BioC 3.6: CHECK report for regioneR on veracruz1

Package: regioneR

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.9.1.tar.gz

StartedAt: 2017-08-16 07:33:07 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:41:09 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 481.6 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_1.9.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.9.1’
* 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        47.335  4.726  56.070
circularRandomizeRegions 47.698  4.042  55.255
maskFromBSGenome         44.330  4.143  49.897
getMask                  43.627  3.826  48.757
* 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-3.6-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	0.077	0.751
circularRandomizeRegions	47.698	4.042	55.255
commonRegions	0.381	0.005	0.513
createFunctionsList	1.827	0.218	2.119
createRandomRegions	0.094	0.001	0.096
emptyCacheRegioneR	0.001	0.000	0.000
extendRegions	0.203	0.001	0.237
filterChromosomes	47.335	4.726	56.070
getChromosomesByOrganism	0.001	0.000	0.001
getGenome	0.033	0.001	0.042
getGenomeAndMask	0.044	0.000	0.045
getMask	43.627	3.826	48.757
joinRegions	0.141	0.001	0.149
listChrTypes	0.021	0.000	0.022
localZScore	3.521	0.268	4.802
maskFromBSGenome	44.330	4.143	49.897
meanDistance	0.071	0.000	0.071
meanInRegions	0.182	0.002	0.189
mergeRegions	0.061	0.001	0.065
numOverlaps	0.133	0.000	0.143
overlapGraphicalSummary	0.133	0.001	0.136
overlapPermTest	0.758	0.068	0.864
overlapRegions	0.061	0.003	0.066
permTest	1.203	0.012	1.244
plot.localZScoreResults	1.104	0.004	1.150
plot.localZScoreResultsList	2.324	0.005	2.401
plot.permTestResults	1.729	0.004	1.793
plot.permTestResultsList	1.733	0.005	1.786
plotRegions	0.034	0.001	0.035
print.permTestResults	0.992	0.003	1.014
randomizeRegions	0.188	0.001	0.190
recomputePermTest	0.703	0.003	0.777
resampleRegions	0.039	0.000	0.039
splitRegions	0.084	0.001	0.088
subtractRegions	0.110	0.001	0.118
toDataframe	0.012	0.000	0.013
toGRanges	0.010	0.001	0.010
uniqueRegions	0.218	0.000	0.228