BioC 3.2: CHECK report for regioneR on oaxaca

Package: regioneR

Version: 1.2.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.2.3.tar.gz

StartedAt: 2016-04-23 03:40:40 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:50:09 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 569.0 seconds

RetCode: 0

Status: WARNINGS

CheckDir: regioneR.Rcheck

Warnings: 1

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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_1.2.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.2.3’
* 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 ... [18s/18s] 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
copySeqLevels: no visible global function definition for ‘seqlevels<-’
copySeqLevels: no visible global function definition for ‘seqlevels’
createRandomRegions: no visible global function definition for
  ‘seqlevels’
filterChromosomes: no visible global function definition for
  ‘keepSeqlevels’
randomizeRegions: no visible global function definition for ‘seqlevels’
randomizeRegions: no visible global function definition for ‘IRanges’
resampleRegions: no visible global function definition for ‘seqlevels’
toGRanges: no visible global function definition for ‘IRanges’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'characterToBSGenome':
characterToBSGenome
  Code: function(genome.name)
  Docs: function(...)
  Argument names in code not in docs:
    genome.name
  Argument names in docs not in code:
    ...
  Mismatches in argument names:
    Position: 1 Code: genome.name Docs: ...

* 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 ... [254s/324s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
filterChromosomes           52.267  5.133  57.517
getMask                     49.069  4.776  53.913
circularRandomizeRegions    48.901  4.318  81.652
maskFromBSGenome            47.784  4.661  52.568
localZScore                  4.244  0.255   6.079
plot.localZScoreResultsList  3.222  0.006   5.714
characterToBSGenome          0.829  0.218  33.782
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [68s/81s]
 [68s/81s] 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.829	0.218	33.782
circularRandomizeRegions	48.901	4.318	81.652
commonRegions	0.276	0.021	0.297
createFunctionsList	1.545	0.230	1.777
createRandomRegions	0.172	0.001	0.174
emptyCacheRegioneR	0.001	0.000	0.001
extendRegions	0.122	0.000	0.123
filterChromosomes	52.267	5.133	57.517
getChromosomesByOrganism	0.002	0.000	0.003
getGenome	0.056	0.001	0.056
getGenomeAndMask	1.304	0.261	1.567
getMask	49.069	4.776	53.913
joinRegions	0.152	0.000	0.152
listChrTypes	0.019	0.000	0.019
localZScore	4.244	0.255	6.079
maskFromBSGenome	47.784	4.661	52.568
meanDistance	0.115	0.000	0.114
meanInRegions	0.159	0.001	0.160
mergeRegions	0.139	0.001	0.141
numOverlaps	0.206	0.000	0.207
overlapGraphicalSummary	0.177	0.000	0.178
overlapPermTest	1.060	0.002	1.094
overlapRegions	0.068	0.000	0.069
permTest	1.647	0.004	1.668
plot.localZScoreResults	1.410	0.003	2.347
plot.localZScoreResultsList	3.222	0.006	5.714
plot.permTestResults	2.434	0.005	4.353
plot.permTestResultsList	2.820	0.007	4.237
plotRegions	0.063	0.001	0.064
print.permTestResults	1.626	0.012	1.642
randomizeRegions	0.248	0.000	0.249
recomputePermTest	0.988	0.002	0.991
resampleRegions	0.063	0.000	0.064
splitRegions	0.110	0.001	0.112
subtractRegions	0.171	0.001	1.033
toDataframe	0.017	0.000	0.017
toGRanges	0.02	0.00	0.02
uniqueRegions	0.329	0.001	0.809

BioC 3.2: CHECK report for regioneR on oaxaca

Summary

Command output