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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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.1.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck’
* using R version 3.2.1 (2015-06-18)
* using platform: x86_64-unknown-linux-gnu (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 ... [13s/13s] 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 ... [127s/127s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
createRandomRegions 19.086 1.165 20.311
filterChromosomes 18.052 1.210 19.398
circularRandomizeRegions 18.088 0.999 19.266
maskFromBSGenome 16.208 1.742 17.993
randomizeRegions 16.121 1.460 17.706
getMask 15.954 1.294 17.285
* 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
‘/home/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck/00check.log’
for details.