Package: splicegear

Version: 1.5.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check splicegear_1.5.0.tar.gz

RetCode: 0

Time: 86.9 seconds

Status: WARNINGS

CheckDir: splicegear.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/splicegear.Rcheck'
* using R version 2.4.0 Under development (unstable) (2006-06-04 r38279)
* checking for file 'splicegear/DESCRIPTION' ... OK
* this is package 'splicegear' version '1.5.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'splicegear' can be installed ... OK
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING
as.data.frame:
  function(x, row.names, optional, ...)
as.data.frame.SpliceExprSet:
  function(x, row.names, optional)

as.data.frame:
  function(x, row.names, optional, ...)
as.data.frame.SpliceSites:
  function(x, row.names, optional)

See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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
  /loc/biocbuild/1.9d/Rpacks/splicegear.Rcheck/00check.log
for details

* 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()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: XML
Loading required package: annotate
[1] TRUE
[1] "SpliceSites"
[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"
[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)