Back to Multiple platform build/check report for BioC 3.19:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-28 17:39 -0400 (Fri, 28 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4362
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 168/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BindingSiteFinder 2.2.0  (landing page)
Mirko Brüggemann
Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024)
git_url: https://git.bioconductor.org/packages/BindingSiteFinder
git_branch: RELEASE_3_19
git_last_commit: 1e3a377
git_last_commit_date: 2024-04-30 11:36:02 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


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: 2.2.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BindingSiteFinder_2.2.0.tar.gz
StartedAt: 2024-06-26 20:56:15 -0400 (Wed, 26 Jun 2024)
EndedAt: 2024-06-26 21:11:12 -0400 (Wed, 26 Jun 2024)
EllapsedTime: 897.1 seconds
RetCode: 0
Status:   OK  
CheckDir: BindingSiteFinder.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BindingSiteFinder_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BindingSiteFinder’ version ‘2.2.0’
* 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 ... OK
* 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                28.914  0.176  29.091
BSFind                     25.811  0.584  26.398
bindingSiteDefinednessPlot 25.431  0.416  25.847
processingStepsFlowChart   23.887  0.032  23.920
calculateBsFoldChange      16.853  0.160  17.015
plotBsVolcano              16.175  0.076  16.250
plotBsMA                   13.104  0.164  13.269
estimateBsWidth             9.219  0.024   9.244
bindingSiteCoveragePlot     8.870  0.216   9.088
estimateBsWidthPlot         8.254  0.028   8.282
plotBsBackgroundFilter      6.731  0.112   6.847
rangeCoveragePlot           4.978  0.063   5.042
* 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: OK


Installation output

BindingSiteFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BindingSiteFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘BindingSiteFinder’ ...
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 1 | SKIP 0 | PASS 236 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 236 ]
> 
> proc.time()
   user  system elapsed 
244.834   2.444 247.270 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.1950.0040.200
BSFind25.811 0.58426.398
add-BSFDataSet1.9850.0162.002
annotateWithScore1.2750.0081.285
assignToGenes1.8190.0001.819
assignToTranscriptRegions2.1520.0032.155
bindingSiteCoveragePlot8.8700.2169.088
bindingSiteDefinednessPlot25.431 0.41625.847
calculateBsBackground4.7590.1564.916
calculateBsFoldChange16.853 0.16017.015
calculateSignalToFlankScore1.3320.0041.336
clipCoverage1.640.001.64
collapseReplicates0.1670.0000.167
combineBSF3.160.003.16
coverageOverRanges0.9090.0030.912
duplicatedSitesPlot0.5670.0000.567
estimateBsWidth9.2190.0249.244
estimateBsWidthPlot8.2540.0288.282
exportTargetGenes0.0220.0040.026
exportToBED0.0260.0000.026
filterBsBackground3.3390.0043.342
geneOverlapsPlot2.4540.0082.463
getMeta0.0290.0000.029
getName0.0250.0030.028
getRanges0.0380.0080.045
getSignal0.0620.0040.067
getSummary1.0770.0121.090
globalScorePlot1.3310.0201.351
imputeBsDifferencesForTestdata2.0080.0042.012
makeBindingSites2.2580.0002.258
makeBsSummaryPlot1.2520.0001.252
mergeCrosslinkDiagnosticsPlot1.4430.0001.442
mergeSummaryPlot3.8890.0483.938
plotBsBackgroundFilter6.7310.1126.847
plotBsMA13.104 0.16413.269
plotBsVolcano16.175 0.07616.250
processingStepsFlowChart23.887 0.03223.920
processingStepsTable0.0580.0000.058
pureClipGeneWiseFilter0.3390.0000.339
pureClipGlobalFilter0.0550.0000.055
pureClipGlobalFilterPlot0.2460.0000.246
quickFigure28.914 0.17629.091
rangeCoveragePlot4.9780.0635.042
reproducibilityCutoffPlot2.3650.0042.369
reproducibilityFilter1.4500.0001.449
reproducibilityFilterPlot1.8110.0041.815
reproducibilitySamplesPlot1.5720.0281.600
reproducibilityScatterPlot3.2190.0003.219
setMeta0.0300.0000.031
setName0.0270.0000.028
setRanges0.0470.0040.051
setSignal0.0730.0040.077
setSummary0.0290.0000.029
show0.0280.0000.028
subset-BSFDataSet0.0390.0000.039
summary0.0470.0000.047
supportRatio3.0930.0043.097
supportRatioPlot3.3230.0003.323
targetGeneSpectrumPlot1.9920.0041.995
transcriptRegionOverlapsPlot2.3040.0042.308
transcriptRegionSpectrumPlot2.2740.0002.274