Package: splicegear

Version: 1.9.0

Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check splicegear_1.9.0.tar.gz

RetCode: 0

Time: 50.6 seconds

Status: WARNINGS

CheckDir: splicegear.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/splicegear.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-08-06 r42439)
* checking for file 'splicegear/DESCRIPTION' ... OK
* this is package 'splicegear' version '1.9.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'splicegear' can be installed ... WARNING
Found the following significant warnings:
  Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
  Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
  Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
  Warning: The exprSet class is deprecated, use ExpressionSet instead
See '/home/biocbuild/bbs-2.1-bioc/meat/splicegear.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 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
grid.plot.SpliceExprSet: no visible binding for global variable
  'm.ylim'
isSpliceSiteOnProbe: no visible global function definition for 'error'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'as.data.frame.SpliceExprSet':
  as.data.frame.SpliceSites as.data.frame.SpliceExprSet

S3 methods shown with full name in documentation object 'barplot.SpliceSites':
  barplot.SpliceSites

S3 methods shown with full name in documentation object 'plot.SpliceExprSet':
  plot.SpliceExprSet

S3 methods shown with full name in documentation object 'plot.SpliceSites':
  plot.Probes plot.SpliceSites

S3 methods shown with full name in documentation object 'plot.SpliceSitesGenomic':
  plot.SpliceSitesGenomic

S3 methods shown with full name in documentation object 'sort.SpliceExprSet':
  sort.SpliceExprSet

S3 methods shown with full name in documentation object 'split.SpliceSites':
  split.SpliceSites

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking data for non-ASCII characters ... OK
* creating splicegear-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating splicegear-manual.tex ... OK
* checking splicegear-manual.tex ... OK

WARNING: There was 1 warning, see
  /home/biocbuild/bbs-2.1-bioc/meat/splicegear.Rcheck/00check.log
for details

* Installing *source* package 'splicegear' ...
** R
** data
** inst
** preparing package for lazy loading
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
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead
Warning: The exprSet class is deprecated, use ExpressionSet instead
** help
Note: unmatched right brace in 'grid.helpers' on or after line 28
Note: unmatched right brace in 'plot.SpliceSitesGenomic' on or after line 6
 >>> 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)