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splicegear

1.8.0

Laurent
Last Changed Date: 2007-04-24 11:21:48 -0700
Last Changed Rev: 24214
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
churchill Solaris 2.9 sparc  ERROR skipped
lemming Windows Server 2003 (32-bit) x64  OK  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) x64  OK  OK  OK 
derby Mac OS X (10.4.9) i686  OK [ OK ]
Package: splicegear
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check splicegear_1.8.0.tar.gz
RetCode: 0
Time: 66.2 seconds
Status: OK
CheckDir: splicegear.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/Users/biocbuild/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 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 ... 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

splicegear.Rcheck/00install.out:

* 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)