[BioC] Rv1.91 or v2.0.0 on MacOS 10.3.5

Robert Gentleman rgentlem at jimmy.harvard.edu
Thu Oct 28 19:25:07 CEST 2004


On Thu, Oct 28, 2004 at 10:33:36AM -0500, Rahul Kakkar wrote:
> This posting is regarding 2 problems, but all dealing with trying to  
> run Bioconductor on MacOS 10.3.x.
> 

  Hi, 
   sorry you are having trouble. 
  One problem you seem to be having is that you do not have tcl/tk 
  installed. Many developers use this so you might want to install
   it. Information is in the R FAQ for OS X (or use the email archive
   for pointers).
   capabilities() #in R should tell you.

l> capabilities()
    jpeg      png    tcltk      X11 http/ftp  sockets   libxml
    fifo 
    TRUE    FALSE     TRUE     TRUE     TRUE     TRUE     TRUE
    TRUE 
  cledit  IEEE754 
    TRUE     TRUE 

   Second, there is some chance that you tried to do this just when we
   updated the repository, and so for that 1 or 2 minutes it is in an
   inconsistent state. You might try again, for example I use OS X
   (and the unstable R, but I have no trouble updating these
   packages). 

   both
    install.packages2("annotate", develOK=T)

     install.packages2("genefilter", develOK=T)

   seem to work for me. Are you sure you are getting R 2.0.0 (as some
   of these errors could happen if downloading recent versions of
   these packages into R 1.9.1). Could you please try just one of
   these two now and see what happens?

   Robert
   

> I initially tried to download and install Rv2.0.0 / Bioconductor.  I  
> included X11 upgrade during the installation.  I used
>  > source("http://www.bioconductor.org/getBioC.R")
>  >getBioC("affy", develOK=TRUE)
> I installed into my user directory rather than the system dir.
> Please see the paste at the end of this email for the output and  
> numerous errors.  In brief, the errors included numerous slot class  
> errors, inability to locate the library "annotate" in any know  
> repository (and subsequently unable to execute packages which depend  
> upon it such as annaffy and geneplotter) and inability to compile  
> certain packages (genefilter, SparseM, Ruuid).  Note that MacOS X  
> Developer Tools is installed.
> 
> "affy" loaded fine, but ReadAffy gave an error:
>  > library(affy)
> Loading required package: Biobase
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
>  > data<-ReadAffy(widget=TRUE)
> Loading required package: tkWidgets
> Loading required package: widgetTools
> Loading required package: tcltk
> Error in fun(...) : this isn't a Tk applicationcouldn't connect to  
> display ":0"
> Error: .onLoad failed in loadNamespace for 'tcltk'
> Error in fun(...) : Package tcltk not able to be loaded!
> Error: .onLoad failed in loadNamespace for 'widgetTools'
> Error: package 'widgetTools' could not be loaded
>  >
> 
> "genefilter" could not be loaded of course:
>  > library(genefilter)
> Loading required package: survival
> Loading required package: splines
> Error in library.dynam(lib, package, package.lib) :
> 	shared library 'genefilter' not found
> In addition: Warning message:
> Package  'genefilter' contains no R code in: loadNamespace(package,  
> c(which.lib.loc, lib.loc))
> Error in library(genefilter) : package/namespace load failed for  
> 'genefilter'
>  >
> 
> Trying to install genefilter via a different means gave the following:
>  > install.packages2("genefilter", develOK=TRUE)
> Warning message:
> Failed to read repdatadesc at  
> http://www.bioconductor.org/repository/devel/package in:  
> loadRepDD(repURL, rddFile, method = method)
> Error in repURL(replisting(object), pos) :
> 	subscript out of bounds
>  >
> 
> Given the numerous errors, I completely uninstalled Rv2 and tried  
> Rv1.9.1 / Biocondcutor.  Downloaded and installed as per some very  
> helpful previous posts  
> (http://files.protsuggest.org/biocond/html/3612.html).  This included  
> installing Bioconductor packages via the "Affy bundle" script under the  
> "Packages" menu in R as well as installing MacOS X developer tools .
> 
> Came across an issue with the function ReadAffy(widget=TRUE):
> 
>  > data<-ReadAffy(widget=TRUE)
> Error in fileBrowser(textToShow = "Choose CEL files", testFun =  
> hasSuffix("[cC][eE][lL]")) :
> 	couldn't find function "tktoplevel"
> Error in end() : couldn't find function "tkgrab.release"
>  > data<-ReadAffy(widget=TRUE)
> Error in fileBrowser(textToShow = "Choose CEL files", testFun =  
> hasSuffix("[cC][eE][lL]")) :
> 	couldn't find function "tktoplevel"
> Error in end() : couldn't find function "tkgrab.release"
>  >
> 
> Note widgetTools (1.4.2) and tkWidgets (1.5.10) are installed.  I  
> suspect this has something to do with X Windows, but I'm not  
> knowledgeable enough to figure this one out.  I did install the X11  
> app, but Im not sure how to use it to run the widget function if this  
> is indeed the issue.
> 
> I would appreciate any assistance in getting R / Bioconductor, either  
> version, to work on my macintosh.
> 
> Obliged,
> 
> -Rahul
> 
> 
> 
> Rahul Kakkar M.D.
> Post-Doctoral Fellow
> 
> Elizabeth M. McNally Laboratory
> Department of Medicine
> University of Chicago Hospitals
> MC 6088
> 5841 S. Maryland Avenue
> Chicago, IL 60637
> 
> P: (773) 702-2684 F: (773) 702-2681 E: rkakkar at uchicago.edu
> 
> 
> 
> OUTPUT FROM >getBioC("affy", develOK=TRUE) COMMAND IN Rv2.0.0:
> 
> 
> R : Copyright 2004, The R Foundation for Statistical Computing
> Version 2.0.0  (2004-10-04), ISBN 3-900051-07-0
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for a HTML browser interface to help.
> Type 'q()' to quit R.
> 
>  > source("http://www.bioconductor.org/getBioC.R")
>  > getBioC("affy", develOK=TRUE)
> Running getBioC version 1.2.66....
> If you encounter problems, first make sure that
> you are running the latest version of getBioC()
> which can be found at: www.bioconductor.org/getBioC.R
> 
> Please direct any concerns or questions to  
> bioconductor at stat.math.ethz.ch.
> 
> Please select an installation directory:
> 1:/Users/rkakkar/Library/R/library
> 2:/Library/Frameworks/R.framework/Resources/library
> Selection: 1
> [1] "Installing reposTools ..."
> * Installing *source* package 'reposTools' ...
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> Loading required package: tools
> [1] "replisting"
> [1] "replisting"
> [1] "repURL"
> Creating a new generic function for "summary" in "reposTools"
> [1] "summary"
> [1] "repReleaseLevel"
> [1] "repReleaseLevel"
> [1] "show"
> [1] "replisting"
> [1] "repURL"
> [1] "numSubReps"
> [1] "numSubReps"
> [1] "repdatadesc"
> [1] "repdatadesc"
> [1] "repdatadesc"
> [1] "summary"
> [1] "depends"
> [1] "depends"
> [1] "suggests"
> [1] "suggests"
> [1] "imports"
> [1] "imports"
> [1] "keywords"
> [1] "keywords"
> [1] "show"
> [1] "ReposList"
> [1] "repList"
> [1] "repList"
> [1] "repList<-"
> [1] "repList<-"
> [1] "numReps"
> [1] "numReps"
> [1] "getRepEntry"
> [1] "getRepEntry"
> [1] "repPkgs"
> [1] "repPkgs"
> [1] "repPkgInfoList"
> [1] "repPkgInfoList"
> [1] "repNames"
> [1] "repNames"
> [1] "repURLs"
> [1] "repURLs"
> [1] "show"
> [1] "ReposEntry"
> [1] "repType"
> [1] "repName"
> [1] "reposThemes"
> [1] "reposThemes"
> [1] "repType"
> [1] "replisting"
> [1] "repdatadesc"
> [1] "repName"
> [1] "repURL"
> [1] "repdataframe"
> [1] "repdataframe"
> [1] "numSubReps"
> [1] "getSubRep"
> [1] "getSubRep"
> [1] "getSubRepList"
> [1] "getSubRepList"
> [1] "depends"
> [1] "suggests"
> [1] "imports"
> [1] "keywords"
> [1] "hasFiles"
> [1] "hasFiles"
> [1] "pkgRVersion"
> [1] "pkgRVersion"
> [1] "repPkgs"
> [1] "repObjects"
> [1] "repObjects"
> [1] "repPkgInfos"
> [1] "repPkgInfos"
> [1] "downloadFile"
> [1] "downloadFile"
> [1] "repReleaseLevel"
> [1] "summary"
> [1] "show"
> [1] "pkgListing"
> [1] "pkgList"
> [1] "pkgList"
> [1] "repList"
> [1] "repListing"
> [1] "repListing"
> [1] "getRepEntry"
> [1] "getRepURL"
> [1] "getRepURL"
> [1] "packages"
> [1] "packages"
> [1] "pkgVersionList"
> [1] "pkgVersionList"
> [1] "summary"
> [1] "show"
> [1] "reposTheme"
> [1] "repThemeName"
> [1] "repThemeName"
> [1] "repThemePkgs"
> [1] "repThemePkgs"
> [1] "repThemeDesc"
> [1] "repThemeDesc"
> [1] "repThemeRepos"
> [1] "repThemeRepos"
> [1] "show"
> [1] "VersionNumber"
> [1] "stringRep"
> [1] "major"
> [1] "minor"
> [1] "revision"
> [1] "stringRep"
> [1] "major"
> [1] "minor"
> [1] "revision"
> [1] "show"
> [1] "as.character"
> [1] "pkgInfo"
> [1] "pkgName"
> [1] "pkgVersion"
> [1] "pkgRelLevel"
> [1] "pkgPath"
> [1] "pkgContains"
> [1] "pkgRelLevel"
> [1] "pkgName"
> [1] "pkgVersion"
> [1] "pkgPath"
> [1] "pkgContains"
> [1] "=="
> [1] "show"
> [1] "localPkg"
> [1] "Package"
> [1] "Package"
> [1] "PkgVersion"
> [1] "PkgVersion"
> [1] "Keywords"
> [1] "Keywords"
> [1] "Depends"
> [1] "Depends"
> [1] "Suggests"
> [1] "Suggests"
> [1] "Imports"
> [1] "Imports"
> [1] "Repos"
> [1] "Repos"
> [1] "Bundle"
> [1] "Bundle"
> [1] "pkgStatusList"
> [1] "show"
> [1] "statusList"
> [1] "statusList"
> [1] "statusList<-"
> [1] "statusList<-"
> [1] "matchesList"
> [1] "matchesList"
> [1] "matchesList<-"
> [1] "matchesList<-"
> [1] "packages"
> [1] "found"
> [1] "found"
> [1] "notFound"
> [1] "notFound"
> [1] "updated"
> [1] "updated"
> [1] "notUpdated"
> [1] "notUpdated"
> [1] "urls"
> [1] "urls"
> [1] "pkgVersions"
> [1] "pkgVersions"
> [1] "foundPkgs"
> [1] "foundPkgs"
> [1] "notFoundPkgs"
> [1] "notFoundPkgs"
> [1] "updatedPkgs"
> [1] "updatedPkgs"
> [1] "getPackage"
> [1] "getPackage"
> [1] "getFound"
> [1] "getFound"
> [1] "getUpdated"
> [1] "getUpdated"
> [1] "getUrl"
> [1] "getUrl"
> [1] "getPkgVersion"
> [1] "getPkgVersion"
> [1] "pkgStatus"
> [1] "package"
> [1] "package"
> [1] "found"
> [1] "updated"
> [1] "URL"
> [1] "URL"
> [1] "pkgVersion"
> [1] "show"
> 
> ** help
>   >>> Building/Updating help pages for package 'reposTools'
>       Formats: text html latex example
>    ReposEntry-class                  text    html    latex   example
>    ReposList-class                   text    html    latex   example
>    VersionNumber-class               text    html    latex   example
>    buildPkgInfo                      text    html    latex   example
>    buildReposEntry                   text    html    latex   example
>    buildVersionNumber                text    html    latex   example
>    checkVers                         text    html    latex   example
>    closeLocLib                       text    html    latex   example
>    download.packages2                text    html    latex   example
>    genRepos                          text    html    latex   example
>    genReposHtml                      text    html    latex   example
>    getDependings                     text    html    latex   example
>    getLocalPkgs                      text    html    latex   example
>    getMaxVersion                     text    html    latex   example
>    getOptReposList                   text    html    latex   example
>    getPkgVers                        text    html    latex   example
>    getReplisting                     text    html    latex   example
>    getReposEntry                     text    html    latex   example
>    getReposList                      text    html    latex   example
>    getReposOption                    text    html    latex   example
>    getRversion                       text    html    latex   example
>    initVersionNumber                 text    html    latex
>    install.packages2                 text    html    latex   example
>    load.locLib                       text    html    latex   example
>    loadDepends                       text    html    latex   example
>    loadRepDD                         text    html    latex   example
>    localPkg-class                    text    html    latex   example
>    note                              text    html    latex   example
>    parseThemesXML                    text    html    latex   example
>    pkgInfo-class                     text    html    latex   example
>    pkgListing-class                  text    html    latex   example
>    pkgStatus-class                   text    html    latex   example
>    pkgStatusList-class               text    html    latex   example
>    repdatadesc-class                 text    html    latex   example
>    replisting-class                  text    html    latex   example
>    reposTheme-class                  text    html    latex   example
>    reposToolsLibPaths                text    html    latex   example
>    repositories                      text    html    latex   example
