##############################################################################
##############################################################################
###
### 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_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BindingSiteFinder.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘2.6.0’
* 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 ... 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                    77.797  0.481  79.621
processingStepsFlowChart       64.827  0.847  74.089
bindingSiteDefinednessPlot     63.783  1.111 123.291
BSFind                         62.111  0.887  63.766
calculateBsFoldChange          39.163  1.287  65.999
plotBsVolcano                  27.565  4.643  40.196
plotBsMA                       26.567  0.867  31.671
geneRegulationPlot             25.878  0.212  27.101
estimateBsWidthPlot            22.284  0.462  24.743
estimateBsWidth                19.268  0.292  20.505
bindingSiteCoveragePlot        17.142  0.462  18.322
rangeCoveragePlot              13.829  0.186  14.240
plotBsBackgroundFilter         12.559  0.249  13.947
reproducibilityScatterPlot     12.607  0.058  12.900
mergeSummaryPlot               11.366  0.361  12.704
calculateBsBackground          10.600  0.386  23.124
combineBSF                      8.224  2.562  12.360
filterBsBackground              9.080  0.222   9.839
supportRatioPlot                8.799  0.085   8.974
supportRatio                    8.081  0.043   8.208
reproducibilityCutoffPlot       7.499  0.057   7.623
geneOverlapsPlot                7.011  0.096   7.377
transcriptRegionSpectrumPlot    6.694  0.044   6.890
transcriptRegionOverlapsPlot    6.404  0.038   6.527
assignToTranscriptRegions       5.920  0.110   6.185
makeBindingSites                5.828  0.059   6.016
targetGeneSpectrumPlot          5.854  0.032   6.018
imputeBsDifferencesForTestdata  5.634  0.077   5.810
reproducibilityFilterPlot       5.414  0.026   5.547
assignToGenes                   5.168  0.039   5.561
add-BSFDataSet                  4.934  0.062   5.175
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/BindingSiteFinder.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BindingSiteFinder
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BindingSiteFinder’ ...
** this is package ‘BindingSiteFinder’ version ‘2.6.0’
** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 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
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: GenomeInfoDb
> 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 
641.125   6.445 670.906