Package: splicegear

Version: 1.5.0

Command: D:\biocbld\1.9d\R\bin\R.exe CMD check splicegear_1.5.0.tar.gz

RetCode: 0

Time: 64.5 seconds

Status: WARNINGS

CheckDir: splicegear.Rcheck

Warnings: 2

* checking for working latex ... OK
* using log directory 'D:/biocbld/1.9d/Rpacks/splicegear.Rcheck'
* using R version 2.4.0 alpha (2006-09-10 r39242)
* 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 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 whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... 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)

sort:
  function(x, decreasing, ...)
sort.SpliceExprSet:
  function(x, fun, reverse)

See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* 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 ... WARNING
Undocumented S4 methods:
  generic 'exprs<-' and siglist 'SpliceExprSet,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* 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 were 2 warnings, see
  D:/biocbld/1.9d/Rpacks/splicegear.Rcheck/00check.log
for details

installing R.css in D:/biocbld/1.9d/Rpacks/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()' 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"
  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\1.9d\Rpacks\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\1.9d\Rpacks\splicegear.Rcheck\00_pkg_src\splicegear\chm\splicegear.chm, 36,601 bytes
Compression decreased file by 36,695 bytes.
  adding MD5 sums

* DONE (splicegear)