Package: siggenes

Version: 1.9.4

Command: /home/biocbuild/2.0d/R/bin/R CMD check siggenes_1.9.4.tar.gz

RetCode: 0

Time: 34.9 seconds

Status: WARNINGS

CheckDir: siggenes.Rcheck

Warnings: 3

* checking for working latex ... OK
* using log directory '/home/biocbuild/2.0d/Rpacks/siggenes.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'siggenes/DESCRIPTION' ... OK
* this is package 'siggenes' version '1.9.4'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'siggenes' can be installed ... WARNING
Found the following significant warnings:
  Warning: \alias{cat.stat} already in sam.snp.Rd -- skipping the one in siggenes-internal.Rd
See '/home/biocbuild/2.0d/Rpacks/siggenes.Rcheck/00install.out' for details.
* 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 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
Rd files with duplicated alias 'cat.stat':
  /home/biocbuild/2.0d/Rpacks/siggenes.Rcheck/00_pkg_src/siggenes/man/sam.snp.Rd
  /home/biocbuild/2.0d/Rpacks/siggenes.Rcheck/00_pkg_src/siggenes/man/siggenes-internal.Rd

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  cat.null cat.null.approx cat.stat.old chisqClass compPermStat
  computeContCols
All user-level objects in a package 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 siggenes-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating siggenes-manual.tex ... OK
* checking siggenes-manual.tex ... OK

WARNING: There were 3 warnings, see
  /home/biocbuild/2.0d/Rpacks/siggenes.Rcheck/00check.log
for details

* Installing *source* package 'siggenes' ...
** R
** inst
** preparing package for lazy loading
Loading required package: multtest
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: survival
Loading required package: splines
Creating a new generic function for "print" in "siggenes"
Creating a new generic function for "identify" in "siggenes"
** help
Warning: \alias{cat.stat} already in sam.snp.Rd -- skipping the one in siggenes-internal.Rd
 >>> Building/Updating help pages for package 'siggenes'
     Formats: text html latex example 
  SAM-class                         text    html    latex   example
  delta.plot                        text    html    latex   example
  ebam                              text    html    latex   example
  ebam.wilc                         text    html    latex   example
  find.a0                           text    html    latex   example
  fudge2                            text    html    latex
  help.sam                          text    html    latex   example
  link.genes                        text    html    latex
  link.siggenes                     text    html    latex
  list.siggenes                     text    html    latex   example
  na.handling                       text    html    latex   example
  na.replace.cont                   text    html    latex
  na.replace.dist                   text    html    latex
  pi0.est                           text    html    latex   example
  qvalue.cal                        text    html    latex   example
  sam                               text    html    latex   example
  sam.dstat                         text    html    latex   example
  sam.plot2                         text    html    latex   example
  sam.snp                           text    html    latex
  sam.wilc                          text    html    latex   example
  sam2excel                         text    html    latex
  sam2html                          text    html    latex
  siggenes-internal                 text    html    latex
  sumSAM-class                      text    html    latex
** building package indices ...
* DONE (siggenes)