>    resolve.depends                   text    html    latex   example
>    save.locLib                       text    html    latex   example
>    saveDfRda                         text    html    latex   example
>    splitDFstrings                    text    html    latex   example
>    syncLocalLibList                  text    html    latex   example
>    themes                            text    html    latex   example
>    unpackExtractPkgDESC              text    html    latex   example
>    userQuery                         text    html    latex   example
>    winConvertSourceRepos             text    html    latex   example
>    writeThemesXML                    text    html    latex   example
> * DONE (reposTools)
> Loading required package: reposTools
> Loading required package: tools
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download widgetTools from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing widgetTools"
> * Installing *source* package 'widgetTools' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning message:
> Undefined slot classes in definition of "widgetView": winid (class "  
> tkwin ") in: .completeClassSlots(ClassDef, where)
> 
> ** help
>   >>> Building/Updating help pages for package 'widgetTools'
>       Formats: text html latex example
>    basicPW-class                     text    html    latex   example
>    button                            text    html    latex   example
>    dropdownList                      text    html    latex   example
>    makeViewer                        text    html    latex   example
>    oneVScrList                       text    html    latex   example
>    safeFileOpen                      text    html    latex   example
>    tooltip                           text    html    latex   example
>    widget-class                      text    html    latex   example
>    widgetView-class                  text    html    latex   example
>    writeText                         text    html    latex   example
> * DONE (widgetTools)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download DynDoc from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing DynDoc"
> * Installing *source* package 'DynDoc' ...
> ** R
> ** save image
> [1] TRUE
> Loading required package: tools
> [1] "DynDoc"
> Warning message:
> Undefined slot classes in definition of "DynDoc": codeChunks (class "  
> chunkList ") in: .completeClassSlots(ClassDef, where)
> [1] "indexEntry"
> [1] "indexEntry"
> [1] "path"
> [1] "path"
> [1] "pdfPath"
> [1] "pdfPath"
> [1] "getDepends"
> [1] "getDepends"
> [1] "getRequires"
> [1] "getRequires"
> [1] "getSuggests"
> [1] "getSuggests"
> [1] "getKeywords"
> [1] "getKeywords"
> [1] "codeChunks"
> [1] "codeChunks"
> [1] "chunks"
> [1] "chunks"
> [1] "setChunk<-"
> [1] "setChunk<-"
> [1] "numChunks"
> [1] "numChunks"
> [1] "getChunk"
> [1] "getChunk"
> [1] "evalChunk"
> [1] "evalChunk"
> Creating a new generic function for "summary" in "DynDoc"
> [1] "summary"
> [1] "show"
> [1] "SweaveOptions"
> [1] "SweaveOptions"
> [1] "getOptions"
> [1] "getOptions"
> [1] "numOptions"
> [1] "numOptions"
> [1] "show"
> [1] "codeChunk"
> [1] "codeChunk"
> [1] "chunk"
> [1] "chunk"
> [1] "chunk<-"
> [1] "chunk<-"
> [1] "chunkName"
> [1] "chunkName"
> [1] "SweaveOptions"
> [1] "getOptions"
> [1] "evalChunk"
> [1] "show"
> [1] "chunkList"
> [1] "chunkList"
> [1] "chunks"
> [1] "numChunks"
> [1] "evalEnv"
> [1] "evalEnv"
> [1] "summary"
> [1] "show"
> [1] "getChunk"
> [1] "setChunk<-"
> [1] "getAllCodeChunks"
> [1] "getAllCodeChunks"
> [1] "evalChunk"
> [1] "Vignette"
> Warning message:
> Undefined slot classes in definition of "Vignette": vigPkgVersion  
> (class " VersionNumber ") in: .completeClassSlots(ClassDef, where)
> [1] "vigPkgVersion"
> [1] "vigPkgVersion"
> [1] "vignetteCode"
> [1] "path"
> [1] "getDepends"
> [1] "chunks"
> [1] "chunkList"
> [1] "setChunk<-"
> [1] "evalEnv"
> [1] "numChunks"
> [1] "getChunk"
> [1] "evalChunk"
> [1] "summary"
> [1] "show"
> 
> ** help
>   >>> Building/Updating help pages for package 'DynDoc'
>       Formats: text html latex example
>    DynDoc-class                      text    html    latex   example
>    SweaveOptions-class               text    html    latex   example
>    Vignette-class                    text    html    latex   example
>    chunkList-class                   text    html    latex   example
>    codeChunk-class                   text    html    latex   example
>    getPkgVigList                     text    html    latex   example
>    getVignette                       text    html    latex   example
>    getVignetteCode                   text    html    latex   example
>    getVignetteHeader                 text    html    latex   example
>    tangleToR                         text    html    latex   example
>    vignetteCode-class                text    html    latex   example
> * DONE (DynDoc)
> [1] "Installation complete"
> [1] "Attempting to download tkWidgets from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing tkWidgets"
> * Installing *source* package 'tkWidgets' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'tkWidgets'
>       Formats: text html latex example
>    DPExplorer                        text    html    latex   example
>    WName                             text    html    latex   example
>    appendSepDir                      text    html    latex   example
>    args2XML                          text    html    latex   example
>    argsWidget                        text    html    latex   example
>    colInfo-class                     text    html    latex   example
>    dataViewer                        text    html    latex   example
>    dbArgsWidget                      text    html    latex   example
>    eExplorer                         text    html    latex   example
>    fileBrowser                       text    html    latex   example
>    fileWizard                        text    html    latex   example
>    getLightTW                        text    html    latex   example
>    getWvalues                        text    html    latex   example
>    guess.sep                         text    html    latex   example
>    hasChar                           text    html    latex   example
>    importPhenoData                   text    html    latex   example
>    importWizard                      text    html    latex   example
>    listSelect                        text    html    latex   example
>    objNameToList                     text    html    latex   example
>    objViewer                         text    html    latex   example
>    objectBrowser                     text    html    latex   example
>    pExplorer                         text    html    latex   example
>    pickFiles                         text    html    latex   example
>    pickItems                         text    html    latex   example
>    pickObjs                          text    html    latex   example
>    setArgsList                       text    html    latex   example
>    stdType                           text    html    latex   example
>    tkMIAME                           text    html    latex
>    tkSampleNames                     text    html    latex
>    tkphenoData                       text    html    latex
>    vExplorer                         text    html    latex   example
>    values.Widget                     text    html    latex   example
>    widgetRender                      text    html    latex   example
> * DONE (tkWidgets)
> [1] "Installation complete"
> [1] "Attempting to download Biobase from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing Biobase"
> * Installing *source* package 'Biobase' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c Rinit.c -o Rinit.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c envir.c -o envir.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> Biobase.so Rinit.o envir.o  -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> Loading required package: tools
> [1] "aggregator"
> [1] "aggenv"
> [1] "aggenv"
> [1] "initfun"
> [1] "initfun"
> [1] "aggfun"
> [1] "aggfun"
> [1] "container"
> [1] "content"
> [1] "content"
> [1] "locked"
> [1] "locked"
> [1] "[[<-"
> [1] "[["
> [1] "length"
> [1] "show"
> [1] "["
> [1] "phenoData"
> [1] "pData"
> [1] "pData"
> [1] "varLabels"
> [1] "varLabels"
> [1] "["
> [1] "[["
> [1] "[[<-"
> [1] "show"
> [1] "MIAME"
> [1] "show"
> [1] "abstract"
> [1] "abstract"
> [1] "samples"
> [1] "samples"
> [1] "hybridizations"
> [1] "hybridizations"
> [1] "normControls"
> [1] "normControls"
> [1] "preproc"
> [1] "preproc"
> [1] "otherInfo"
> [1] "otherInfo"
> [1] "expinfo"
> [1] "expinfo"
> [1] "characterORMIAME"
> [1] "exprMatrix"
> [1] "exprSet"
> [1] "update2MIAME"
> [1] "update2MIAME"
> [1] "exprs"
> [1] "exprs"
> [1] "se.exprs"
> [1] "se.exprs"
> [1] "exprs<-"
> [1] "exprs<-"
> [1] "se.exprs<-"
> [1] "se.exprs<-"
> [1] "notes"
> [1] "notes"
> [1] "notes<-"
> [1] "notes<-"
> [1] "description"
> [1] "description"
> [1] "description<-"
> [1] "description<-"
> [1] "abstract"
> [1] "phenoData"
> [1] "phenoData"
> [1] "phenoData<-"
> [1] "phenoData<-"
> [1] "pData"
> [1] "pData<-"
> [1] "pData<-"
> [1] "[[<-"
> [1] "[["
> [1] "pData<-"
> [1] "sampleNames"
> [1] "sampleNames"
> [1] "sampleNames<-"
> [1] "sampleNames<-"
> [1] "geneNames"
> [1] "geneNames"
> [1] "geneNames<-"
> [1] "geneNames<-"
> [1] "varLabels"
> [1] "annotation"
> [1] "annotation"
> [1] "annotation<-"
> [1] "annotation<-"
> [1] "["
> [1] "show"
> [1] "iter"
> [1] "iter"
> [1] "iter"
> [1] "iter"
> [1] "split"
> [1] "split"
> [1] "split"
> [1] "split"
> [1] "write.exprs"
> [1] "write.exprs"
> [1] "exprs2excel"
> [1] "exprs2excel"
> [1] "exprList"
> [1] "eSet"
> [1] "eList"
> [1] "eList"
> [1] "eList<-"
> [1] "eList<-"
> [1] "eList<-"
> [1] "eList<-"
> [1] "getExpData"
> [1] "getExpData"
> [1] "exprs"
> [1] "["
> [1] "show"
> [1] "phenoData"
> [1] "phenoData<-"
> [1] "pData"
> [1] "pData<-"
> [1] "combine"
> [1] "combine"
> [1] "combine"
> [1] "combine"
> [1] "combine"
> 
> ** help
>   >>> Building/Updating help pages for package 'Biobase'
>       Formats: text html latex example
>    Aggregate                         text    html    latex   example
>    aaMap                             text    html    latex   example
>    addVig2Menu                       text    html    latex   example
>    aggregator-class                  text    html    latex
>    as.data.frame.exprSet             text    html    latex   example
>    characterORmiame-class            text    html    latex
>    combine                           text    html    latex   example
>    container-class                   text    html    latex   example
>    contents                          text    html    latex   example
>    copyEnv                           text    html    latex   example
>    copySubstitute                    text    html    latex   example
>    createPackage                     text    html    latex   example
>    dumpPackTxt                       text    html    latex   example
>    eSet-class                        text    html    latex   example
>    esApply                           text    html    latex   example
>    eset                              text    html    latex   example
>    exprList-class                    text    html    latex   example
>    exprMatrix-class                  text    html    latex
>    exprSet-class                     text    html    latex   example
>    geneData                          text    html    latex   example
>    getPkgVigs                        text    html    latex   example
>    iter-methods                      text    html    latex
>    miame-class                       text    html    latex
>    multiassign                       text    html    latex   example
>    openPDF                           text    html    latex   example
>    openVignette                      text    html    latex   example
>    package.version                   text    html    latex   example
>    phenoData-class                   text    html    latex
>    read.MIAME                        text    html    latex   example
>    read.exprSet                      text    html    latex   example
>    read.phenoData                    text    html    latex   example
>    testBioCConnection                text    html    latex   example
> * DONE (Biobase)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download hgu95av2cdf from  
> http://www.bioconductor.org/data/cdfenvs/repos/"
> [1] "Download complete."
