BioC 3.3: CHECK report for regioneR on oaxaca

Package: regioneR

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.4.2.tar.gz

StartedAt: 2016-10-13 05:36:27 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:44:55 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 508.2 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_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/regioneR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.4.2’
* 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
overlapRegions: no visible global function definition for ‘queryHits’
overlapRegions: no visible global function definition for ‘subjectHits’
removeOverlapping: no visible global function definition for
  ‘queryHits’
removeOverlapping: no visible global function definition for
  ‘subjectHits’
toGRanges : <anonymous>: no visible global function definition for
  ‘read.delim’
toGRanges : <anonymous> : <anonymous>: no visible global function
  definition for ‘read.csv’
Undefined global functions or variables:
  queryHits read.csv read.delim subjectHits
Consider adding
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file.
* 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        51.867  5.241  59.256
circularRandomizeRegions 49.811  5.180  78.191
maskFromBSGenome         47.688  4.672  52.534
getMask                  47.805  4.520  52.515
characterToBSGenome       0.939  0.113  10.941
* 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-3.3-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	0.939	0.113	10.941
circularRandomizeRegions	49.811	5.180	78.191
commonRegions	0.268	0.021	0.345
createFunctionsList	1.602	0.243	2.057
createRandomRegions	0.140	0.022	0.165
emptyCacheRegioneR	0.001	0.000	0.001
extendRegions	0.125	0.001	0.126
filterChromosomes	51.867	5.241	59.256
getChromosomesByOrganism	0.001	0.000	0.002
getGenome	0.042	0.000	0.043
getGenomeAndMask	0.540	0.066	0.606
getMask	47.805	4.520	52.515
joinRegions	0.104	0.001	0.105
listChrTypes	0.015	0.001	0.016
localZScore	3.412	0.259	4.712
maskFromBSGenome	47.688	4.672	52.534
meanDistance	0.092	0.000	0.092
meanInRegions	0.132	0.001	0.133
mergeRegions	0.099	0.001	0.100
numOverlaps	0.170	0.000	0.171
overlapGraphicalSummary	0.122	0.000	0.139
overlapPermTest	0.731	0.002	0.967
overlapRegions	0.049	0.001	0.050
permTest	1.088	0.002	1.098
plot.localZScoreResults	1.330	0.002	1.334
plot.localZScoreResultsList	2.842	0.052	2.903
plot.permTestResults	2.013	0.006	2.023
plot.permTestResultsList	2.298	0.005	2.786
plotRegions	0.044	0.001	0.077
print.permTestResults	1.261	0.003	2.376
randomizeRegions	0.212	0.001	0.383
recomputePermTest	0.817	0.003	1.443
resampleRegions	0.048	0.000	0.101
splitRegions	0.093	0.000	0.169
subtractRegions	0.162	0.001	0.305
toDataframe	0.016	0.001	0.024
toGRanges	0.019	0.000	0.048
uniqueRegions	0.310	0.001	0.587