Package: splicegear

Version: 1.8.0

Command: /home/biocbuild/bbs-2.0-bioc/R/bin/R CMD build splicegear

RetCode: 0

Time: 6.5 seconds

Status: OK

PackageFile: splicegear_1.8.0.tar.gz

* checking for file 'splicegear/DESCRIPTION' ... OK
* preparing 'splicegear':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* Installing *source* package 'splicegear' ...
** R
** data
** inst
** save image
Loading required package: grid
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: XML
Loading required package: annotate
[1] TRUE
[1] "SpliceSites"
Warning messages:
1: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead 
2: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead 
3: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead 
[1] "show"
[1] "plot"
[1] "plot"
[1] "initialize"
[1] "grid.plot"
[1] "grid.plot"
[1] "Probes"
[1] "initialize"
[1] "show"
[1] "plot"
[1] "plot"
[1] "grid.plot"
[1] "grid.plot"
[1] "SpliceSitesGenomic"
[1] "plot"
[1] TRUE
[1] "SpliceExprSet"
Warning message:
The exprSet class is deprecated, use ExpressionSet instead 
[1] "spliceSites"
[1] "spliceSites"
[1] "exprs"
[1] "exprs<-"
[1] "show"
[1] "plot"
[1] "grid.plot"
** help
 >>> Building/Updating help pages for package 'splicegear'
     Formats: text html latex example 
  Probes-class                      text    html    latex   example
  SpliceExprSet-class               text    html    latex   example
  SpliceSites-class                 text    html    latex   example
  SpliceSitesGenomic-class          text    html    latex   example
  as.data.frame.SpliceExprSet       text    html    latex   example
  barplot.SpliceSites               text    html    latex   example
  buildSpliceSites                  text    html    latex   example
  getRelSignStrength                text    html    latex   example
  grid.helpers                      text    html    latex
  grid.plot.SpliceSites             text    html    latex   example
  isProbeOnSpliceSite               text    html    latex   example
  matchprobes2Probes                text    html    latex
  plot.SpliceExprSet                text    html    latex   example
  plot.SpliceSites                  text    html    latex   example
  plot.SpliceSitesGenomic           text    html    latex   example
  sort.SpliceExprSet                text    html    latex   example
  spliceset                         text    html    latex   example
  split.SpliceSites                 text    html    latex   example
** building package indices ...
* DONE (splicegear)
* creating vignettes ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building 'splicegear_1.8.0.tar.gz'