BioC 2.12: CHECK report for splicegear on george2

Package: splicegear

Version: 1.32.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings splicegear_1.32.0.tar.gz

StartedAt: 2013-10-09 05:08:18 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:11:40 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 201.6 seconds

RetCode: 0

Status:  OK

CheckDir: splicegear.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/splicegear.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘splicegear/DESCRIPTION’ ... OK
* this is package ‘splicegear’ version ‘1.32.0’
* 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 ‘splicegear’ can be installed ... [17s/21s] 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

buildSpliceSites: warning in matrix(unlist(spsiteIpos[spsiteIpos.i]),
  nc = 2, byrow = TRUE): partial argument match of 'nc' to 'ncol'
getRelSignStrength: warning in matrix(NaN, nc = ncol(x), nr = nrow(x)):
  partial argument match of 'nr' to 'nrow'
getRelSignStrength: warning in matrix(NaN, nc = ncol(x), nr = nrow(x)):
  partial argument match of 'nc' to 'ncol'
grid.plot.Probes: warning in viewport(xscale = xlim, yscale = ylim, w =
  0.9, h = 0.9): partial argument match of 'w' to 'width'
grid.plot.Probes: warning in viewport(xscale = xlim, yscale = ylim, w =
  0.9, h = 0.9): partial argument match of 'h' to 'height'
grid.plot.SpliceSites: warning in viewport(xscale = xlim, yscale =
  ylim, w = 0.9, h = 0.9): partial argument match of 'w' to 'width'
grid.plot.SpliceSites: warning in viewport(xscale = xlim, yscale =
  ylim, w = 0.9, h = 0.9): partial argument match of 'h' to 'height'
plot.SpliceExprSet: warning in layout(matrix(c(1, 2), 1, 2), width =
  fig.xratio, height = fig.yratio): partial argument match of 'width'
  to 'widths'
plot.SpliceExprSet: warning in layout(matrix(c(1, 2), 1, 2), width =
  fig.xratio, height = fig.yratio): partial argument match of 'height'
  to 'heights'
* checking Rd files ... NOTE
prepare_Rd: isProbeOnSpliceSite.Rd:18-19: Dropping empty section \details
prepare_Rd: isProbeOnSpliceSite.Rd:31-33: Dropping empty section \examples
prepare_Rd: sort.SpliceExprSet.Rd:18-20: Dropping empty section \details
prepare_Rd: spliceset.Rd:29-31: Dropping empty section \source
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [11s/11s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/splicegear.Rcheck/00check.log’
for details.

* installing *source* package ‘splicegear’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘splicegear’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: ignoring .First.lib() for package ‘splicegear’
* DONE (splicegear)

name	user	system	elapsed
Probes-class	0.424	0.008	0.438
SpliceExprSet-class	0.068	0.004	0.072
SpliceSites-class	0.46	0.00	0.46
SpliceSitesGenomic-class	0.028	0.004	0.033
as.data.frame.SpliceExprSet	0.120	0.000	0.118
barplot.SpliceSites	0.024	0.000	0.025
buildSpliceSites	1.064	0.028	1.098
getRelSignStrength	0.120	0.008	0.128
grid.plot.SpliceSites	0.432	0.004	0.434
plot.SpliceExprSet	0.104	0.000	0.105
plot.SpliceSites	0.032	0.000	0.034
plot.SpliceSitesGenomic	0.04	0.00	0.04
sort.SpliceExprSet	0.016	0.000	0.016
spliceset	0.048	0.008	0.062
split.SpliceSites	0.020	0.004	0.025