> [1] "Installing hgu95av2cdf"
> * Installing *source* package 'hgu95av2cdf' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'hgu95av2cdf'
>       Formats: text html latex example
>    geometry                          text    html    latex   example
>    hgu95av2cdf                       text    html    latex
> * DONE (hgu95av2cdf)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download hgu133acdf from  
> http://www.bioconductor.org/data/cdfenvs/repos/"
> [1] "Download complete."
> [1] "Installing hgu133acdf"
> * Installing *source* package 'hgu133acdf' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'hgu133acdf'
>       Formats: text html latex example
>    geometry                          text    html    latex   example
>    hgu133acdf                        text    html    latex
> * DONE (hgu133acdf)
> [1] "Installation complete"
> [1] "Attempting to download affydata from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing affydata"
> * Installing *source* package 'affydata' ...
> ** R
> ** data
> ** inst
> ** help
>   >>> Building/Updating help pages for package 'affydata'
>       Formats: text html latex example
>    Dilution                          text    html    latex
>       missing link(s):  AffyBatch AffyBatch
> * DONE (affydata)
> [1] "Installation complete"
> [1] "Attempting to download affy from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing affy"
> * Installing *source* package 'affy' ...
> creating cache ./config.cache
> checking how to run the C preprocessor... cc -E
> checking for main in -lz... yes
> checking for zlib.h... yes
> checking if zlib version >= 1.1.3... yes
> updating cache ./config.cache
> creating ./config.status
> creating src/Makevars
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c  
> chipbackground.c -o chipbackground.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c  
> getall_locations.c -o getall_locations.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c  
> mas5calls.c -o mas5calls.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c qnorm.c -o  
> qnorm.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c  
> read_abatch.c -o read_abatch.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c rma2.c -o  
> rma2.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c  
> rma_background2.c -o rma_background2.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c  
> rma_common.c -o rma_common.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o  
> read_abatch.o rma2.o rma_background2.o rma_common.o -lz  -lcc_dynamic  
> -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /usr/lib/libz.dylib(crc32.o) definition of _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /usr/lib/libz.dylib(crc32.o) definition of _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflateInit_
> /usr/lib/libz.dylib(deflate.o) definition of _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> ld: warning multiple definitions of symbol _deflateCopy
> /usr/lib/libz.dylib(deflate.o) definition of _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateParams
> /usr/lib/libz.dylib(deflate.o) definition of _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> ld: warning multiple definitions of symbol _deflateReset
> /usr/lib/libz.dylib(deflate.o) definition of _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /usr/lib/libz.dylib(deflate.o) definition of _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateEnd
> /usr/lib/libz.dylib(deflate.o) definition of _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflate
> /usr/lib/libz.dylib(deflate.o) definition of _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> ld: warning multiple definitions of symbol _deflateInit2_
> /usr/lib/libz.dylib(deflate.o) definition of _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> ld: warning multiple definitions of symbol _gzwrite
> /usr/lib/libz.dylib(gzio.o) definition of _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> ld: warning multiple definitions of symbol _gztell
> /usr/lib/libz.dylib(gzio.o) definition of _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> ld: warning multiple definitions of symbol _gzseek
> /usr/lib/libz.dylib(gzio.o) definition of _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> ld: warning multiple definitions of symbol _gzread
> /usr/lib/libz.dylib(gzio.o) definition of _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> ld: warning multiple definitions of symbol _gzopen
> /usr/lib/libz.dylib(gzio.o) definition of _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> ld: warning multiple definitions of symbol _gzgetc
> /usr/lib/libz.dylib(gzio.o) definition of _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzeof
> /usr/lib/libz.dylib(gzio.o) definition of _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /usr/lib/libz.dylib(gzio.o) definition of _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /usr/lib/libz.dylib(gzio.o) definition of _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /usr/lib/libz.dylib(gzio.o) definition of _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /usr/lib/libz.dylib(gzio.o) definition of _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgets
> /usr/lib/libz.dylib(gzio.o) definition of _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> ld: warning multiple definitions of symbol _gzprintf
> /usr/lib/libz.dylib(gzio.o) definition of _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /usr/lib/libz.dylib(gzio.o) definition of _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /usr/lib/libz.dylib(gzio.o) definition of _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> ld: warning multiple definitions of symbol _gzrewind
> /usr/lib/libz.dylib(gzio.o) definition of _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzsetparams
> /usr/lib/libz.dylib(gzio.o) definition of _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /usr/lib/libz.dylib(inflate.o) definition of _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /usr/lib/libz.dylib(inflate.o) definition of _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> ld: warning multiple definitions of symbol _inflateInit2_
> /usr/lib/libz.dylib(inflate.o) definition of _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> ld: warning multiple definitions of symbol _inflateEnd
> /usr/lib/libz.dylib(inflate.o) definition of _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateReset
> /usr/lib/libz.dylib(inflate.o) definition of _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /usr/lib/libz.dylib(inflate.o) definition of _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /usr/lib/libz.dylib(inflate.o) definition of _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateSync
> /usr/lib/libz.dylib(inflate.o) definition of _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> ld: warning multiple definitions of symbol _adler32
> /usr/lib/libz.dylib(adler32.o) definition of _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> ld: warning multiple definitions of symbol _zError
> /usr/lib/libz.dylib(zutil.o) definition of _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /usr/lib/libz.dylib(zutil.o) definition of _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ** R
> ** data
> ** demo
> ** inst
> ** save image
> [1] TRUE
> [1] TRUE
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> [1] TRUE
> Loading required package: reposTools
> [1] "ProgressBarText"
> [1] "initialize"
> [1] "open"
> [1] "open"
> [1] "update"
> [1] "update"
> [1] "close"
> [1] "close"
> [1] "AffyBatch"
> [1] "cdfName"
> [1] "cdfName"
> [1] "intensity"
> [1] "intensity"
> [1] "intensity<-"
> [1] "intensity<-"
> [1] "length"
> [1] "ncol"
> [1] "ncol"
> [1] "nrow"
> [1] "nrow"
> [1] "geneNames"
> [1] "geneNames<-"
> [1] "show"
> [1] "indexProbes"
> [1] "indexProbes"
> [1] "pmindex"
> [1] "pmindex"
> [1] "mmindex"
> [1] "mmindex"
> [1] "probeNames"
> [1] "probeNames"
> [1] "probes"
> [1] "probes"
> [1] "pm"
> [1] "pm"
> [1] "pm<-"
> [1] "pm<-"
> [1] "mm"
> [1] "mm"
> [1] "mm<-"
> [1] "mm<-"
> [1] "probeset"
> [1] "probeset"
> [1] "["
> [1] "[<-"
> [1] "bg.correct"
> [1] "bg.correct"
> [1] "normalize.methods"
> [1] "normalize.methods"
> [1] "normalize"
> [1] "normalize"
> [1] "computeExprSet"
> [1] "computeExprSet"
> [1] "image"
> [1] "image"
> [1] "boxplot"
> [1] "boxplot"
> [1] "hist"
> [1] "hist"
> [1] "mas5calls"
> [1] "mas5calls"
> [1] "Mbox"
> [1] "Mbox"
> [1] "MAplot"
> [1] "MAplot"
> [1] "ProbeSet"
> [1] "show"
> [1] "colnames"
> [1] "sampleNames"
> [1] "colnames"
> [1] "pm"
> [1] "pm<-"
> [1] "mm"
> [1] "mm<-"
> [1] "express.summary.stat"
> [1] "express.summary.stat"
> [1] "barplot"
> [1] "barplot"
> [1] "mas5calls"
> 
> ** help
>   >>> Building/Updating help pages for package 'affy'
>       Formats: text html latex example
>    .setAffyOptions                   text    html    latex   example
>    AffyBatch-class                   text    html    latex   example
>    AffyRNAdeg                        text    html    latex   example
>    MAplot                            text    html    latex   example
>    ProbeSet-class                    text    html    latex   example
>    ProgressBarText-class             text    html    latex   example
>    SpikeIn                           text    html    latex
>    affy-options                      text    html    latex   example
>    affy.scalevalue.exprSet           text    html    latex
>    affybatch.example                 text    html    latex
>    barplot.ProbeSet                  text    html    latex   example
>    bg.adjust                         text    html    latex
>    bgc                               text    html    latex   example
>    cdfFromBioC                       text    html    latex   example
>    cdfenv.example                    text    html    latex
>    cleancdfname                      text    html    latex   example
>    debug.affy123                     text    html    latex
>    expresso                          text    html    latex   example
>    expressoWidget                    text    html    latex   example
>    fit.li.wong                       text    html    latex   example
>    generateExprSet-methods           text    html    latex   example
>    generateExprVal-methods           text    html    latex   example
>    generateExprVal.method.avgdiff    text    html    latex   example
>    generateExprVal.method.playerout  text    html    latex
>    hlog                              text    html    latex
>    justrma                           text    html    latex   example
>       missing link(s):  read.celfile
>    list.celfiles                     text    html    latex   example
>    loess.normalize                   text    html    latex
>    maffy.normalise                   text    html    latex   example
>    maffy.subset                      text    html    latex   example
>    mas5                              text    html    latex   example
>    mas5calls                         text    html    latex   example
>    merge.AffyBatch                   text    html    latex   example
>    multiloess                        text    html    latex
>    mva.pairs                         text    html    latex   example
>    normalize-methods                 text    html    latex   example
>    normalize                         text    html    latex
>    normalize.constant                text    html    latex
>    normalize.contrast                text    html    latex   example
>    normalize.invariantset            text    html    latex
>    normalize.loess                   text    html    latex   example
>    normalize.qspline                 text    html    latex
>    normalize.quantiles               text    html    latex
>    normalize.quantiles.robust        text    html    latex
>    pairs.AffyBatch                   text    html    latex   example
>    plot.ProbeSet                     text    html    latex   example
>    plot.density                      text    html    latex   example
>    plotLocation                      text    html    latex   example
>    pmcorrect                         text    html    latex   example
