BioC 3.5: CHECK report for regioneR on toluca2

Package: regioneR

Version: 1.7.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.7.3.tar.gz

StartedAt: 2017-04-23 08:49:29 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:58:20 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 531.2 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_1.7.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/regioneR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.3’
* 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
circularRandomizeRegions 49.381  4.376  59.823
filterChromosomes        48.468  5.185  58.378
maskFromBSGenome         45.809  4.508  50.546
getMask                  44.961  4.261  52.735
localZScore               4.388  0.301   5.894
* 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	0.649	0.084	0.762
circularRandomizeRegions	49.381	4.376	59.823
commonRegions	0.426	0.084	0.515
createFunctionsList	1.936	0.245	2.232
createRandomRegions	0.130	0.002	0.133
emptyCacheRegioneR	0.000	0.000	0.001
extendRegions	0.231	0.001	0.234
filterChromosomes	48.468	5.185	58.378
getChromosomesByOrganism	0.001	0.001	0.002
getGenome	0.040	0.000	0.041
getGenomeAndMask	0.056	0.001	0.057
getMask	44.961	4.261	52.735
joinRegions	0.131	0.001	0.135
listChrTypes	0.023	0.000	0.023
localZScore	4.388	0.301	5.894
maskFromBSGenome	45.809	4.508	50.546
meanDistance	0.083	0.000	0.084
meanInRegions	0.226	0.001	0.227
mergeRegions	0.091	0.001	0.093
numOverlaps	0.163	0.067	0.231
overlapGraphicalSummary	0.165	0.001	0.170
overlapPermTest	0.796	0.005	0.812
overlapRegions	0.055	0.001	0.056
permTest	1.333	0.003	1.347
plot.localZScoreResults	1.309	0.004	1.326
plot.localZScoreResultsList	2.745	0.005	2.764
plot.permTestResults	1.960	0.005	1.978
plot.permTestResultsList	2.178	0.005	2.194
plotRegions	0.042	0.000	0.042
print.permTestResults	1.320	0.004	1.337
randomizeRegions	0.212	0.001	0.214
recomputePermTest	0.770	0.003	0.775
resampleRegions	0.038	0.000	0.039
splitRegions	0.091	0.001	0.093
subtractRegions	0.159	0.001	0.162
toDataframe	0.014	0.000	0.013
toGRanges	0.018	0.001	0.018
uniqueRegions	0.279	0.001	0.281