Multiple platform build/check report for BioC 3.8 - CHECK report for regioneR on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:regioneR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings regioneR_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/regioneR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.14.0’
* 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 ‘regioneR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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 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 or elapsed time > 5s
                           user system elapsed
maskFromBSGenome         61.430  6.865  68.829
circularRandomizeRegions 61.208  5.418  68.427
filterChromosomes        59.524  5.778  66.591
getMask                  58.128  5.341  63.978
localZScore               3.396  0.371   5.623
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.8-bioc/meat/regioneR.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL regioneR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘regioneR’ ...
** 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
* DONE (regioneR)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

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(regioneR)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("regioneR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 75.513   6.030  82.244

Example timings

name	user	system	elapsed
characterToBSGenome	1.957	0.226	2.230
circularRandomizeRegions	61.208	5.418	68.427
commonRegions	0.254	0.002	0.259
createFunctionsList	0.906	0.117	1.148
createRandomRegions	0.243	0.002	0.270
emptyCacheRegioneR	0.001	0.001	0.001
extendRegions	0.103	0.001	0.106
filterChromosomes	59.524	5.778	66.591
getChromosomesByOrganism	0.001	0.000	0.001
getGenome	0.027	0.000	0.028
getGenomeAndMask	0.712	0.123	0.842
getMask	58.128	5.341	63.978
joinRegions	0.131	0.001	0.133
listChrTypes	0.009	0.001	0.009
localZScore	3.396	0.371	5.623
maskFromBSGenome	61.430	6.865	68.829
meanDistance	0.088	0.001	0.089
meanInRegions	0.154	0.001	0.156
mergeRegions	0.093	0.002	0.101
numOverlaps	0.179	0.001	0.183
overlapGraphicalSummary	0.109	0.001	0.111
overlapPermTest	0.874	0.024	0.903
overlapRegions	0.046	0.001	0.047
permTest	1.162	0.024	1.193
plot.localZScoreResults	1.273	0.005	1.287
plot.localZScoreResultsList	2.854	0.011	2.917
plot.permTestResults	1.934	0.006	1.958
plot.permTestResultsList	2.175	0.006	2.200
plotRegions	0.044	0.001	0.045
print.permTestResults	1.164	0.002	1.176
randomizeRegions	0.236	0.001	0.240
recomputePermTest	0.798	0.002	0.806
resampleRegions	0.045	0.001	0.046
splitRegions	0.058	0.001	0.060
subtractRegions	0.166	0.001	0.168
toDataframe	0.019	0.000	0.019
toGRanges	0.490	0.012	0.625
uniqueRegions	0.377	0.002	0.380

CHECK report for regioneR on merida1

Summary

Command output

Installation output

Tests output

Example timings