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This page was generated on 2024-03-01 11:36:17 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 166/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BindingSiteFinder 2.1.0  (landing page)
Mirko Brüggemann
Snapshot Date: 2024-02-28 14:00:14 -0500 (Wed, 28 Feb 2024)
git_url: https://git.bioconductor.org/packages/BindingSiteFinder
git_branch: devel
git_last_commit: 8230907
git_last_commit_date: 2023-10-24 11:35:05 -0500 (Tue, 24 Oct 2023)
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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 2.1.0
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_2.1.0.tar.gz
StartedAt: 2024-02-28 20:19:20 -0500 (Wed, 28 Feb 2024)
EndedAt: 2024-02-28 20:35:02 -0500 (Wed, 28 Feb 2024)
EllapsedTime: 942.0 seconds
RetCode: 0
Status:   OK  
CheckDir: BindingSiteFinder.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_2.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BindingSiteFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BindingSiteFinder’ version ‘2.1.0’
* 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 R 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                30.062  0.104  30.167
BSFind                     27.280  0.836  28.123
bindingSiteDefinednessPlot 27.279  0.649  27.928
processingStepsFlowChart   24.865  0.112  24.983
plotBsMA                   17.594  0.084  17.679
calculateBsFoldChange      15.941  0.064  16.006
plotBsVolcano              10.102  0.084  10.187
bindingSiteCoveragePlot     9.020  0.435   9.463
estimateBsWidth             9.227  0.172   9.399
estimateBsWidthPlot         8.735  0.204   8.939
plotBsBackgroundFilter      5.741  0.084   5.827
mergeSummaryPlot            5.454  0.028   5.669
rangeCoveragePlot           5.263  0.048   5.312
* 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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 
257.414   2.380 259.792 

Example timings

BindingSiteFinder.Rcheck/BindingSiteFinder-Ex.timings

nameusersystemelapsed
BSFDataSet0.1980.0110.210
BSFind27.280 0.83628.123
add-BSFDataSet2.2430.0162.259
annotateWithScore1.4080.0051.415
assignToGenes1.9940.1162.110
assignToTranscriptRegions2.2870.1242.411
bindingSiteCoveragePlot9.0200.4359.463
bindingSiteDefinednessPlot27.279 0.64927.928
calculateBsBackground4.6990.0204.719
calculateBsFoldChange15.941 0.06416.006
calculateSignalToFlankScore1.4170.0121.429
clipCoverage1.7290.0001.730
collapseReplicates0.1830.0000.183
combineBSF2.9910.0163.007
coverageOverRanges0.9180.0000.919
duplicatedSitesPlot0.5710.0070.579
estimateBsWidth9.2270.1729.399
estimateBsWidthPlot8.7350.2048.939
exportTargetGenes0.0270.0000.026
exportToBED0.0270.0010.027
filterBsBackground3.5390.0083.547
geneOverlapsPlot3.5290.0193.549
getMeta0.0270.0040.030
getName0.0290.0000.028
getRanges0.0430.0040.047
getSignal0.0700.0000.071
getSummary1.1390.0041.143
globalScorePlot1.4100.0041.415
imputeBsDifferencesForTestdata2.1850.0042.189
makeBindingSites4.0570.0044.062
makeBsSummaryPlot1.9920.0001.992
mergeCrosslinkDiagnosticsPlot1.6680.0041.673
mergeSummaryPlot5.4540.0285.669
plotBsBackgroundFilter5.7410.0845.827
plotBsMA17.594 0.08417.679
plotBsVolcano10.102 0.08410.187
processingStepsFlowChart24.865 0.11224.983
processingStepsTable0.0610.0000.061
pureClipGeneWiseFilter0.3530.0040.356
pureClipGlobalFilter0.0570.0000.057
pureClipGlobalFilterPlot0.2600.0000.261
quickFigure30.062 0.10430.167
rangeCoveragePlot5.2630.0485.312
reproducibilityCutoffPlot2.4740.0042.479
reproducibilityFilter1.5220.0041.526
reproducibilityFilterPlot1.8710.0001.871
reproducibilitySamplesPlot1.6500.0361.685
reproducibilityScatterPlot3.4660.0163.482
setMeta0.0320.0000.031
setName0.0280.0000.028
setRanges0.0480.0040.053
setSignal0.0490.0040.053
setSummary0.0290.0000.028
show0.0280.0000.028
subset-BSFDataSet0.0400.0000.039
summary0.0430.0040.047
supportRatio3.2290.0003.228
supportRatioPlot3.5170.0403.556
targetGeneSpectrumPlot2.1440.0082.151
transcriptRegionOverlapsPlot2.4290.0002.429
transcriptRegionSpectrumPlot2.4690.0002.468