BioC 3.5: CHECK report for regioneR on veracruz2

Package: regioneR

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.8.1.tar.gz

StartedAt: 2017-08-16 07:16:50 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:25:02 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 492.8 seconds

RetCode: 0

Status:  OK

CheckDir: regioneR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/regioneR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.8.1’
* 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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
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 ... NOTE
commonRegions: no visible global function definition for ‘hasArg’
createFunctionsList: no visible global function definition for ‘hasArg’
extendRegions: no visible global function definition for ‘hasArg’
joinRegions: no visible global function definition for ‘hasArg’
localZScore: no visible global function definition for ‘hasArg’
meanDistance: no visible global function definition for ‘hasArg’
meanInRegions: no visible global function definition for ‘hasArg’
mergeRegions: no visible global function definition for ‘hasArg’
numOverlaps: no visible global function definition for ‘hasArg’
overlapGraphicalSummary: no visible global function definition for
  ‘hasArg’
overlapPermTest: no visible global function definition for ‘hasArg’
overlapRegions: no visible global function definition for ‘hasArg’
overlapRegions: no visible global function definition for ‘queryHits’
overlapRegions: no visible global function definition for ‘subjectHits’
permTest: no visible global function definition for ‘hasArg’
plot.localZScoreResultsList: no visible global function definition for
  ‘is’
plot.permTestResultsList: no visible global function definition for
  ‘is’
plotRegions: no visible global function definition for ‘hasArg’
randomizeRegions: no visible global function definition for ‘hasArg’
removeOverlapping: no visible global function definition for
  ‘queryHits’
removeOverlapping: no visible global function definition for
  ‘subjectHits’
resampleRegions: no visible global function definition for ‘hasArg’
splitRegions: no visible global function definition for ‘hasArg’
subtractRegions: no visible global function definition for ‘hasArg’
toDataframe: no visible global function definition for ‘hasArg’
toDataframe: no visible global function definition for ‘is’
toGRanges: no visible global function definition for ‘hasArg’
toGRanges: no visible global function definition for ‘is’
toGRanges : <anonymous>: no visible global function definition for
  ‘read.delim’
toGRanges : <anonymous> : <anonymous>: no visible global function
  definition for ‘read.csv’
uniqueRegions: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  hasArg is queryHits read.csv read.delim subjectHits
Consider adding
  importFrom("methods", "hasArg", "is")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
filterChromosomes        48.229  4.750  56.627
circularRandomizeRegions 48.720  4.152  56.536
maskFromBSGenome         46.311  4.397  52.037
getMask                  46.043  4.289  51.701
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/regioneR.Rcheck/00check.log’
for details.

* installing *source* package ‘regioneR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (regioneR)

name	user	system	elapsed
characterToBSGenome	0.679	0.087	0.780
circularRandomizeRegions	48.720	4.152	56.536
commonRegions	0.337	0.003	0.348
createFunctionsList	1.754	0.212	2.036
createRandomRegions	0.110	0.001	0.111
emptyCacheRegioneR	0.001	0.000	0.001
extendRegions	0.195	0.001	0.202
filterChromosomes	48.229	4.750	56.627
getChromosomesByOrganism	0.001	0.001	0.001
getGenome	0.034	0.000	0.035
getGenomeAndMask	1.070	0.175	1.293
getMask	46.043	4.289	51.701
joinRegions	0.129	0.001	0.133
listChrTypes	0.020	0.000	0.021
localZScore	3.501	0.282	4.867
maskFromBSGenome	46.311	4.397	52.037
meanDistance	0.080	0.001	0.082
meanInRegions	0.183	0.004	0.190
mergeRegions	0.075	0.002	0.081
numOverlaps	0.126	0.002	0.139
overlapGraphicalSummary	0.149	0.002	0.159
overlapPermTest	0.667	0.016	0.704
overlapRegions	0.043	0.001	0.045
permTest	1.156	0.023	1.210
plot.localZScoreResults	1.144	0.024	1.188
plot.localZScoreResultsList	2.304	0.046	2.389
plot.permTestResults	1.677	0.030	1.753
plot.permTestResultsList	1.730	0.005	1.805
plotRegions	0.033	0.001	0.034
print.permTestResults	1.090	0.002	1.115
randomizeRegions	0.176	0.001	0.180
recomputePermTest	0.616	0.002	0.648
resampleRegions	0.027	0.000	0.027
splitRegions	0.058	0.001	0.059
subtractRegions	0.128	0.001	0.135
toDataframe	0.013	0.000	0.013
toGRanges	0.012	0.000	0.012
uniqueRegions	0.218	0.000	0.231