>    ppsetApply                        text    html    latex   example
>    probeMatch-methods                text    html    latex
>    probeNames-methods                text    html    latex
>    read.affybatch                    text    html    latex   example
>    read.probematrix                  text    html    latex   example
>    rma                               text    html    latex   example
>    simplemultiLoess                  text    html    latex
>    summary                           text    html    latex
>    tukey.biweight                    text    html    latex
>    whatcdf                           text    html    latex
>    xy2indices                        text    html    latex   example
> * DONE (affy)
> [1] "Installation complete"
> [1] "Attempting to download affyPLM from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing affyPLM"
> * Installing *source* package 'affyPLM' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c LESN.c -o LESN.o
> LESN.c:190: warning: static declaration for `log2' follows non-static
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c SCAB.c -o SCAB.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c avg_log.c -o avg_log.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c biweight.c -o biweight.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c chipbackground.c -o  
> chipbackground.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c do_PLMrlm.c -o  
> do_PLMrlm.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c do_PLMrma.c -o  
> do_PLMrma.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c do_PLMthreestep.c -o  
> do_PLMthreestep.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c idealmismatch.c -o  
> idealmismatch.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c lm.c -o lm.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c lm_threestep.c -o  
> lm_threestep.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c log_avg.c -o log_avg.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c matrix_functions.c -o  
> matrix_functions.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c medianPM.c -o medianPM.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c median_logPM.c -o  
> median_logPM.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c medianpolish.c -o  
> medianpolish.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c nthLargestPM.c -o  
> nthLargestPM.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c preprocess.c -o  
> preprocess.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c psi_fns.c -o psi_fns.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c qnorm.c -o qnorm.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c qnorm_probeset.c -o  
> qnorm_probeset.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rlm.c -o rlm.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rlm_PLM.c -o rlm_PLM.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rlm_anova.c -o  
> rlm_anova.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rlm_se.c -o rlm_se.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rlm_threestep.c -o  
> rlm_threestep.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rmaPLM_pseudo.c -o  
> rmaPLM_pseudo.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rma_PLM.c -o rma_PLM.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rma_background2.c -o  
> rma_background2.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c rma_common.c -o  
> rma_common.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c scaling.c -o scaling.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c threestep.c -o  
> threestep.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c threestep_PLM.c -o  
> threestep_PLM.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c threestep_common.c -o  
> threestep_common.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c threestep_summary.c -o  
> threestep_summary.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c  
> threestep_summary_methods.c -o threestep_summary_methods.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c weightedkerneldensity.c  
> -o weightedkerneldensity.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> affyPLM.so LESN.o SCAB.o avg_log.o biweight.o chipbackground.o  
> do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm.o  
> lm_threestep.o log_avg.o matrix_functions.o medianPM.o median_logPM.o  
> medianpolish.o nthLargestPM.o preprocess.o psi_fns.o qnorm.o  
> qnorm_probeset.o rlm.o rlm_PLM.o rlm_anova.o rlm_se.o rlm_threestep.o  
> rmaPLM_pseudo.o rma_PLM.o rma_background2.o rma_common.o scaling.o  
> threestep.o threestep_PLM.o threestep_common.o threestep_summary.o  
> threestep_summary_methods.o weightedkerneldensity.o  -framework vecLib  
> -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** inst
> ** save image
> [1] TRUE
> [1] TRUE
> [1] TRUE
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> [1] TRUE
> Loading required package: reposTools
> [1] TRUE
> [1] TRUE
> [1] "PLMset"
> [1] "cdfName"
> Creating a new generic function for "weights" in "affyPLM"
> [1] "weights"
> [1] "weights<-"
> [1] "weights<-"
> [1] "coefs"
> [1] "coefs"
> [1] "coefs<-"
> [1] "coefs<-"
> [1] "coefs.probe"
> [1] "coefs.probe"
> [1] "se"
> [1] "se"
> [1] "se.probe"
> [1] "se.probe"
> [1] "se<-"
> [1] "se<-"
> [1] "indexProbes"
> [1] "indexProbesProcessed"
> [1] "indexProbesProcessed"
> [1] "image"
> [1] "boxplot"
> [1] "show"
> [1] "coefs.const"
> [1] "coefs.const"
> [1] "se.const"
> [1] "se.const"
> [1] "summary"
> [1] "Mbox"
> [1] "resid<-"
> [1] "resid<-"
> Creating a new generic function for "resid" in "affyPLM"
> [1] "resid"
> [1] "residuals<-"
> [1] "residuals<-"
> Creating a new generic function for "residuals" in "affyPLM"
> [1] "residuals"
> [1] "normvec"
> [1] "normvec"
> [1] "varcov"
> [1] "varcov"
> [1] "residSE"
> [1] "residSE"
> [1] "sampleNames<-"
> [1] "model.description"
> [1] "model.description"
> [1] "MAplot"
> 
> ** help
>   >>> Building/Updating help pages for package 'affyPLM'
>       Formats: text html latex example
>    MAplot                            text    html    latex
>    PLMset-class                      text    html    latex   example
>    PLMset2exprSet                    text    html    latex   example
>    affyPLM-internal                  text    html    latex
>    bg.correct.LESN                   text    html    latex   example
>    fitPLM                            text    html    latex   example
>    normalize.exprSet                 text    html    latex   example
>    normalize.quantiles.probeset      text    html    latex
>    normalize.scaling                 text    html    latex   example
>    pseudo                            text    html    latex   example
>    rmaPLM                            text    html    latex   example
>    threestep                         text    html    latex   example
>    threestepPLM                      text    html    latex   example
> * DONE (affyPLM)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download GO from  
> http://www.bioconductor.org/data/metaData-devel/"
> [1] "Download complete."
> [1] "Installing GO"
> * Installing *source* package 'GO' ...
> ** R
> ** data
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'GO'
>       Formats: text html latex example
>    GO                                text    html    latex
>    GOALLLOCUSID                      text    html    latex   example
>    GOBPANCESTOR                      text    html    latex   example
>    GOBPCHILDREN                      text    html    latex   example
>    GOBPOFFSPRING                     text    html    latex   example
>    GOBPPARENTS                       text    html    latex   example
>    GOCCANCESTOR                      text    html    latex   example
>    GOCCCHILDREN                      text    html    latex   example
>    GOCCOFFSPRING                     text    html    latex   example
>    GOCCPARENTS                       text    html    latex   example
>    GOLOCUSID                         text    html    latex   example
>    GOLOCUSID2ALLGO                   text    html    latex   example
>    GOLOCUSID2GO                      text    html    latex   example
>    GOMFANCESTOR                      text    html    latex   example
>    GOMFCHILDREN                      text    html    latex   example
>    GOMFOFFSPRING                     text    html    latex   example
>    GOMFPARENTS                       text    html    latex   example
>    GOQC                              text    html    latex
>    GOTERM                            text    html    latex   example
> * DONE (GO)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download KEGG from  
> http://www.bioconductor.org/data/metaData-devel/"
> [1] "Download complete."
> [1] "Installing KEGG"
> * Installing *source* package 'KEGG' ...
> ** R
> ** data
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'KEGG'
>       Formats: text html latex example
>    KEGG                              text    html    latex
>    KEGGENZYMEID2GO                   text    html    latex   example
>    KEGGEXTID2PATHID                  text    html    latex   example
>    KEGGGO2ENZYMEID                   text    html    latex   example
>    KEGGPATHID2EXTID                  text    html    latex   example
>    KEGGPATHID2NAME                   text    html    latex   example
>    KEGGPATHNAME2ID                   text    html    latex   example
>    KEGGQC                            text    html    latex
> * DONE (KEGG)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download hgu95av2 from  
> http://www.bioconductor.org/data/metaData-devel/"
> [1] "Download complete."
> [1] "Installing hgu95av2"
> * Installing *source* package 'hgu95av2' ...
> ** R
> ** data
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'hgu95av2'
>       Formats: text html latex example
>    hgu95av2                          text    html    latex
>    hgu95av2ACCNUM                    text    html    latex   example
>    hgu95av2CHR                       text    html    latex   example
>    hgu95av2CHRLENGTHS                text    html    latex   example
>    hgu95av2CHRLOC                    text    html    latex   example
>    hgu95av2ENZYME                    text    html    latex   example
>    hgu95av2ENZYME2PROBE              text    html    latex   example
>    hgu95av2GENENAME                  text    html    latex   example
>    hgu95av2GO                        text    html    latex   example
>    hgu95av2GO2ALLPROBES              text    html    latex   example
>    hgu95av2GO2PROBE                  text    html    latex   example
>    hgu95av2GRIF                      text    html    latex   example
>    hgu95av2LOCUSID                   text    html    latex   example
>    hgu95av2MAP                       text    html    latex   example
>    hgu95av2OMIM                      text    html    latex   example
>    hgu95av2ORGANISM                  text    html    latex   example
>    hgu95av2PATH                      text    html    latex   example
>    hgu95av2PATH2PROBE                text    html    latex   example
>    hgu95av2PMID                      text    html    latex   example
>    hgu95av2PMID2PROBE                text    html    latex   example
>    hgu95av2QC                        text    html    latex
>    hgu95av2REFSEQ                    text    html    latex   example
>    hgu95av2SUMFUNC                   text    html    latex   example
>    hgu95av2SYMBOL                    text    html    latex   example
>    hgu95av2UNIGENE                   text    html    latex   example
> * DONE (hgu95av2)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download genefilter from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing genefilter"
> * Installing *source* package 'genefilter' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c genedist.c -o genedist.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c init.c -o init.o
> g77   -fno-common  -g -O2 -c ttest.f -o ttest.o
> make: g77: Command not found
> make: *** [ttest.o] Error 127
> ERROR: compilation failed for package 'genefilter'
> Note: Package genefilter not found in any known repository.
