Package: exonmap

Version: 1.0.07

Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check exonmap_1.0.07.tar.gz

RetCode: 0

Time: 88.5 seconds

Status: WARNINGS

CheckDir: exonmap.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-bioc/meat/exonmap.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'exonmap/DESCRIPTION' ... OK
* this is package 'exonmap' version '1.0.07'
* 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 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 ... WARNING
Codoc mismatches from documentation object 'splanova':
splanova
  Code: function(x, genesin, group, base, thr = 0.05, probes.min = 4,
                 exonic = TRUE, debug = 0)
  Docs: function(x, genesin, group, base, thr = 0.05, probes.min = 4,
                 exonic = T, debug = 0)
  Mismatches in argument default values:
    Name: exonic Code: TRUE Docs: T

* checking Rd \usage sections ... OK
* 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

WARNING: There was 1 warning, see
  D:/biocbld/bbs-2.0-bioc/meat/exonmap.Rcheck/00check.log
for details

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


---------- Making package exonmap ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'exonmap'
     Formats: text html latex example chm 
  PC-class                          text    html    latex   example chm
  Splanova-class                    text    html    latex   example chm
  X.toY                             text    html    latex   example chm
  array.subset                      text    html    latex   example chm
  gene.details                      text    html    latex   example chm
  gene.legend                       text    html    latex   example chm
  gene.strip                        text    html    latex   example chm
  gene.to.exon.probeset             text    html    latex   example chm
  group.indices                     text    html    latex   example chm
  pc                                text    html    latex   example chm
  plot.gene                         text    html    latex   example chm
  plot.gene.graph                   text    html    latex   example chm
  probeset.stats                    text    html    latex   example chm
  probesets.in.range                text    html    latex   example chm
  read.exon                         text    html    latex   example chm
  select.probewise                  text    html    latex   example chm
  splanova                          text    html    latex   example chm
  splicing.index                    text    html    latex   example chm
  x.rma                             text    html    latex           chm
  xmapDatabase                      text    html    latex   example chm
  xmapGene                          text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

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


Compile time: 0 minutes, 0 seconds
22	Topics
97	Local links
18	Internet links
1	Graphic


Created d:\biocbld\bbs-2.0-bioc\meat\exonmap.Rcheck\00_pkg_src\exonmap\chm\exonmap.chm, 43,700 bytes
Compression decreased file by 45,206 bytes.
  preparing package exonmap 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: simpleaffy
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: RColorBrewer
Loading required package: RMySQL
Loading required package: DBI
Loading required package: plier
  adding MD5 sums

* DONE (exonmap)