Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-08-21 11:38 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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: 2025-08-18 13:40 -0400 (Mon, 18 Aug 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 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for BindingSiteFinder on nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BindingSiteFinder_2.6.0.tar.gz
StartedAt: 2025-08-20 20:27:17 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 20:43:17 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 959.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BindingSiteFinder.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BindingSiteFinder_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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
bindingSiteDefinednessPlot 38.097  1.828  44.729
quickFigure                31.217  0.273  31.573
BSFind                     26.941  0.928  27.872
processingStepsFlowChart   26.471  0.062  26.784
calculateBsFoldChange      17.970  0.906  18.877
plotBsMA                   11.110  0.026  11.138
plotBsVolcano              10.820  0.027  10.849
geneRegulationPlot         10.469  0.020  10.490
bindingSiteCoveragePlot    10.053  0.318  10.374
estimateBsWidthPlot        10.087  0.156  10.244
estimateBsWidth             9.790  0.143   9.934
rangeCoveragePlot           5.512  0.026   5.540
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/BindingSiteFinder.Rcheck/00check.log’
for details.


Installation output

BindingSiteFinder.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BindingSiteFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
264.843   2.007 266.851 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.1670.0060.175
BSFind26.941 0.92827.872
add-BSFDataSet2.1960.0482.246
annotateWithScore1.4440.0211.468
assignToGenes1.9690.0161.985
assignToTranscriptRegions2.3080.0072.316
bindingSiteCoveragePlot10.053 0.31810.374
bindingSiteDefinednessPlot38.097 1.82844.729
calculateBsBackground4.6450.0264.671
calculateBsFoldChange17.970 0.90618.877
calculateSignalToFlankScore1.4890.0121.501
clipCoverage1.8060.0021.808
collapseReplicates0.1700.0030.172
combineBSF3.1360.0513.187
coverageOverRanges0.9770.0040.982
duplicatedSitesPlot0.5820.0090.591
estimateBsWidth9.7900.1439.934
estimateBsWidthPlot10.087 0.15610.244
exportTargetGenes0.0240.0000.024
exportToBED0.0250.0000.025
filterBsBackground3.6920.0023.695
geneOverlapsPlot2.6830.0042.687
geneRegulationPlot10.469 0.02010.490
getMeta0.0270.0000.027
getName0.0240.0010.025
getRanges0.0420.0020.044
getSignal0.0680.0020.070
getSummary1.1670.0041.171
globalScorePlot1.4450.0011.446
imputeBsDifferencesForTestdata2.1840.0022.186
makeBindingSites2.5130.0252.539
makeBsSummaryPlot1.3480.0041.353
mergeCrosslinkDiagnosticsPlot1.3400.0021.342
mergeSummaryPlot3.8040.0043.809
plotBsBackgroundFilter4.6960.0704.767
plotBsMA11.110 0.02611.138
plotBsVolcano10.820 0.02710.849
processingStepsFlowChart26.471 0.06226.784
processingStepsTable0.0580.0020.060
pureClipGeneWiseFilter0.3920.0090.402
pureClipGlobalFilter0.0560.0010.057
pureClipGlobalFilterPlot0.2690.0020.270
quickFigure31.217 0.27331.573
rangeCoveragePlot5.5120.0265.540
reproducibilityCutoffPlot2.5280.0012.529
reproducibilityFilter1.6520.0051.657
reproducibilityFilterPlot2.1120.0012.122
reproducibilitySamplesPlot1.6840.0021.687
reproducibilityScatterPlot3.6740.0063.680
setMeta0.0290.0010.029
setName0.0240.0010.026
setRanges0.0500.0010.050
setSignal0.0520.0000.053
setSummary0.0260.0010.026
show0.0250.0010.026
subset-BSFDataSet0.0390.0000.039
summary0.0450.0020.047
supportRatio3.4070.0253.432
supportRatioPlot3.6160.0063.624
targetGeneSpectrumPlot2.2370.0052.242
transcriptRegionOverlapsPlot2.5600.0162.576
transcriptRegionSpectrumPlot2.5260.0042.529