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This page was generated on 2025-09-22 12:04 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 174/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BindingSiteFinder 2.7.1  (landing page)
Mirko Brüggemann
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 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: 2025-09-21 19:33:57 -0400 (Sun, 21 Sep 2025)
EndedAt: 2025-09-21 19:53:46 -0400 (Sun, 21 Sep 2025)
EllapsedTime: 1188.5 seconds
RetCode: 0
Status:   OK  
CheckDir: BindingSiteFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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                42.574  0.912  51.096
BSFind                     36.034  0.591  36.930
processingStepsFlowChart   31.555  3.201  59.372
bindingSiteDefinednessPlot 33.082  0.583  44.596
calculateBsFoldChange      19.440  0.543  28.394
estimateBsWidth            11.929  3.407  68.685
plotBsMA                   13.216  0.290  15.511
plotBsVolcano              12.590  0.346  14.661
geneRegulationPlot         12.383  0.448  14.268
bindingSiteCoveragePlot    11.225  0.464  11.780
estimateBsWidthPlot         9.538  0.926  29.545
rangeCoveragePlot           7.744  0.154   8.029
reproducibilityScatterPlot  6.518  0.088   6.676
plotBsBackgroundFilter      5.469  0.299  11.800
supportRatioPlot            5.028  0.076   5.157
calculateBsBackground       4.763  0.072   6.713
filterBsBackground          4.488  0.279  10.386
mergeSummaryPlot            4.212  0.092   5.154
geneOverlapsPlot            3.253  0.312   7.482
* 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 
333.779   4.720 340.460 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.2130.0070.220
BSFind36.034 0.59136.930
add-BSFDataSet2.8550.0542.940
annotateWithScore1.8450.0221.895
assignToGenes2.3270.0262.370
assignToTranscriptRegions2.9070.0552.984
bindingSiteCoveragePlot11.225 0.46411.780
bindingSiteDefinednessPlot33.082 0.58344.596
calculateBsBackground4.7630.0726.713
calculateBsFoldChange19.440 0.54328.394
calculateSignalToFlankScore1.9270.0923.497
clipCoverage2.0760.0733.663
collapseReplicates0.1500.0160.779
combineBSF2.5530.0793.894
coverageOverRanges0.9510.0311.569
duplicatedSitesPlot0.7760.0482.147
estimateBsWidth11.929 3.40768.685
estimateBsWidthPlot 9.538 0.92629.545
exportTargetGenes0.0370.0070.100
exportToBED0.0510.0050.126
filterBsBackground 4.488 0.27910.386
geneOverlapsPlot3.2530.3127.482
geneRegulationPlot12.383 0.44814.268
getMeta0.0460.0040.052
getName0.0430.0030.046
getRanges0.0690.0180.105
getSignal0.1180.0160.139
getSummary1.1190.0241.288
globalScorePlot1.8590.0462.018
imputeBsDifferencesForTestdata2.3180.1332.867
makeBindingSites2.9820.0933.688
makeBsSummaryPlot1.8260.0451.910
mergeCrosslinkDiagnosticsPlot1.8010.0271.854
mergeSummaryPlot4.2120.0925.154
plotBsBackgroundFilter 5.469 0.29911.800
plotBsMA13.216 0.29015.511
plotBsVolcano12.590 0.34614.661
processingStepsFlowChart31.555 3.20159.372
processingStepsTable0.0980.0070.156
pureClipGeneWiseFilter0.4890.0190.605
pureClipGlobalFilter0.0920.0030.098
pureClipGlobalFilterPlot0.5460.0540.820
quickFigure42.574 0.91251.096
rangeCoveragePlot7.7440.1548.029
reproducibilityCutoffPlot3.9160.0674.084
reproducibilityFilter2.1120.0242.153
reproducibilityFilterPlot2.8480.0282.898
reproducibilitySamplesPlot3.5620.0603.653
reproducibilityScatterPlot6.5180.0886.676
setMeta0.0520.0030.056
setName0.0510.0020.053
setRanges0.0800.0030.084
setSignal0.1130.0050.119
setSummary0.0490.0030.053
show0.0500.0030.053
subset-BSFDataSet0.0630.0020.066
summary0.0770.0030.082
supportRatio4.6170.0724.735
supportRatioPlot5.0280.0765.157
targetGeneSpectrumPlot3.1760.0443.250
transcriptRegionOverlapsPlot3.4140.0443.491
transcriptRegionSpectrumPlot3.8700.0934.019