Package: altcdfenvs

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes altcdfenvs_2.6.0.tar.gz

StartedAt: 2009-10-20 16:52:23 -0700 (Tue, 20 Oct 2009)

EndedAt: 2009-10-20 16:55:40 -0700 (Tue, 20 Oct 2009)

EllapsedTime: 196.8 seconds

RetCode: 0

Status: OK

CheckDir: altcdfenvs.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.6.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'altcdfenvs' 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 whether the name space 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 files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* Installing *source* package ‘altcdfenvs’ ...
** R
** data
** inst
** preparing package for lazy loading

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: AnnotationDbi
Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 cbind,
	 duplicated,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rank,
	 rbind,
	 rep.int,
	 sapply,
	 sort,
	 table,
	 unique 


*** Deprecation warning ***
The matchprobes package is deprecated and will not be supported
anymore starting with Bioconductor 2.4. Please switch to using the
Biostrings package for efficient string manipulations. If you need
to build a probe package, please see the makeProbePackage vignette
in the AnnotationDbi package.

Loading required package: affyio
Loading required package: graph

Attaching package: 'graph'


	The following object(s) are masked from package:Biostrings :

	 complement 


Attaching package: 'hypergraph'


	The following object(s) are masked from package:IRanges :

	 head,
	 tail 


	The following object(s) are masked from package:AnnotationDbi :

	 head,
	 tail 


	The following object(s) are masked from package:utils :

	 head,
	 tail 

NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
Warning in matchSignature(signature, fdef, where) :
  in the method signature for function "toHypergraph" no definition for class: “CdfEnvAffy”
Creating a new generic function for "plot" in "altcdfenvs"
** help
*** installing help indices
 >>> Building/Updating help pages for package 'altcdfenvs'
     Formats: text html latex example 
  AffyProbesMatch-class             text    html    latex   example
  CdfEnvAffy-class                  text    html    latex   example
  appendCdfEnvAffy                  text    html    latex   example
  buildCdfEnv.biostrings            text    html    latex
  cdfenv                            text    html    latex   example
  cdfenvEx                          text    html    latex   example
  copyCdfEnvAffy                    text    html    latex
Note: removing empty section \details in file 'countduplicated.Rd'
Note: removing empty section \examples in file 'countduplicated.Rd'
  countduplicated                   text    html    latex
  geneNames                         text    html    latex
  getxy.probeseq                    text    html    latex   example
Note: removing empty section \details in file 'index2xy.Rd'
Note: removing empty section \section{Warning} in file 'index2xy.Rd'
  index2xy                          text    html    latex   example
Note: removing empty section \examples in file 'indexProbes.CdfEnvAffy.Rd'
  indexProbes.CdfEnvAffy            text    html    latex
Note: removing empty section \note in file 'matchAffyProbes.Rd'
  matchAffyProbes                   text    html    latex   example
  plot.CdfEnvAffy                   text    html    latex   example
  removeIndex                       text    html    latex   example
  toHypergraph                      text    html    latex
  unique.CdfEnvAffy                 text    html    latex   example
  utils.FASTA                       text    html    latex   example
Note: removing empty section \value in file 'validAffyBatch.Rd'
  validAffyBatch                    text    html    latex   example
** building package indices ...
* DONE (altcdfenvs)