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download Biostrings from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing Biostrings"
> * Installing *source* package 'Biostrings' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c biostring.c -o  
> biostring.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> Biostrings.so biostring.o  -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** data
> ** save image
> [1] "BioAlphabet"
> [1] "gapletter<-"
> [1] "gapletter<-"
> [1] "initialize"
> [1] "NucleotideAlphabet"
> [1] "initialize"
> [1] "AminoAcidAlphabet"
> [1] "BioPatternAlphabet"
> [1] "gapletter<-"
> [1] "initialize"
> [1] "BioString"
> Creating a new generic function for "as.matrix" in "Biostrings"
> [1] "as.matrix"
> [1] "BioStringNewValues"
> [1] "BioStringNewValues"
> [1] "BioStringNewValues"
> [1] "BioStringNewValues"
> [1] "initialize"
> [1] "length"
> [1] "["
> [1] "[["
> Creating a new generic function for "substr" in "Biostrings"
> [1] "substr"
> Creating a new generic function for "substring" in "Biostrings"
> [1] "substring"
> [1] "as.character"
> Creating a new generic function for "nchar" in "Biostrings"
> [1] "nchar"
> [1] "show"
> [1] "matchDNAPattern"
> [1] "matchDNAPattern"
> [1] "matchDNAPattern"
> [1] "matchDNAPattern"
> [1] "allSameLetter"
> [1] "allSameLetter"
> [1] "allSameLetter"
> [1] "allSameLetter"
> [1] "anySameLetter"
> [1] "anySameLetter"
> [1] "anySameLetter"
> [1] "anySameLetter"
> [1] "LongestCommonPrefix"
> [1] "["
> 
> ** help
>   >>> Building/Updating help pages for package 'Biostrings'
>       Formats: text html latex example
>    AminoAcidAlphabet-class           text    html    latex
>    BioAlphabet-class                 text    html    latex   example
>    BioPatternAlphabet-class          text    html    latex   example
>    BioString-class                   text    html    latex   example
>    BioStringNewValues                text    html    latex   example
>    DNAAlphabet                       text    html    latex   example
>    DNAPatternAlphabet                text    html    latex   example
>    DNASuffixArray                    text    html    latex   example
>    LongestCommonPrefix-class         text    html    latex   example
>    LongestCommonPrefix               text    html    latex   example
>    NucleotideAlphabet-class          text    html    latex   example
>    NucleotideString                  text    html    latex   example
>    allSameLetter                     text    html    latex   example
>    alphabetFrequency                 text    html    latex   example
>    anySameLetter                     text    html    latex   example
>    gapletterReplace                  text    html    latex   example
>    matchDNAPattern                   text    html    latex   example
>    reverseComplement                 text    html    latex   example
>    sortDNAString                     text    html    latex   example
>    yeastSEQCHR1                      text    html    latex   example
> * DONE (Biostrings)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download rae230a from  
> http://www.bioconductor.org/data/metaData-devel/"
> [1] "Download complete."
> [1] "Installing rae230a"
> * Installing *source* package 'rae230a' ...
> ** R
> ** data
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'rae230a'
>       Formats: text html latex example
>    rae230a                           text    html    latex
>    rae230aACCNUM                     text    html    latex   example
>    rae230aCHR                        text    html    latex   example
>    rae230aCHRLENGTHS                 text    html    latex   example
>    rae230aCHRLOC                     text    html    latex   example
>    rae230aENZYME                     text    html    latex   example
>    rae230aENZYME2PROBE               text    html    latex   example
>    rae230aGENENAME                   text    html    latex   example
>    rae230aGO                         text    html    latex   example
>    rae230aGO2ALLPROBES               text    html    latex   example
>    rae230aGO2PROBE                   text    html    latex   example
>    rae230aGRIF                       text    html    latex   example
>    rae230aLOCUSID                    text    html    latex   example
>    rae230aMAP                        text    html    latex   example
>    rae230aOMIM                       text    html    latex   example
>    rae230aORGANISM                   text    html    latex   example
>    rae230aPATH                       text    html    latex   example
>    rae230aPATH2PROBE                 text    html    latex   example
>    rae230aPMID                       text    html    latex   example
>    rae230aPMID2PROBE                 text    html    latex   example
>    rae230aQC                         text    html    latex
>    rae230aREFSEQ                     text    html    latex   example
>    rae230aSUMFUNC                    text    html    latex   example
>    rae230aSYMBOL                     text    html    latex   example
>    rae230aUNIGENE                    text    html    latex   example
> * DONE (rae230a)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download hgu95av2probe from  
> http://www.bioconductor.org/data/probes/Packages/"
> [1] "Download complete."
> [1] "Installing hgu95av2probe"
> * Installing *source* package 'hgu95av2probe' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'hgu95av2probe'
>       Formats: text html latex example
>    hgu95av2probe                     text    html    latex   example
> * DONE (hgu95av2probe)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download hu6800cdf from  
> http://www.bioconductor.org/data/cdfenvs/repos/"
> [1] "Download complete."
> [1] "Installing hu6800cdf"
> * Installing *source* package 'hu6800cdf' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'hu6800cdf'
>       Formats: text html latex example
>    geometry                          text    html    latex   example
>    hu6800cdf                         text    html    latex
> [1] "Installation complete"
> * DONE (hu6800cdf)
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download hu6800probe from  
> http://www.bioconductor.org/data/probes/Packages/"
> [1] "Download complete."
> [1] "Installing hu6800probe"
> * Installing *source* package 'hu6800probe' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'hu6800probe'
>       Formats: text html latex example
>    hu6800probe                       text    html    latex   example
> * DONE (hu6800probe)
> [1] "Installation complete"
> [1] "Attempting to download matchprobes from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing matchprobes"
> * Installing *source* package 'matchprobes' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c main.c -o main.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c strutils.c -o strutils.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> matchprobes.so main.o strutils.o  -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** data
> ** inst
> ** save image
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> [1] TRUE
> 
> ** help
>   >>> Building/Updating help pages for package 'matchprobes'
>       Formats: text html latex example
>    basecontent                       text    html    latex   example
>    combineAffyBatch                  text    html    latex   example
>    complementSeq                     text    html    latex   example
>    getProbeDataAffy                  text    html    latex   example
>    makeProbePackage                  text    html    latex   example
>    matchprobes                       text    html    latex   example
>    print.probetable                  text    html    latex   example
>    reverseSeq                        text    html    latex   example
> * DONE (matchprobes)
> [1] "Installation complete"
> [1] "Attempting to download rae230aprobe from  
> http://www.bioconductor.org/data/probes/Packages/"
> [1] "Download complete."
> [1] "Installing rae230aprobe"
> * Installing *source* package 'rae230aprobe' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'rae230aprobe'
>       Formats: text html latex example
>    rae230aprobe                      text    html    latex   example
> * DONE (rae230aprobe)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: Package XML not found in any known repository.
> Note: Package annotate not found in any known repository.
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download multtest from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing multtest"
> * Installing *source* package 'multtest' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c Rpack.c -o  
> Rpack.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c  
> block_sampling_fixed.c -o block_sampling_fixed.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c bootloop.c  
> -o bootloop.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c mt.c -o  
> mt.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c  
> pairt_sampling.c -o pairt_sampling.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c  
> pairt_sampling_fixed.c -o pairt_sampling_fixed.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c random.c  
> -o random.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c sampling.c  
> -o sampling.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c  
> sampling_fixed.c -o sampling_fixed.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c  
> stat_func.c -o stat_func.o
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include  -O -DUSEDOUBLE -fno-common  -g -O2 -c  
> stat_order.c -o stat_order.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> multtest.so Rpack.o block_sampling_fixed.o bootloop.o mt.o  
> pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o  
> sampling_fixed.o stat_func.o stat_order.o -lm -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> [1] "MTP"
> Creating a new generic function for "print" in "multtest"
> [1] "print"
> Creating a new generic function for "plot" in "multtest"
> [1] "plot"
> Creating a new generic function for "summary" in "multtest"
> [1] "summary"
> [1] "["
> Creating a new generic function for "as.list" in "multtest"
> [1] "as.list"
> 
> ** help
>   >>> Building/Updating help pages for package 'multtest'
>       Formats: text html latex example
>    MTP-class                         text    html    latex   example
>    MTP-methods                       text    html    latex
>    MTP                               text    html    latex   example
>    boot.resample                     text    html    latex   example
>    fwer2gfwer                        text    html    latex   example
>    get.index                         text    html    latex   example
>    golub                             text    html    latex
>    meanX                             text    html    latex   example
>    mt.internal                       text    html    latex
>    mt.maxT                           text    html    latex   example
>    mt.plot                           text    html    latex   example
>    mt.rawp2adjp                      text    html    latex   example
>    mt.reject                         text    html    latex   example
>    mt.sample.teststat                text    html    latex   example
>    mt.teststat                       text    html    latex   example
>    ss.maxT                           text    html    latex   example
>    wapply                            text    html    latex   example
> * DONE (multtest)
> [1] "Installation complete"
> [1] "Attempting to download annaffy from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing annaffy"
> * Installing *source* package 'annaffy' ...
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> Loading required package: GO
> Loading required package: KEGG
> Error: package 'annotate' required by 'annaffy' could not be found
> Execution halted
> cat: stdout: Broken pipe
> ERROR: execution of package source for 'annaffy' failed
> [1] "Attempting to download gcrma from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing gcrma"
> * Installing *source* package 'gcrma' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c computeAffinities.c -o  
> computeAffinities.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> gcrma.so computeAffinities.o  -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'gcrma'
>       Formats: text html latex example
>    affinity.spline.coefs             text    html    latex
>    bg.adjust.affinities              text    html    latex
>    bg.parameters.ns                  text    html    latex
>    compute.affinities                text    html    latex
>    fast.bkg                          text    html    latex
>    gcrma                             text    html    latex   example
>    getCDF                            text    html    latex
>    justGCRMA                         text    html    latex   example
> * DONE (gcrma)
> [1] "Installation complete"
> [1] "Attempting to download makecdfenv from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing makecdfenv"
> * Installing *source* package 'makecdfenv' ...
