BioC 2.12: CHECK report for motifRG on petty

Package: motifRG

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch motifRG_1.4.0.tar.gz

StartedAt: 2013-10-08 23:07:58 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:14:10 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 372.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: motifRG.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/motifRG.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'motifRG/DESCRIPTION' ... OK
* this is package 'motifRG' version '1.4.0'
* 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 'motifRG' can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated 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
matchPWMCoor: no visible global function definition for 'GRanges'
* 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 'findMotif':
findMotif
  Code: function(all.seq, category, weights = rep(1, length(all.seq)),
                 start.width = 6, min.cutoff = 5, min.ratio = 1.3,
                 min.frac = 0.01, both.strand = T, flank = 2, max.motif
                 = 5, mask = T, other.data = NULL, start.nmer = NULL,
                 enriched.only = F, n.bootstrap = 5, bootstrap.pvalue =
                 0.1, is.parallel = T, mc.cores = 4, min.info = 10,
                 max.width = 15, discretize = T)
  Docs: function(all.seq, category, weights = rep(1, length(all.seq)),
                 start.width = 6, min.cutoff = 5, min.ratio = 1.3,
                 min.frac = 0.01, both.strand = T, flank = 2, max.motif
                 = 5, mask = T, other.data = NULL, start.nmer = NULL,
                 enriched.only = F, n.bootstrap = 5, bootstrap.pvalue =
                 0.1, is.parallel = T, mc.cores = 4, min.info = 10,
                 max.width = 15, discretize = TRUE)
  Mismatches in argument default values:
    Name: 'discretize' Code: T Docs: TRUE

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [269s/193s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
findMotif      160.500 90.668 168.201
refinePWMMotif   6.972  0.662   8.198
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/motifRG.Rcheck/00check.log'
for details.

* installing *source* package 'motifRG' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifRG)

name	user	system	elapsed
control.seq	0.183	0.026	0.591
ctcf.seq	0.180	0.021	0.416
findMotif	160.500	90.668	168.201
motifLatexTable	0.606	0.040	0.684
plotMotif	0.177	0.010	0.198
refinePWMMotif	6.972	0.662	8.198
summaryMotif	0.144	0.007	0.291