BioC 3.5: CHECK report for regioneR on oaxaca

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: 2017-03-04 07:56:19 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:05:13 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 534.7 seconds

RetCode: 0

Status:  OK

CheckDir: regioneR.Rcheck

Warnings: 0

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


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/regioneR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 50.055  4.621  70.272
filterChromosomes        49.427  4.948  55.676
maskFromBSGenome         45.662  3.874  50.749
getMask                  44.697  3.768  61.684
characterToBSGenome       0.680  0.095   9.432
* 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	0.680	0.095	9.432
circularRandomizeRegions	50.055	4.621	70.272
commonRegions	0.374	0.057	0.432
createFunctionsList	1.746	0.218	1.964
createRandomRegions	0.116	0.001	0.116
emptyCacheRegioneR	0.001	0.000	0.000
extendRegions	0.201	0.001	0.201
filterChromosomes	49.427	4.948	55.676
getChromosomesByOrganism	0.001	0.000	0.001
getGenome	0.036	0.001	0.036
getGenomeAndMask	0.055	0.001	0.057
getMask	44.697	3.768	61.684
joinRegions	0.104	0.001	0.146
listChrTypes	0.013	0.000	0.014
localZScore	3.220	0.255	4.629
maskFromBSGenome	45.662	3.874	50.749
meanDistance	0.081	0.000	0.081
meanInRegions	0.157	0.000	0.157
mergeRegions	0.084	0.001	0.086
numOverlaps	0.125	0.056	0.180
overlapGraphicalSummary	0.137	0.001	0.139
overlapPermTest	0.825	0.004	0.832
overlapRegions	0.055	0.000	0.056
permTest	1.384	0.003	1.388
plot.localZScoreResults	1.176	0.002	1.179
plot.localZScoreResultsList	2.765	0.004	2.773
plot.permTestResults	1.733	0.004	1.743
plot.permTestResultsList	1.913	0.005	1.921
plotRegions	0.033	0.000	0.034
print.permTestResults	1.225	0.002	1.229
randomizeRegions	0.193	0.001	0.194
recomputePermTest	0.710	0.002	0.711
resampleRegions	0.030	0.001	0.031
splitRegions	0.059	0.000	0.059
subtractRegions	0.149	0.001	0.150
toDataframe	0.014	0.000	0.015
toGRanges	0.021	0.000	0.021
uniqueRegions	0.234	0.001	0.237