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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 174/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BindingSiteFinder 2.6.0  (landing page)
Mirko Brüggemann
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/BindingSiteFinder
git_branch: RELEASE_3_21
git_last_commit: efff5d6
git_last_commit_date: 2025-04-15 12:35:25 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for BindingSiteFinder on merida1

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: 2.6.0
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_2.6.0.tar.gz
StartedAt: 2025-10-14 00:32:53 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 01:06:38 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 2024.9 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_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘2.6.0’
* 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                    77.082  0.687  78.503
processingStepsFlowChart       65.589  4.351  84.731
bindingSiteDefinednessPlot     63.567  0.749 102.545
BSFind                         63.000  0.833  64.851
calculateBsFoldChange          36.888  1.087  72.494
plotBsMA                       28.150  0.554  30.892
geneRegulationPlot             26.194  2.223  28.816
plotBsVolcano                  25.818  1.423  28.816
estimateBsWidthPlot            20.809  0.323  21.442
estimateBsWidth                19.134  0.506  20.497
bindingSiteCoveragePlot        15.843  0.461  16.402
rangeCoveragePlot              14.072  0.142  14.288
reproducibilityScatterPlot     12.968  0.130  13.415
plotBsBackgroundFilter         12.662  0.267  14.086
calculateBsBackground          10.839  0.241  21.649
mergeSummaryPlot                9.974  0.319  11.298
supportRatioPlot                8.857  0.060   9.271
filterBsBackground              8.669  0.118   8.974
supportRatio                    8.246  0.062   8.596
reproducibilityCutoffPlot       7.474  0.060   7.686
geneOverlapsPlot                7.042  0.177   7.430
transcriptRegionSpectrumPlot    6.537  0.044   6.670
transcriptRegionOverlapsPlot    6.385  0.041   6.458
combineBSF                      5.761  0.274   9.625
targetGeneSpectrumPlot          5.829  0.027   5.882
imputeBsDifferencesForTestdata  5.547  0.047   5.710
reproducibilityFilterPlot       5.505  0.037   5.621
assignToTranscriptRegions       5.142  0.068   5.221
makeBindingSites                4.920  0.061   5.120
clipCoverage                    4.208  0.136   8.778
calculateSignalToFlankScore     3.377  0.145   7.524
* 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-3.21-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 ‘2.6.0’
** 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 RC (2025-06-05 r88288) -- "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: GenomeInfoDb
> 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 
641.193   6.658 666.292 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.3530.0080.379
BSFind63.000 0.83364.851
add-BSFDataSet4.7680.0514.842
annotateWithScore3.4300.0233.539
assignToGenes4.8350.0264.876
assignToTranscriptRegions5.1420.0685.221
bindingSiteCoveragePlot15.843 0.46116.402
bindingSiteDefinednessPlot 63.567 0.749102.545
calculateBsBackground10.839 0.24121.649
calculateBsFoldChange36.888 1.08772.494
calculateSignalToFlankScore3.3770.1457.524
clipCoverage4.2080.1368.778
collapseReplicates0.2810.0210.904
combineBSF5.7610.2749.625
coverageOverRanges2.1280.0482.227
duplicatedSitesPlot1.5280.0831.622
estimateBsWidth19.134 0.50620.497
estimateBsWidthPlot20.809 0.32321.442
exportTargetGenes0.0330.0030.036
exportToBED0.0370.0020.039
filterBsBackground8.6690.1188.974
geneOverlapsPlot7.0420.1777.430
geneRegulationPlot26.194 2.22328.816
getMeta0.0280.0030.034
getName0.0250.0020.049
getRanges0.0530.0030.059
getSignal0.0860.0040.105
getSummary2.1470.0522.407
globalScorePlot3.3640.0403.525
imputeBsDifferencesForTestdata5.5470.0475.710
makeBindingSites4.9200.0615.120
makeBsSummaryPlot3.0090.0383.248
mergeCrosslinkDiagnosticsPlot3.0540.0413.195
mergeSummaryPlot 9.974 0.31911.298
plotBsBackgroundFilter12.662 0.26714.086
plotBsMA28.150 0.55430.892
plotBsVolcano25.818 1.42328.816
processingStepsFlowChart65.589 4.35184.731
processingStepsTable0.1110.0020.113
pureClipGeneWiseFilter0.8460.0200.932
pureClipGlobalFilter0.1050.0020.109
pureClipGlobalFilterPlot0.9780.0060.992
quickFigure77.082 0.68778.503
rangeCoveragePlot14.072 0.14214.288
reproducibilityCutoffPlot7.4740.0607.686
reproducibilityFilter3.8550.0283.903
reproducibilityFilterPlot5.5050.0375.621
reproducibilitySamplesPlot4.2670.0274.361
reproducibilityScatterPlot12.968 0.13013.415
setMeta0.0480.0030.052
setName0.0400.0030.044
setRanges0.1010.0030.104
setSignal0.1110.0050.140
setSummary0.0420.0020.059
show0.0410.0030.056
subset-BSFDataSet0.0690.0030.079
summary0.0860.0030.091
supportRatio8.2460.0628.596
supportRatioPlot8.8570.0609.271
targetGeneSpectrumPlot5.8290.0275.882
transcriptRegionOverlapsPlot6.3850.0416.458
transcriptRegionSpectrumPlot6.5370.0446.670