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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BindingSiteFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BindingSiteFinder_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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                    78.081  1.166  90.004
processingStepsFlowChart       67.040  6.966  99.383
bindingSiteDefinednessPlot     67.568  1.349  92.695
BSFind                         66.966  1.038  80.213
calculateBsFoldChange          40.009  1.944  89.562
plotBsMA                       28.793  3.990  38.290
plotBsVolcano                  26.868  2.477  35.390
estimateBsWidth                22.328  4.496  53.924
estimateBsWidthPlot            20.729  0.904  23.783
bindingSiteCoveragePlot        17.546  0.635  22.238
rangeCoveragePlot              15.121  2.212  21.215
calculateBsBackground          13.185  0.208  26.545
plotBsBackgroundFilter         11.546  0.438  14.189
filterBsBackground              9.425  0.296  10.585
mergeSummaryPlot                9.388  0.159  10.356
reproducibilityScatterPlot      9.064  0.101  10.452
supportRatioPlot                8.775  0.096  10.358
supportRatio                    8.462  0.279  10.129
globalScorePlot                 5.116  2.352   8.475
geneOverlapsPlot                6.570  0.206  13.607
transcriptRegionSpectrumPlot    6.613  0.063   7.816
transcriptRegionOverlapsPlot    6.564  0.075   7.443
combineBSF                      6.361  0.216  13.010
reproducibilityCutoffPlot       6.337  0.083   7.679
assignToTranscriptRegions       6.196  0.074   7.855
imputeBsDifferencesForTestdata  5.761  0.202   6.717
makeBindingSites                5.810  0.102   6.283
targetGeneSpectrumPlot          5.746  0.082   6.519
assignToGenes                   5.412  0.078   6.796
add-BSFDataSet                  5.120  0.078   5.981
reproducibilityFilterPlot       4.947  0.054   5.810
reproducibilitySamplesPlot      4.322  0.049   5.113
clipCoverage                    4.212  0.130   8.971
calculateSignalToFlankScore     3.268  0.140   8.340
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BindingSiteFinder
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
667.235   7.813 784.245