> creating cache ./config.cache
> checking how to run the C preprocessor... cc -E
> checking for main in -lz... yes
> checking for zlib.h... yes
> checking if zlib version >= 1.1.3... yes
> updating cache ./config.cache
> creating ./config.status
> creating src/Makevars
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -DHAVE_ZLIB=1  -I/usr/local/include   -fno-common  -g -O2 -c  
> read_cdffile.c -o read_cdffile.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> makecdfenv.so read_cdffile.o -lz  -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _crc32
> /usr/lib/libz.dylib(crc32.o) definition of _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /usr/lib/libz.dylib(crc32.o) definition of _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflateInit_
> /usr/lib/libz.dylib(deflate.o) definition of _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> ld: warning multiple definitions of symbol _deflateCopy
> /usr/lib/libz.dylib(deflate.o) definition of _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateParams
> /usr/lib/libz.dylib(deflate.o) definition of _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> ld: warning multiple definitions of symbol _deflateReset
> /usr/lib/libz.dylib(deflate.o) definition of _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /usr/lib/libz.dylib(deflate.o) definition of _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateEnd
> /usr/lib/libz.dylib(deflate.o) definition of _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflate
> /usr/lib/libz.dylib(deflate.o) definition of _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> ld: warning multiple definitions of symbol _deflateInit2_
> /usr/lib/libz.dylib(deflate.o) definition of _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> ld: warning multiple definitions of symbol _gzwrite
> /usr/lib/libz.dylib(gzio.o) definition of _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> ld: warning multiple definitions of symbol _gztell
> /usr/lib/libz.dylib(gzio.o) definition of _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> ld: warning multiple definitions of symbol _gzseek
> /usr/lib/libz.dylib(gzio.o) definition of _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> ld: warning multiple definitions of symbol _gzread
> /usr/lib/libz.dylib(gzio.o) definition of _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> ld: warning multiple definitions of symbol _gzopen
> /usr/lib/libz.dylib(gzio.o) definition of _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> ld: warning multiple definitions of symbol _gzgetc
> /usr/lib/libz.dylib(gzio.o) definition of _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzeof
> /usr/lib/libz.dylib(gzio.o) definition of _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /usr/lib/libz.dylib(gzio.o) definition of _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /usr/lib/libz.dylib(gzio.o) definition of _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /usr/lib/libz.dylib(gzio.o) definition of _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /usr/lib/libz.dylib(gzio.o) definition of _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgets
> /usr/lib/libz.dylib(gzio.o) definition of _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> ld: warning multiple definitions of symbol _gzprintf
> /usr/lib/libz.dylib(gzio.o) definition of _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /usr/lib/libz.dylib(gzio.o) definition of _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /usr/lib/libz.dylib(gzio.o) definition of _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> ld: warning multiple definitions of symbol _gzrewind
> /usr/lib/libz.dylib(gzio.o) definition of _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzsetparams
> /usr/lib/libz.dylib(gzio.o) definition of _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /usr/lib/libz.dylib(inflate.o) definition of _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /usr/lib/libz.dylib(inflate.o) definition of _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> ld: warning multiple definitions of symbol _inflateInit2_
> /usr/lib/libz.dylib(inflate.o) definition of _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> ld: warning multiple definitions of symbol _inflateEnd
> /usr/lib/libz.dylib(inflate.o) definition of _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateReset
> /usr/lib/libz.dylib(inflate.o) definition of _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /usr/lib/libz.dylib(inflate.o) definition of _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /usr/lib/libz.dylib(inflate.o) definition of _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateSync
> /usr/lib/libz.dylib(inflate.o) definition of _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> ld: warning multiple definitions of symbol _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> ld: warning multiple definitions of symbol _adler32
> /usr/lib/libz.dylib(adler32.o) definition of _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> ld: warning multiple definitions of symbol _zError
> /usr/lib/libz.dylib(zutil.o) definition of _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /usr/lib/libz.dylib(zutil.o) definition of _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> Loading required package: reposTools
> [1] TRUE
> [1] TRUE
> [1] "Cdf"
> [1] "name.levels"
> [1] "name.levels"
> [1] "name.levels<-"
> [1] "name.levels<-"
> [1] "pbase"
> [1] "pbase"
> [1] "pbase<-"
> [1] "pbase<-"
> [1] "pbase.levels"
> [1] "pbase.levels"
> [1] "pbase.levels<-"
> [1] "pbase.levels<-"
> [1] "tbase"
> [1] "tbase"
> [1] "tbase<-"
> [1] "tbase<-"
> [1] "tbase.levels"
> [1] "tbase.levels"
> [1] "tbase.levels<-"
> [1] "tbase.levels<-"
> [1] "show"
> 
> ** help
>   >>> Building/Updating help pages for package 'makecdfenv'
>       Formats: text html latex example
>    Cdf-class                         text    html    latex
>    getInfoInAffyFile                 text    html    latex
>    make.cdf.env                      text    html    latex   example
>    make.cdf.package                  text    html    latex   example
>    pmormm                            text    html    latex
>    read.cdffile                      text    html    latex   example
> * DONE (makecdfenv)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: Package XML not found in any known repository.
> Note: Package annotate not found in any known repository.
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download Ruuid from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing Ruuid"
> * Installing *source* package 'Ruuid' ...
> creating cache ./config.cache
> checking for glib-config... no
> checking how to run the C preprocessor... cc -E
> checking for /usr/include/unistd.h... yes
> updating cache ./config.cache
> creating ./config.status
> creating src/Makevars
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
> -I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include    
> -fno-common  -g -O2 -c Rinit.c -o Rinit.o
> In file included from Ruuid.h:5,
>                   from Rinit.c:1:
> uuidP.h:24:18: glib.h: No such file or directory
> In file included from Ruuid.h:5,
>                   from Rinit.c:1:
> uuidP.h:36: error: parse error before "guint32"
> uuidP.h:36: warning: no semicolon at end of struct or union
> uuidP.h:37: warning: data definition has no type or storage class
> uuidP.h:38: error: parse error before "time_hi_and_version"
> uuidP.h:38: warning: data definition has no type or storage class
> uuidP.h:39: error: parse error before "clock_seq"
> uuidP.h:39: warning: data definition has no type or storage class
> uuidP.h:40: error: parse error before "node"
> uuidP.h:40: warning: data definition has no type or storage class
> uuidP.h:41: error: parse error before '}' token
> make: *** [Rinit.o] Error 1
> ERROR: compilation failed for package 'Ruuid'
> Note: Package Ruuid not found in any known repository.
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download SparseM from  
> http://www.bioconductor.org//CRANrepository"
> [1] "Download complete."
> [1] "Installing SparseM"
> * Installing *source* package 'SparseM' ...
> ** libs
> g77   -fno-common  -g -O2 -c bckslv.f -o bckslv.o
> make: g77: Command not found
> make: *** [bckslv.o] Error 127
> ERROR: compilation failed for package 'SparseM'
> Note: Package SparseM not found in any known repository.
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: Package XML not found in any known repository.
> Note: Package graph not found in any known repository.
> Note: Package Rgraphviz not found in any known repository.
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download fibroEset from  
> http://www.bioconductor.org/data/experimental/repos/"
> [1] "Download complete."
> [1] "Installing fibroEset"
> * Installing *source* package 'fibroEset' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'fibroEset'
>       Formats: text html latex example
>    fibroEset                         text    html    latex   example
> * DONE (fibroEset)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download hu6800 from  
> http://www.bioconductor.org/data/metaData-devel/"
> [1] "Download complete."
> [1] "Installing hu6800"
> * Installing *source* package 'hu6800' ...
> ** R
> ** data
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'hu6800'
>       Formats: text html latex example
>    hu6800                            text    html    latex
>    hu6800ACCNUM                      text    html    latex   example
>    hu6800CHR                         text    html    latex   example
>    hu6800CHRLENGTHS                  text    html    latex   example
>    hu6800CHRLOC                      text    html    latex   example
>    hu6800ENZYME                      text    html    latex   example
>    hu6800ENZYME2PROBE                text    html    latex   example
>    hu6800GENENAME                    text    html    latex   example
>    hu6800GO                          text    html    latex   example
>    hu6800GO2ALLPROBES                text    html    latex   example
>    hu6800GO2PROBE                    text    html    latex   example
>    hu6800GRIF                        text    html    latex   example
>    hu6800LOCUSID                     text    html    latex   example
>    hu6800MAP                         text    html    latex   example
>    hu6800OMIM                        text    html    latex   example
>    hu6800ORGANISM                    text    html    latex   example
>    hu6800PATH                        text    html    latex   example
>    hu6800PATH2PROBE                  text    html    latex   example
>    hu6800PMID                        text    html    latex   example
>    hu6800PMID2PROBE                  text    html    latex   example
>    hu6800QC                          text    html    latex
>    hu6800REFSEQ                      text    html    latex   example
>    hu6800SUMFUNC                     text    html    latex   example
>    hu6800SYMBOL                      text    html    latex   example
>    hu6800UNIGENE                     text    html    latex   example
> * DONE (hu6800)
> [1] "Installation complete"
> [1] "Attempting to download geneplotter from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing geneplotter"
> * Installing *source* package 'geneplotter' ...
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> [1] TRUE
> Loading required package: annotate
> Error: geneplotter requires annotate
> In addition: Warning message:
> There is no package called 'annotate' in: library(package,  
> character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts,
> Execution halted
> /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1:  7714  
> Broken pipe             cat  
> "/Users/rkakkar/Library/R/library/geneplotter/R/geneplotter"
> ERROR: execution of package source for 'geneplotter' failed
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download golubEsets from  
> http://www.bioconductor.org/data/experimental/repos/"
> [1] "Download complete."
> [1] "Installing golubEsets"
> * Installing *source* package 'golubEsets' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'golubEsets'
>       Formats: text html latex example
>    golubMerge                        text    html    latex   example
>    golubTest                         text    html    latex   example
>    golubTrain                        text    html    latex   example
> [1] "Installation complete"
> * DONE (golubEsets)
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download xtable from  
> http://www.bioconductor.org//CRANrepository"
> [1] "Download complete."
> [1] "Installing xtable"
> * Installing *source* package 'xtable' ...
> ** R
> ** data
> ** help
>   >>> Building/Updating help pages for package 'xtable'
>       Formats: text html latex example
>    print.xtable                      text    html    latex
>    string                            text    html    latex
>    table.attributes                  text    html    latex
>    tli                               text    html    latex
>    xtable                            text    html    latex   example
> * DONE (xtable)
> [1] "Installation complete"
> [1] "Attempting to download edd from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing edd"
> * Installing *source* package 'edd' ...
> ** R
> ** inst
> ** save image
> [1] TRUE
> Loading required package: golubEsets
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> Loading required package: Biobase
> Loading required package: class
> Loading required package: nnet
> Loading required package: xtable
> [1] "eddDist"
> [1] "stub"
> [1] "stub"
> [1] "plotlim"
> [1] "plotlim"
> [1] "tag"
> [1] "tag"
> [1] "latexTag"
> [1] "latexTag"
> [1] "parms"
> [1] "parms"
> [1] "med"
> [1] "med"
> [1] "Mad"
> [1] "Mad"
> [1] "CDFname"
> [1] "CDFname"
> [1] "qfName"
> [1] "qfName"
> [1] "qfun"
> [1] "qfun"
> [1] "genName"
> [1][1] "Installation complete"
>   "genName"
> [1] "testVec"
> [1] "testVec"
> 
> ** help
>   >>> Building/Updating help pages for package 'edd'
>       Formats: text html latex example
>    centerScale                       text    html    latex   example
>    edd                               text    html    latex   example
>    eddDist-class                     text    html    latex   example
>    eddObsolete                       text    html    latex   example
>    flatQQNorm                        text    html    latex   example
>    latEDtable                        text    html    latex   example
>    makeCandmat.raw                   text    html    latex   example
>    maxKSp                            text    html    latex   example
>    plotED                            text    html    latex   example
> * DONE (edd)
> [1] "Attempting to download ROC from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing ROC"
> * Installing *source* package 'ROC' ...
> ** R
> ** inst
> ** save image
> [1] TRUE
> [1] TRUE
> [1] "rocc"
> [1] "plot"
> [1] "plot"
> 
> ** help
>   >>> Building/Updating help pages for package 'ROC'
>       Formats: text html latex example
>    AUC                               text    html    latex   example
>    plot-methods                      text    html    latex   example
>    rocc-class                        text    html    latex   example
>    rocdemo.sca                       text    html    latex   example
>    trapezint                         text    html    latex   example
> [1] "Installation complete"
> * DONE (ROC)
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download statmod from  
> http://www.bioconductor.org//CRANrepository"
> [1] "Download complete."
> [1] "Installing statmod"
> * Installing *source* package 'statmod' ...
