Package: exonmap

Version: 1.2.01

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check exonmap_1.2.01.tar.gz

RetCode: 0

Time: 81.0 seconds

Status: OK

CheckDir: exonmap.Rcheck

Warnings: 0

* checking for working latex ... OK
* using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/exonmap.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'exonmap/DESCRIPTION' ... OK
* this is package 'exonmap' version '1.2.01'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'exonmap' 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 ... NOTE
.doStoredProcedureFetch: no visible binding for global variable
  '.ExonmapConnection'
.doStoredProcedureOtherFeaturesFetch: no visible binding for global
  variable '.ExonmapOtherFeaturesConnection'
.xmapDisconnect: no visible binding for global variable
  '.ExonmapConnection'
.xmapOtherFeaturesDisconnect: no visible binding for global variable
  '.ExonmapOtherFeaturesConnection'
exon.details: no visible binding for global variable 'a'
xmapBridge: no visible binding for global variable '.ExonmapSpecies'
* 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 'plot.gene':
  plot.gene

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

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 exonmap-Ex.R ... OK
* checking examples ... OK
* creating exonmap-manual.tex ... OK
* checking exonmap-manual.tex ... OK

* Installing *source* package 'exonmap' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: affy
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: affyio
Loading required package: preprocessCore
Loading required package: simpleaffy
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: gcrma
Loading required package: matchprobes
Loading required package: RColorBrewer
Loading required package: RMySQL
Loading required package: DBI
Loading required package: plier
** help
 >>> Building/Updating help pages for package 'exonmap'
     Formats: text html latex example 
  PC-class                          text    html    latex   example
  Splanova-class                    text    html    latex   example
  X.toY                             text    html    latex   example
  array.subset                      text    html    latex   example
  gene.details                      text    html    latex   example
  gene.legend                       text    html    latex   example
  gene.strip                        text    html    latex   example
  gene.to.exon.probeset             text    html    latex   example
  group.indices                     text    html    latex   example
  pc                                text    html    latex   example
  plot.gene                         text    html    latex   example
  plot.gene.graph                   text    html    latex   example
  probeset.stats                    text    html    latex   example
  probesets.in.range                text    html    latex   example
  read.exon                         text    html    latex   example
  select.probewise                  text    html    latex   example
  splanova                          text    html    latex   example
  splicing.index                    text    html    latex   example
  x.rma                             text    html    latex
  xmapBridge                        text    html    latex   example
  xmapDatabase                      text    html    latex   example
  xmapGene                          text    html    latex   example
** building package indices ...
* DONE (exonmap)