Package: splicegear

Version: 1.8.0

Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check splicegear_1.8.0.tar.gz

RetCode: 0

Time: 78.0 seconds

Status: OK

CheckDir: splicegear.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-bioc/meat/splicegear.Rcheck'
* using R version 2.5.0 (2007-04-23)
* checking for file 'splicegear/DESCRIPTION' ... OK
* this is package 'splicegear' version '1.8.0'
* 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 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 ... OK
* 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 ... OK
* 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

installing R.css in D:/biocbld/bbs-2.0-bioc/meat/splicegear.Rcheck


---------- Making package splicegear ------------
  adding build stamp to DESCRIPTION
  installing R files
  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"
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'splicegear'
     Formats: text html latex example chm 
  Probes-class                      text    html    latex   example chm
  SpliceExprSet-class               text    html    latex   example chm
  SpliceSites-class                 text    html    latex   example chm
  SpliceSitesGenomic-class          text    html    latex   example chm
  as.data.frame.SpliceExprSet       text    html    latex   example chm
  barplot.SpliceSites               text    html    latex   example chm
  buildSpliceSites                  text    html    latex   example chm
  getRelSignStrength                text    html    latex   example chm
  grid.helpers                      text    html    latex           chm
  grid.plot.SpliceSites             text    html    latex   example chm
  isProbeOnSpliceSite               text    html    latex   example chm
  matchprobes2Probes                text    html    latex           chm
  plot.SpliceExprSet                text    html    latex   example chm
  plot.SpliceSites                  text    html    latex   example chm
  plot.SpliceSitesGenomic           text    html    latex   example chm
  sort.SpliceExprSet                text    html    latex   example chm
  spliceset                         text    html    latex   example chm
  split.SpliceSites                 text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.0-bioc\meat\splicegear.Rcheck\00_pkg_src\splicegear\chm\splicegear.chm


Compile time: 0 minutes, 0 seconds
19	Topics
105	Local links
0	Internet links
1	Graphic


Created d:\biocbld\bbs-2.0-bioc\meat\splicegear.Rcheck\00_pkg_src\splicegear\chm\splicegear.chm, 36,573 bytes
Compression decreased file by 38,159 bytes.
  adding MD5 sums

* DONE (splicegear)