regioneR 1.1.1 Bernat Gel
Snapshot Date: 2015-06-21 16:31:12 -0700 (Sun, 21 Jun 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/regioneR | Last Changed Rev: 104558 / Revision: 105281 | Last Changed Date: 2015-06-04 06:39:34 -0700 (Thu, 04 Jun 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | | |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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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_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck’
* using R version 3.2.1 (2015-06-18)
* 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 ‘1.1.1’
* 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 ... [17s/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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
plot:
function(x, ...)
plot.localZScoreResults:
function(lz, main, num.x.labels, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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 ‘seqlevels’
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 'plot.localZScoreResults':
plot.localZScoreResults
Code: function(lz, main = "", num.x.labels = 5, ...)
Docs: function(x, ...)
Argument names in code not in docs:
lz main num.x.labels
Argument names in docs not in code:
x
Mismatches in argument names:
Position: 1 Code: lz Docs: x
Position: 2 Code: main Docs: ...
Codoc mismatches from documentation object 'plot.permTestResults':
plot.permTestResults
Code: function(x, pvalthres = 0.05, plotType = "Tailed", main = "",
xlab = NULL, ylab = "", ...)
Docs: function(x, pvalthres = 0.05, plotType = "Area", ...)
Argument names in code not in docs:
main xlab ylab
Mismatches in argument names:
Position: 4 Code: main Docs: ...
Mismatches in argument default values:
Name: 'plotType' Code: "Tailed" Docs: "Area"
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
‘figure’
Please remove from your package.
* checking examples ... [357s/392s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
createRandomRegions 53.289 5.179 58.726
filterChromosomes 51.781 4.957 56.855
circularRandomizeRegions 51.811 4.524 76.780
maskFromBSGenome 50.419 4.769 56.197
getMask 50.050 4.248 60.443
randomizeRegions 48.761 4.666 53.554
characterToBSGenome 0.525 0.083 8.036
* 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 WARNINGs, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck/00check.log’
for details.