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: 2017-10-18 08:04:02 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 08:12:26 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 503.4 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 3.4.2 (2017-09-28)
* 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        48.986  4.977  56.951
circularRandomizeRegions 49.032  4.404  56.710
getMask                  46.004  4.537  51.929
maskFromBSGenome         44.547  4.638  50.644
localZScore               3.654  0.305   5.074
* 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	0.705	0.087	0.899
circularRandomizeRegions	49.032	4.404	56.710
commonRegions	0.386	0.003	0.403
createFunctionsList	1.804	0.239	2.299
createRandomRegions	0.111	0.001	0.114
emptyCacheRegioneR	0.001	0.000	0.001
extendRegions	0.217	0.003	0.270
filterChromosomes	48.986	4.977	56.951
getChromosomesByOrganism	0.001	0.000	0.001
getGenome	0.034	0.001	0.034
getGenomeAndMask	1.116	0.199	1.352
getMask	46.004	4.537	51.929
joinRegions	0.121	0.001	0.125
listChrTypes	0.019	0.000	0.020
localZScore	3.654	0.305	5.074
maskFromBSGenome	44.547	4.638	50.644
meanDistance	0.073	0.000	0.075
meanInRegions	0.181	0.001	0.187
mergeRegions	0.077	0.001	0.081
numOverlaps	0.136	0.001	0.138
overlapGraphicalSummary	0.143	0.001	0.148
overlapPermTest	0.687	0.003	0.706
overlapRegions	0.046	0.000	0.048
permTest	1.250	0.010	1.329
plot.localZScoreResults	1.112	0.006	1.152
plot.localZScoreResultsList	2.380	0.012	2.460
plot.permTestResults	1.798	0.060	1.908
plot.permTestResultsList	2.028	0.013	2.101
plotRegions	0.036	0.001	0.038
print.permTestResults	1.136	0.007	1.189
randomizeRegions	0.201	0.002	0.205
recomputePermTest	0.760	0.005	0.797
resampleRegions	0.040	0.000	0.041
splitRegions	0.078	0.001	0.082
subtractRegions	0.157	0.002	0.165
toDataframe	0.013	0.000	0.013
toGRanges	0.017	0.001	0.017
uniqueRegions	0.232	0.002	0.239