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This page was generated on 2025-10-03 12:03 -0400 (Fri, 03 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4845
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4632
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4577
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4576
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 175/2337HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BindingSiteFinder 2.7.1  (landing page)
Mirko Brüggemann
Snapshot Date: 2025-10-02 13:45 -0400 (Thu, 02 Oct 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: 2025-10-02 21:24:43 -0400 (Thu, 02 Oct 2025)
EndedAt: 2025-10-02 21:49:05 -0400 (Thu, 02 Oct 2025)
EllapsedTime: 1462.6 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
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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
quickFigure                41.989  0.252  46.357
bindingSiteDefinednessPlot 38.208  0.439  40.299
BSFind                     38.017  0.414  44.947
processingStepsFlowChart   35.533  0.388  37.550
calculateBsFoldChange      24.954  0.201  26.379
plotBsVolcano              14.486  0.115  17.253
plotBsMA                   14.356  0.092  16.527
geneRegulationPlot         14.138  0.245  17.204
estimateBsWidth            13.211  0.062  16.579
estimateBsWidthPlot        12.640  0.256  14.728
bindingSiteCoveragePlot    12.283  0.342  13.032
reproducibilityScatterPlot  7.796  0.133   9.491
rangeCoveragePlot           7.790  0.070   8.778
calculateBsBackground       6.788  0.035   7.147
plotBsBackgroundFilter      6.222  0.070   6.841
supportRatioPlot            5.188  0.021   5.351
filterBsBackground          5.008  0.177   5.759
mergeSummaryPlot            4.997  0.005   5.974
supportRatio                4.630  0.030   5.030
combineBSF                  4.128  0.009   5.217
* 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

##############################################################################
##############################################################################
###
### 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 Patched (2025-08-23 r88802) -- "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 
382.245   5.592 402.953 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.2460.0080.280
BSFind38.017 0.41444.947
add-BSFDataSet2.6810.1163.177
annotateWithScore1.7740.0102.775
assignToGenes2.8510.0093.064
assignToTranscriptRegions2.8630.0053.231
bindingSiteCoveragePlot12.283 0.34213.032
bindingSiteDefinednessPlot38.208 0.43940.299
calculateBsBackground6.7880.0357.147
calculateBsFoldChange24.954 0.20126.379
calculateSignalToFlankScore2.4800.0032.536
clipCoverage2.3550.0072.666
collapseReplicates0.2600.0040.265
combineBSF4.1280.0095.217
coverageOverRanges1.5320.0031.537
duplicatedSitesPlot0.9580.0060.986
estimateBsWidth13.211 0.06216.579
estimateBsWidthPlot12.640 0.25614.728
exportTargetGenes0.0780.0040.081
exportToBED0.0800.0030.083
filterBsBackground5.0080.1775.759
geneOverlapsPlot3.3340.1663.927
geneRegulationPlot14.138 0.24517.204
getMeta0.0620.0040.163
getName0.0670.0010.096
getRanges0.0980.0040.102
getSignal0.1620.0230.185
getSummary1.4230.0391.481
globalScorePlot2.0300.0132.798
imputeBsDifferencesForTestdata2.6670.0383.049
makeBindingSites3.3350.0373.422
makeBsSummaryPlot2.2080.0092.253
mergeCrosslinkDiagnosticsPlot1.7700.0062.063
mergeSummaryPlot4.9970.0055.974
plotBsBackgroundFilter6.2220.0706.841
plotBsMA14.356 0.09216.527
plotBsVolcano14.486 0.11517.253
processingStepsFlowChart35.533 0.38837.550
processingStepsTable0.0980.0080.106
pureClipGeneWiseFilter0.4860.0020.530
pureClipGlobalFilter0.1000.0050.104
pureClipGlobalFilterPlot0.5330.0080.591
quickFigure41.989 0.25246.357
rangeCoveragePlot7.7900.0708.778
reproducibilityCutoffPlot3.6460.0124.719
reproducibilityFilter2.1800.0012.202
reproducibilityFilterPlot2.8880.0243.450
reproducibilitySamplesPlot2.1250.0103.282
reproducibilityScatterPlot7.7960.1339.491
setMeta0.0830.0060.089
setName0.0820.0030.085
setRanges0.1170.0040.121
setSignal0.1240.0030.127
setSummary0.0760.0070.082
show0.0800.0040.084
subset-BSFDataSet0.0970.0070.103
summary0.1120.0040.116
supportRatio4.630.035.03
supportRatioPlot5.1880.0215.351
targetGeneSpectrumPlot3.5190.0133.587
transcriptRegionOverlapsPlot3.1680.0213.306
transcriptRegionSpectrumPlot3.1850.0083.372