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

Rahul Kakkar rkakkar at uchicago.edu
Thu Oct 28 17:33:36 CEST 2004


This posting is regarding 2 problems, but all dealing with trying to  
run Bioconductor on MacOS 10.3.x.

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
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   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
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   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
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   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
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   stat.bwss                         text    html    latex
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   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
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   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
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   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
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   dupcor                            text    html    latex   example
   ebayes                            text    html    latex   example
   exprset2                          text    html    latex
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   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
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   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
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   ma2D                              text    html    latex   example
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   maCompCoord                       text    html    latex   example
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   maCoord2Ind                       text    html    latex   example
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   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
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   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)
 > 


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