> ** R
> ** data
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'statmod'
>       Formats: text html latex example
>    1Introduction                     text    html    latex
>    digammaf                          text    html    latex   example
>    gauss.quad                        text    html    latex   example
>    gauss.quad.prob                   text    html    latex   example
>    glmgam                            text    html    latex   example
>    growthcurve                       text    html    latex   example
>    hommel.test                       text    html    latex   example
>    invgauss                          text    html    latex   example
>    logmdigamma                       text    html    latex   example
>    matvec                            text    html    latex   example
>    meanT                             text    html    latex   example
>    power                             text    html    latex   example
>    qresiduals                        text    html    latex   example
>    ranblock                          text    html    latex   example
>    remlscor                          text    html    latex   example
>    remlscorgamma                     text    html    latex   example
>    sage.test                         text    html    latex   example
>    tweedie                           text    html    latex   example
>    welding                           text    html    latex
> * DONE (statmod)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download sma from  
> http://www.bioconductor.org//CRANrepository"
> [1] "Download complete."
> [1] "Installing sma"
> * Installing *source* package 'sma' ...
> ** R
> ** data
> [1] "Installation complete"
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'sma'
>       Formats: text html latex example
>    MouseArray                        text    html    latex
>    id2image                          text    html    latex   example
>    init.addinfo                      text    html    latex   example
>    init.ctl.index                    text    html    latex   example
>    init.data                         text    html    latex   example
>    init.grid                         text    html    latex   example
>    init.names                        text    html    latex   example
>    init.read.exp                     text    html    latex   example
>    is.odd                            text    html    latex   example
>    na                                text    html    latex
>    plot.bayesian                     text    html    latex   example
>    plot.confband.lines               text    html    latex   example
>    plot.confband.points              text    html    latex   example
>    plot.confband.text                text    html    latex   example
>    plot.cor                          text    html    latex
>    plot.mat                          text    html    latex   example
>    plot.mva                          text    html    latex   example
>    plot.print.tip.lowess             text    html    latex   example
>    plot.qq                           text    html    latex   example
>    plot.qqline                       text    html    latex   example
>    plot.scale.box                    text    html    latex   example
>    plot.single.slide                 text    html    latex   example
>    plot.smooth.line                  text    html    latex   example
>    plot.spatial                      text    html    latex   example
>    plot.svb                          text    html    latex   example
>    plot.t2                           text    html    latex   example
>    read.genepix                      text    html    latex
>    read.spot                         text    html    latex   example
>    rgcolors.func                     text    html    latex   example
>    sma-internal                      text    html    latex
>    stat.Chen                         text    html    latex   example
>    stat.ChurSap                      text    html    latex   example
>    stat.Newton                       text    html    latex   example
>    stat.bay.est                      text    html    latex   example
>    stat.bayesian                     text    html    latex   example
>    stat.bwss                         text    html    latex
>    stat.diag.da                      text    html    latex
>    stat.gnames                       text    html    latex   example
>    stat.ma                           text    html    latex   example
>    stat.norm.exp                     text    html    latex   example
>    stat.t2                           text    html    latex   example
>    write.spot                        text    html    latex   example
> * DONE (sma)
> [1] "Attempting to download limma from  
> http://www.bioconductor.org//CRANrepository"
> [1] "Download complete."
> [1] "Installing limma"
> * Installing *source* package 'limma' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> 
> ** help
>   >>> Building/Updating help pages for package 'limma'
>       Formats: text html latex example
>    1introduction                     text    html    latex
>    2classes                          text    html    latex
>    3reading                          text    html    latex
>    4normalization                    text    html    latex
>    5linearmodels                     text    html    latex
>    6SingleChannel                    text    html    latex
>    7diagnostics                      text    html    latex
>    8Other                            text    html    latex
>    LargeDataObject                   text    html    latex   example
>    PrintLayout                       text    html    latex   example
>    TestResults                       text    html    latex
>    anova-method                      text    html    latex
>    asmalist                          text    html    latex
>    auROC                             text    html    latex   example
>    backgroundcorrect                 text    html    latex   example
>    blockDiag                         text    html    latex   example
>    bwss                              text    html    latex
>    bwss.matrix                       text    html    latex
>    cbind                             text    html    latex   example
>    changelog                         text    html    latex
>    channel2M                         text    html    latex   example
>    classifytests-deprecated          text    html    latex
>    classifytests                     text    html    latex   example
>    contrasts.fit                     text    html    latex   example
>    controlStatus                     text    html    latex   example
>    decideTests                       text    html    latex
>    designMatrix-deprecated           text    html    latex
>    dim                               text    html    latex   example
>    dimnames                          text    html    latex
>    dupcor                            text    html    latex   example
>    ebayes                            text    html    latex   example
>    exprset2                          text    html    latex
>    fitfdist                          text    html    latex
>    fitnormexp                        text    html    latex   example
>    geneSetTest                       text    html    latex   example
>    getSpacing                        text    html    latex   example
>    getlayout                         text    html    latex   example
>    gls.series                        text    html    latex   example
>    gridspotrc                        text    html    latex
>    heatdiagram                       text    html    latex   example
>    helpMethods                       text    html    latex   example
>    imageplot                         text    html    latex   example
>    imageplot3by2                     text    html    latex
>    intraspotCorrelation              text    html    latex   example
>    isfullrank                        text    html    latex   example
>    isnumeric                         text    html    latex   example
>    kooperberg                        text    html    latex   example
>    limmaguideURL                     text    html    latex
>    lm.series                         text    html    latex   example
>    lmFit                             text    html    latex
>    lmscFit                           text    html    latex   example
>    loessfit                          text    html    latex   example
>    m.spot                            text    html    latex
>    m2logliknormexp                   text    html    latex
>    ma3x3                             text    html    latex   example
>    makeContrasts                     text    html    latex   example
>    makeunique                        text    html    latex   example
>    malist                            text    html    latex
>    marraylm                          text    html    latex
>    matvec                            text    html    latex   example
>    merge                             text    html    latex   example
>    modelMatrix                       text    html    latex   example
>    modifyWeights                     text    html    latex   example
>    normalizeRobustSpline             text    html    latex   example
>    normalizeWithinArrays             text    html    latex   example
>    normalizebetweenarrays            text    html    latex   example
>    normalizeprintorder               text    html    latex   example
>    normalizequantiles                text    html    latex
>    normalizescale                    text    html    latex   example
>    plotDensities                     text    html    latex   example
>    plotma                            text    html    latex   example
>    plotma3by2                        text    html    latex
>    plotprinttiploess                 text    html    latex
>    poolvar                           text    html    latex   example
>    printHead                         text    html    latex
>    printorder                        text    html    latex   example
>    protectMetachar                   text    html    latex   example
>    qqt                               text    html    latex   example
>    qualwt                            text    html    latex   example
>    read.maimages                     text    html    latex   example
>    read.matrix                       text    html    latex
>    read.series                       text    html    latex
>    readGPRHeader                     text    html    latex
>    readImaGeneHeader                 text    html    latex
>    readSpotTypes                     text    html    latex
>    readTargets                       text    html    latex
>    readgal                           text    html    latex   example
>    removeext                         text    html    latex   example
>    rg.genepix                        text    html    latex
>    rg.quantarray                     text    html    latex
>    rg.series.spot                    text    html    latex
>    rg.spot                           text    html    latex
>    rglist                            text    html    latex
>    rlm.series                        text    html    latex   example
>    signalnormexp                     text    html    latex
>    splitName                         text    html    latex   example
>    squeezeVar                        text    html    latex   example
>    subsetting                        text    html    latex   example
>    summary                           text    html    latex
>    targetsA2C                        text    html    latex   example
>    tmixture                          text    html    latex
>    toptable                          text    html    latex   example
>    trigammainverse                   text    html    latex   example
>    trimWhiteSpace                    text    html    latex   example
>    uniquegenelist                    text    html    latex   example
>    unwrapdups                        text    html    latex   example
>    venn                              text    html    latex   example
>    writefit                          text    html    latex
>    zscore                            text    html    latex   example
> * DONE (limma)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> [1] "Attempting to download marray from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing marray"
> * Installing *source* package 'marray' ...
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> [1] TRUE
> [1] "marrayInfo"
> [1] "marrayLayout"
> [1] "marrayRaw"
> [1] "marrayNorm"
> [1] "maLabels"
> [1] "maLabels"
> [1] "maInfo"
> [1] "maInfo"
> [1] "maNotes"
> [1] "maNotes"
> [1] "maNspots"
> [1] "maNspots"
> [1] "maNgr"
> [1] "maNgr"
> [1] "maNgc"
> [1] "maNgc"
> [1] "maNsr"
> [1] "maNsr"
> [1] "maNsc"
> [1] "maNsc"
> [1] "maSub"
> [1] "maSub"
> [1] "maPlate"
> [1] "maPlate"
> [1] "maControls"
> [1] "maControls"
> [1] "maNotes"
> [1] "maGridRow"
> [1] "maGridRow"
> [1] "maGridCol"
> [1] "maGridCol"
> [1] "maSpotRow"
> [1] "maSpotRow"
> [1] "maSpotCol"
> [1] "maSpotCol"
> [1] "maPrintTip"
> [1] "maPrintTip"
> [1] "maRf"
> [1] "maRf"
> [1] "maGf"
> [1] "maGf"
> [1] "maRb"
> [1] "maRb"
> [1] "maGb"
> [1] "maGb"
> [1] "maW"
> [1] "maW"
> [1] "maLR"
> [1] "maLR"
> [1] "maLG"
> [1] "maLG"
> [1] "maM"
> [1] "maM"
> [1] "maA"
> [1] "maA"
> [1] "maLayout"
> [1] "maLayout"
> [1] "maNspots"
> [1] "maNgr"
> [1] "maNgc"
> [1] "maNsr"
> [1] "maNsc"
> [1] "maGridRow"
> [1] "maGridCol"
> [1] "maSpotRow"
> [1] "maSpotCol"
> [1] "maPrintTip"
> [1] "maSub"
> [1] "maPlate"
> [1] "maControls"
> [1] "maNsamples"
> [1] "maNsamples"
> [1] "maGnames"
