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Package 19/294HostnameOS / ArchBUILDCHECKBUILD BIN
altcdfenvs 2.4.0
Laurent Gautier
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/altcdfenvs
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  OK  OK 
Package: altcdfenvs
Version: 2.4.0
Command: E:\biocbld\bbs-2.3-bioc\R\bin\R.exe CMD check --no-vignettes altcdfenvs_2.4.0.tar.gz
StartedAt: 2009-04-18 18:01:33 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:04:22 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 169.4 seconds
RetCode: 0
Status: OK
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.3-bioc/meat/altcdfenvs.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* checking for file 'altcdfenvs/DESCRIPTION' ... OK
* this is package 'altcdfenvs' version '2.4.0'
* 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 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 ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating altcdfenvs-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating altcdfenvs-manual.tex ... OK
* checking altcdfenvs-manual.tex using pdflatex ... OK

altcdfenvs.Rcheck/00install.out:

installing R.css in E:/biocbld/bbs-2.3-bioc/meat/altcdfenvs.Rcheck


---------- Making package altcdfenvs ------------
  adding build stamp to DESCRIPTION
  installing R files
  installing inst files
  installing data files
  preparing package altcdfenvs for lazy loading
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: affy
Loading required package: matchprobes
Loading required package: makecdfenv
Loading required package: affyio
Loading required package: Biostrings
Loading required package: IRanges

Attaching package: 'IRanges'


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

	 annotation 


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

	 cbind,
	 rbind,
	 sapply 


Attaching package: 'Biostrings'


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

	 chartr,
	 order,
	 substr,
	 substring 

Loading required package: hypergraph
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:Biostrings :

	 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"
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'altcdfenvs'
     Formats: text html latex example chm 
  AffyProbesMatch-class             text    html    latex   example chm
  CdfEnvAffy-class                  text    html    latex   example chm
  appendCdfEnvAffy                  text    html    latex   example chm
  buildCdfEnv.biostrings            text    html    latex           chm
  cdfenv                            text    html    latex   example chm
  cdfenvEx                          text    html    latex   example chm
  copyCdfEnvAffy                    text    html    latex           chm
Note: removing empty section \details in file 'countduplicated.Rd'
Note: removing empty section \examples in file 'countduplicated.Rd'
Note: removing empty section \details in file 'countduplicated.Rd'
Note: removing empty section \examples in file 'countduplicated.Rd'
  countduplicated                   text    html    latex           chm
  geneNames                         text    html    latex           chm
  getxy.probeseq                    text    html    latex   example chm
Note: removing empty section \details in file 'index2xy.Rd'
Note: removing empty section \section{Warning} in file 'index2xy.Rd'
Note: removing empty section \details in file 'index2xy.Rd'
Note: removing empty section \section{Warning} in file 'index2xy.Rd'
  index2xy                          text    html    latex   example chm
Note: removing empty section \examples in file 'indexProbes.CdfEnvAffy.Rd'
Note: removing empty section \examples in file 'indexProbes.CdfEnvAffy.Rd'
  indexProbes.CdfEnvAffy            text    html    latex           chm
Note: removing empty section \note in file 'matchAffyProbes.Rd'
Note: removing empty section \note in file 'matchAffyProbes.Rd'
  matchAffyProbes                   text    html    latex   example chm
  plot.CdfEnvAffy                   text    html    latex   example chm
  removeIndex                       text    html    latex   example chm
  toHypergraph                      text    html    latex           chm
  unique.CdfEnvAffy                 text    html    latex   example chm
  utils.FASTA                       text    html    latex   example chm
Note: removing empty section \value in file 'validAffyBatch.Rd'
Note: removing empty section \value in file 'validAffyBatch.Rd'
  validAffyBatch                    text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling e:\biocbld\bbs-2.3-bioc\meat\altcdfenvs.Rcheck\00_pkg_src\altcdfenvs\chm\altcdfenvs.chm


Compile time: 0 minutes, 0 seconds
20	Topics
81	Local links
0	Internet links
1	Graphic


Created e:\biocbld\bbs-2.3-bioc\meat\altcdfenvs.Rcheck\00_pkg_src\altcdfenvs\chm\altcdfenvs.chm, 36,267 bytes
Compression decreased file by 35,229 bytes.
  adding MD5 sums

* DONE (altcdfenvs)