411.930
duplicatedSitesPlot0.6990.1793.995
estimateBsWidth 12.751 11.824150.572
estimateBsWidthPlot10.800 0.82616.989
exportTargetGenes0.0400.0050.102
exportToBED0.0370.0030.047
filterBsBackground3.9770.1556.339
geneOverlapsPlot2.7460.1686.146
geneRegulationPlot12.088 0.29514.253
getMeta0.0460.0050.124
getName0.0440.0020.046
getRanges0.0720.0080.131
getSignal0.1210.0130.138
getSummary1.0890.0211.306
globalScorePlot1.5230.0321.953
imputeBsDifferencesForTestdata2.0810.0933.010
makeBindingSites2.7130.0643.052
makeBsSummaryPlot1.7480.0391.959
mergeCrosslinkDiagnosticsPlot1.6830.0251.780
mergeSummaryPlot4.9980.0965.478
plotBsBackgroundFilter5.5570.2559.141
plotBsMA12.773 0.25313.851
plotBsVolcano12.004 0.36414.553
processingStepsFlowChart34.819 3.66381.275
processingStepsTable0.0950.0040.100
pureClipGeneWiseFilter0.4920.0070.517
pureClipGlobalFilter0.0840.0030.087
pureClipGlobalFilterPlot0.5740.0140.593
quickFigure43.587 0.66144.810
rangeCoveragePlot8.2760.1738.552
reproducibilityCutoffPlot5.5840.1355.781
reproducibilityFilter2.0360.0322.087
reproducibilityFilterPlot2.8160.0502.892
reproducibilitySamplesPlot2.1630.0342.216
reproducibilityScatterPlot6.6660.0846.801
setMeta0.0470.0020.049
setName0.0470.0020.049
setRanges0.0780.0030.080
setSignal0.0810.0020.084
setSummary0.0430.0020.046
show0.0470.0020.050
subset-BSFDataSet0.0610.0020.062
summary0.0700.0030.073
supportRatio4.1140.0494.188
supportRatioPlot4.5460.0494.623
targetGeneSpectrumPlot2.6910.0282.734
transcriptRegionOverlapsPlot3.0460.0573.118
transcriptRegionSpectrumPlot3.3340.0443.400