> [1] "maGnames"
> [1] "maTargets"
> [1] "maTargets"
> [1] "maNotes"
> [1] "maA"
> [1] "maM"
> [1] "maMloc"
> [1] "maMloc"
> [1] "maMscale"
> [1] "maMscale"
> [1] "maW"
> [1] "maLR"
> [1] "maLG"
> [1] "maLayout"
> [1] "maNspots"
> [1] "maNgr"
> [1] "maNgc"
> [1] "maNsr"
> [1] "maNsc"
> [1] "maGridRow"
> [1] "maGridCol"
> [1] "maSpotRow"
> [1] "maSpotCol"
> [1] "maPrintTip"
> [1] "maSub"
> [1] "maPlate"
> [1] "maControls"
> [1] "maNsamples"
> [1] "maGnames"
> [1] "maTargets"
> [1] "maNotes"
> [1] "maNormCall"
> [1] "maNormCall"
> [1] "maLabels<-"
> [1] "maLabels<-"
> [1] "maLabels<-"
> [1] "maInfo<-"
> [1] "maInfo<-"
> [1] "maNgr<-"
> [1] "maNgr<-"
> [1] "maNgr<-"
> [1] "maNgr<-"
> [1] "maNgc<-"
> [1] "maNgc<-"
> [1] "maNgc<-"
> [1] "maNgc<-"
> [1] "maNsr<-"
> [1] "maNsr<-"
> [1] "maNsr<-"
> [1] "maNsr<-"
> [1] "maNsc<-"
> [1] "maNsc<-"
> [1] "maNsc<-"
> [1] "maNsc<-"
> [1] "maNspots<-"
> [1] "maNspots<-"
> [1] "maNspots<-"
> [1] "maNspots<-"
> [1] "maSub<-"
> [1] "maSub<-"
> [1] "maSub<-"
> [1] "maSub<-"
> [1] "maSub<-"
> [1] "maPlate<-"
> [1] "maPlate<-"
> [1] "maPlate<-"
> [1] "maPlate<-"
> [1] "maControls<-"
> [1] "maControls<-"
> [1] "maControls<-"
> [1] "maControls<-"
> [1] "maLayout<-"
> [1] "maLayout<-"
> [1] "maLayout<-"
> [1] "maGnames<-"
> [1] "maGnames<-"
> [1] "maGnames<-"
> [1] "maTargets<-"
> [1] "maTargets<-"
> [1] "maTargets<-"
> [1] "maW<-"
> [1] "maW<-"
> [1] "maW<-"
> [1] "maGf<-"
> [1] "maGf<-"
> [1] "maRf<-"
> [1] "maRf<-"
> [1] "maGb<-"
> [1] "maGb<-"
> [1] "maGb<-"
> [1] "maRb<-"
> [1] "maRb<-"
> [1] "maRb<-"
> [1] "maA<-"
> [1] "maA<-"
> [1] "maM<-"
> [1] "maM<-"
> [1] "maMloc<-"
> [1] "maMloc<-"
> [1] "maMscale<-"
> [1] "maMscale<-"
> [1] "maNotes<-"
> [1] "maNotes<-"
> [1] "maNotes<-"
> [1] "maNotes<-"
> [1] "maNotes<-"
> [1] "summary"
> [1] "summary"
> [1] "summary"
> [1] "summary"
> [1] "summary"
> [1] "ShowLargeObject"
> [1] "show"
> [1] "["
> [1] "["
> [1] "["
> [1] "["
> [1] "boxplot"
> [1] "boxplot"
> [1] "boxplot"
> [1] "image"
> [1] "image"
> [1] "image"
> [1] "points"
> [1] "points"
> [1] "points"
> [1] "text"
> [1] "text"
> [1] "text"
> [1] "lines"
> [1] "lines"
> [1] "lines"
> 
> ** help
>   >>> Building/Updating help pages for package 'marray'
>       Formats: text html latex example
>    [-methods                         text    html    latex
>    boxplot                           text    html    latex   example
>    cbind                             text    html    latex   example
>    coerce-methods                    text    html    latex
>    dim                               text    html    latex   example
>    findID                            text    html    latex   example
>    htmlPage                          text    html    latex   example
>    image                             text    html    latex   example
>    ma2D                              text    html    latex   example
>    maBoxplot                         text    html    latex   example
>    maColorBar                        text    html    latex   example
>    maCompCoord                       text    html    latex   example
>    maCompInd                         text    html    latex   example
>    maCompLayout                      text    html    latex   example
>    maCompNormA                       text    html    latex   example
>    maCompPlate                       text    html    latex   example
>    maCoord2Ind                       text    html    latex   example
>    maDefaultPar                      text    html    latex   example
>    maDotsDefaults                    text    html    latex   example
>    maDotsMatch                       text    html    latex   example
>    maGenControls                     text    html    latex   example
>    maGeneTable                       text    html    latex   example
>    maImage                           text    html    latex   example
>    maImage.func                      text    html    latex   example
>    maInd2Coord                       text    html    latex   example
>    maLegendLines                     text    html    latex   example
>    maLoess                           text    html    latex   example
>    maLoessLines                      text    html    latex   example
>    maMAD                             text    html    latex   example
>    maMed                             text    html    latex   example
>    maNA                              text    html    latex
>    maNorm                            text    html    latex   example
>    maNorm2D                          text    html    latex   example
>    maNormLoess                       text    html    latex   example
>    maNormMAD                         text    html    latex   example
>    maNormMain                        text    html    latex   example
>    maNormMed                         text    html    latex   example
>    maNormScale                       text    html    latex   example
>    maNum2Logic                       text    html    latex   example
>    maPalette                         text    html    latex   example
>    maPlot                            text    html    latex   example
>    maPlot.func                       text    html    latex   example
>    maSelectGnames                    text    html    latex   example
>    maText                            text    html    latex   example
>    maTop                             text    html    latex   example
>    maTwoSamples                      text    html    latex
>    mapGeneInfo                       text    html    latex   example
>    marray-internal                   text    html    latex
>    marrayInfo-class                  text    html    latex   example
>    marrayLayout-class                text    html    latex   example
>    marrayNorm-class                  text    html    latex   example
>    marrayRaw-class                   text    html    latex   example
>    opVersionID                       text    html    latex   example
>    plotMA                            text    html    latex   example
>    print-methods                     text    html    latex
>    read.Galfile                      text    html    latex   example
>    read.marrayInfo                   text    html    latex   example
>    read.marrayLayout                 text    html    latex   example
>    read.marrayRaw                    text    html    latex   example
>    rm.na                             text    html    latex   example
>    showLargeObject                   text    html    latex   example
>    stat.confband.text                text    html    latex   example
>    stat.gnames                       text    html    latex   example
>    swirl                             text    html    latex
>    write.list                        text    html    latex   example
>    write.marray                      text    html    latex   example
>    write.xls                         text    html    latex   example
> Warning in load(zfile, envir = envir) : no input is available
> * DONE (marray)
> [1] "Installation complete"
> [1] "Attempting to download vsn from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing vsn"
> * Installing *source* package 'vsn' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c vsn.c -o vsn.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o  
> vsn.so vsn.o  -lcc_dynamic -framework R
> ld: warning multiple definitions of symbol _xerbla_
> /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of  
> _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/R(deflate.lo) definition of  
> _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/R(inflate.lo) definition of  
> _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ 
> libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** data
> ** inst
> ** save image
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
> 	 Vignettes contain introductory material.  To view,
> 	 simply type: openVignette()
> 	 For details on reading vignettes, see
> 	 the openVignette help page.
> 
> ** help
>   >>> Building/Updating help pages for package 'vsn'
>       Formats: text html latex example
>    getIntensityMatrix                text    html    latex   example
>    kidney                            text    html    latex   example
>    log.na                            text    html    latex   example
>    lymphoma                          text    html    latex   example
>    meanSdPlot                        text    html    latex   example
>    nchoosek                          text    html    latex   example
>    normalize.AffyBatch.vsn           text    html    latex   example
>    rowSds                            text    html    latex   example
>    sagmbSimulateData                 text    html    latex   example
>    sqr                               text    html    latex   example
>    vsn                               text    html    latex   example
>    vsnPlotPar                        text    html    latex   example
>    vsnh                              text    html    latex   example
> * DONE (vsn)
> [1] "Installation complete"
> [1] "Attempting to download globaltest from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing globaltest"
> * Installing *source* package 'globaltest' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Creating a new generic function for "names" in "globaltest"
> Creating a new generic function for "names<-" in "globaltest"
> Creating a new generic function for "scale" in "globaltest"
> Creating a new generic function for "plot" in "globaltest"
> 
> ** help
>   >>> Building/Updating help pages for package 'globaltest'
>       Formats: text html latex example
>    checkerboard                      text    html    latex   example
>    exampleX                          text    html    latex
>    exampleY                          text    html    latex
>    geneplot                          text    html    latex   example
>    globaltest                        text    html    latex   example
>    gt.barplot-class                  text    html    latex
>    gt.result-class                   text    html    latex
>    permutations                      text    html    latex   example
>    regressionplot                    text    html    latex   example
>    sampleplot                        text    html    latex   example
>    sampling                          text    html    latex   example
> * DONE (globaltest)
> [1] "Installation complete"
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: Package SJava not found in any known repository.
> [1] "Attempting to download RMAGEML from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing RMAGEML"
> 
> gzip: /tmp/Rtmp553/RMAGEML_2.1.0.tar.gz: not in gzip format
> ERROR: cannot extract package from '/tmp/Rtmp553/RMAGEML_2.1.0.tar.gz'
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: You did not specify a download type.  Using a default value of:  
> Source
> This will be fine for almost all users
> 
> Note: Package XML not found in any known repository.
> Note: Package annotate not found in any known repository.
> [1] "Attempting to download siggenes from  
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing siggenes"
> 
> gzip: /tmp/Rtmp553/siggenes_1.2.10.tar.gz: not in gzip format
> ERROR: cannot extract package from '/tmp/Rtmp553/siggenes_1.2.10.tar.gz'
> [1] "Attempting to download pamr from  
> http://www.bioconductor.org//CRANrepository"
> [1] "Download complete."
> [1] "Installing pamr"
> * Installing *source* package 'pamr' ...
> ** libs
> gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include  
>   -I/usr/local/include   -fno-common  -g -O2 -c cox_func.c -o cox_func.o
> g77   -fno-common  -g -O2 -c knnimpute.f -o knnimpute.o
> make: g77: Command not found
> make: *** [knnimpute.o] Error 127
> ERROR: compilation failed for package 'pamr'
>  From URL:  http://www.bioconductor.org/repository/devel/package/Source
> 	widgetTools version 1.4.7
> 	DynDoc version 1.4.1
> 	tkWidgets version 1.5.19
> 	Biobase version 1.4.22
> 	affydata version 1.4.0
> 	affy version 1.5.8
> 	affyPLM version 1.2.2
> 	genefilter version 1.4.5
> 	Biostrings version 1.0.0
> 	matchprobes version 1.0.12
> 	multtest version 1.5.2
> 	annaffy version 1.0.11
> 	gcrma version 1.1.1
> 	makecdfenv version 1.4.8
> 	Ruuid version 1.4.5
> 	geneplotter version 1.4.2
> 	edd version 1.4.2
> 	ROC version 1.0.12
> 	marray version 1.5.21
> 	vsn version 1.5.0
> 	globaltest version 3.0.1
> 	RMAGEML version 2.1.0
> 	siggenes version 1.2.10
> 
>  From URL:  http://www.bioconductor.org/data/cdfenvs/repos/
> 	hgu95av2cdf version 1.4.3
> 	hgu133acdf version 1.4.3
> 	hu6800cdf version 1.4.3
> 
>  From URL:  http://www.bioconductor.org/data/metaData-devel/
> 	GO version 1.6.5
> 	KEGG version 1.6.5
> 	hgu95av2 version 1.6.5
> 	rae230a version 1.6.5
> 	hu6800 version 1.6.5
> 
>  From URL:  http://www.bioconductor.org/data/probes/Packages/
> 	hgu95av2probe version 1.0
> 	hu6800probe version 1.0
> 	rae230aprobe version 1.0
> 
>  From URL:  http://www.bioconductor.org//CRANrepository
> 	SparseM version 0.52
> 	xtable version 1.2-4
> 	statmod version 1.1.0
> 	sma version 0.5.14
> 	limma version 1.8.1
> 	pamr version 1.22
> 
>  From URL:  http://www.bioconductor.org/data/experimental/repos/
> 	fibroEset version 1.0
> 	golubEsets version 1.0
> 
> Packages that were not updated:
> 	annotate
> 	graph
> 	Rgraphviz
> 
> There were 13 warnings (use warnings() to see them)
>  > 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

-- 
+---------------------------------------------------------------------------+
| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
+---------------------------------------------------------------------------+



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