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This page was generated on 2025-08-18 12:03 -0400 (Mon, 18 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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: 2025-08-17 13:45 -0400 (Sun, 17 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 24.04.3 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    ERROR  


CHECK results for BindingSiteFinder on nebbiolo2

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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BindingSiteFinder_2.7.1.tar.gz
StartedAt: 2025-08-17 20:21:01 -0400 (Sun, 17 Aug 2025)
EndedAt: 2025-08-17 20:37:01 -0400 (Sun, 17 Aug 2025)
EllapsedTime: 960.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BindingSiteFinder.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BindingSiteFinder_2.7.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-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 ‘2.7.1’
* 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 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 38.494  0.587  44.944
quickFigure                30.541  0.062  30.642
processingStepsFlowChart   26.924  0.114  27.040
BSFind                     26.507  0.282  26.791
calculateBsFoldChange      16.523  0.042  16.567
plotBsMA                   10.896  0.039  10.936
plotBsVolcano              10.515  0.021  10.538
geneRegulationPlot         10.256  0.057  10.314
estimateBsWidthPlot        10.005  0.049  10.054
estimateBsWidth             9.550  0.113   9.664
bindingSiteCoveragePlot     9.172  0.079   9.251
rangeCoveragePlot           5.918  0.036   6.002
* 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-3.22-bioc/meat/BindingSiteFinder.Rcheck/00check.log’
for details.


Installation output

BindingSiteFinder.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BindingSiteFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-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: 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 
268.040   2.602 270.966 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.220.020.24
BSFind26.507 0.28226.791
add-BSFDataSet2.1490.0132.163
annotateWithScore1.3960.0061.402
assignToGenes1.9850.0041.991
assignToTranscriptRegions2.3380.0032.344
bindingSiteCoveragePlot9.1720.0799.251
bindingSiteDefinednessPlot38.494 0.58744.944
calculateBsBackground4.680.014.69
calculateBsFoldChange16.523 0.04216.567
calculateSignalToFlankScore1.5390.0251.564
clipCoverage1.7980.0081.805
collapseReplicates0.2120.0020.213
combineBSF3.1270.0113.138
coverageOverRanges0.9670.0030.970
duplicatedSitesPlot0.5950.0030.599
estimateBsWidth9.5500.1139.664
estimateBsWidthPlot10.005 0.04910.054
exportTargetGenes0.0480.0040.051
exportToBED0.0480.0040.052
filterBsBackground3.6290.0023.632
geneOverlapsPlot2.6880.0072.696
geneRegulationPlot10.256 0.05710.314
getMeta0.0490.0060.055
getName0.0520.0020.053
getRanges0.0700.0010.071
getSignal0.0910.0020.093
getSummary1.1770.0041.181
globalScorePlot1.4810.0031.485
imputeBsDifferencesForTestdata2.1450.0042.150
makeBindingSites2.5450.0042.549
makeBsSummaryPlot1.2980.0051.303
mergeCrosslinkDiagnosticsPlot1.3380.0021.340
mergeSummaryPlot3.9080.0033.911
plotBsBackgroundFilter4.6160.0494.670
plotBsMA10.896 0.03910.936
plotBsVolcano10.515 0.02110.538
processingStepsFlowChart26.924 0.11427.040
processingStepsTable0.0840.0030.086
pureClipGeneWiseFilter0.3830.0020.384
pureClipGlobalFilter0.0790.0050.084
pureClipGlobalFilterPlot0.3210.0030.324
quickFigure30.541 0.06230.642
rangeCoveragePlot5.9180.0366.002
reproducibilityCutoffPlot2.5340.0042.538
reproducibilityFilter1.5990.0041.603
reproducibilityFilterPlot2.0080.0492.057
reproducibilitySamplesPlot1.8340.0091.843
reproducibilityScatterPlot3.8120.0063.819
setMeta0.0520.0060.057
setName0.0510.0030.054
setRanges0.0770.0030.081
setSignal0.0790.0030.083
setSummary0.0470.0080.054
show0.1020.0080.109
subset-BSFDataSet0.0710.0030.073
summary0.0730.0050.078
supportRatio3.4980.0473.546
supportRatioPlot3.6240.0023.627
targetGeneSpectrumPlot3.5370.1513.688
transcriptRegionOverlapsPlot2.5450.0182.563
transcriptRegionSpectrumPlot2.4840.0052.489