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@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@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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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." 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[1] "Installing sma" * Installing *source* package 'sma' ... ** R ** data [1] "Installation complete" ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'sma' Formats: text html latex example MouseArray text html latex id2image text html latex example init.addinfo text html latex example init.ctl.index text html latex example init.data text html latex example init.grid text html latex example init.names text html latex example init.read.exp text html latex example is.odd text html latex example na text html latex plot.bayesian text html latex example plot.confband.lines text html latex example plot.confband.points text html latex example plot.confband.text text html latex example plot.cor text html latex plot.mat text html latex example plot.mva text html latex example plot.print.tip.lowess text html latex example plot.qq text html latex example plot.qqline text html latex example plot.scale.box text html latex example plot.single.slide text html latex example plot.smooth.line text html latex example plot.spatial text html latex example plot.svb text html latex example plot.t2 text html latex example read.genepix text html latex read.spot text html latex example rgcolors.func text html latex example sma-internal text html latex stat.Chen text html latex example stat.ChurSap text html latex example stat.Newton text html latex example stat.bay.est text html latex example stat.bayesian text html latex example stat.bwss text html latex stat.diag.da text html latex stat.gnames text html latex example stat.ma text html latex example stat.norm.exp text html latex example stat.t2 text html latex example write.spot text html latex example * DONE (sma) [1] "Attempting to download limma from http://www.bioconductor.org//CRANrepository" [1] "Download complete." [1] "Installing limma" * Installing *source* package 'limma' ... ** R ** inst ** preparing package for lazy loading ** help >>> Building/Updating help pages for package 'limma' Formats: text html latex example 1introduction text html latex 2classes text html latex 3reading text html latex 4normalization text html latex 5linearmodels text html latex 6SingleChannel text html latex 7diagnostics text html latex 8Other text html latex LargeDataObject text html latex example PrintLayout text html latex example TestResults text html latex anova-method text html latex asmalist text html latex auROC text html latex example backgroundcorrect text html latex example blockDiag text html latex example bwss text html latex bwss.matrix text html latex cbind text html latex example changelog text html latex channel2M text html latex example classifytests-deprecated text html latex classifytests text html latex example contrasts.fit text html latex example controlStatus text html latex example decideTests text html latex designMatrix-deprecated text html latex dim text html latex example dimnames text html latex dupcor text html latex example ebayes text html latex example exprset2 text html latex fitfdist text html latex fitnormexp text html latex example geneSetTest text html latex example getSpacing text html latex example getlayout text html latex example gls.series text html latex example gridspotrc text html latex heatdiagram text html latex example helpMethods text html latex example imageplot text html latex example imageplot3by2 text html latex intraspotCorrelation text html latex example isfullrank text html latex example isnumeric text html latex example kooperberg text html latex example limmaguideURL text html latex lm.series text html latex example lmFit text html latex lmscFit text html latex example loessfit text html latex example m.spot text html latex m2logliknormexp text html latex ma3x3 text html latex example makeContrasts text html latex example makeunique text html latex example malist text html latex marraylm text html latex matvec text html latex example merge text html latex example modelMatrix text html latex example modifyWeights text html latex example normalizeRobustSpline text html latex example normalizeWithinArrays text html latex example normalizebetweenarrays text html latex example normalizeprintorder text html latex example normalizequantiles text html latex normalizescale text html latex example plotDensities text html latex example plotma text html latex example plotma3by2 text html latex plotprinttiploess text html latex poolvar text html latex example printHead text html latex printorder text html latex example protectMetachar text html latex example qqt text html latex example qualwt text html latex example read.maimages text html latex example read.matrix text html latex read.series text html latex readGPRHeader text html latex readImaGeneHeader text html latex readSpotTypes text html latex readTargets text html latex readgal text html latex example removeext text html latex example rg.genepix text html latex rg.quantarray text html latex rg.series.spot text html latex rg.spot text html latex rglist text html latex rlm.series text html latex example signalnormexp text html latex splitName text html latex example squeezeVar text html latex example subsetting text html latex example summary text html latex targetsA2C text html latex example tmixture text html latex toptable text html latex example trigammainverse text html latex example trimWhiteSpace text html latex example uniquegenelist text html latex example unwrapdups text html latex example venn text html latex example writefit text html latex zscore text html latex example * DONE (limma) [1] "Installation complete" Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download marray from http://www.bioconductor.org/repository/devel/package/Source" [1] "Download complete." [1] "Installing marray" * Installing *source* package 'marray' ... ** R ** data ** inst ** save image [1] TRUE [1] TRUE [1] "marrayInfo" [1] "marrayLayout" [1] "marrayRaw" [1] "marrayNorm" [1] "maLabels" [1] "maLabels" [1] "maInfo" [1] "maInfo" [1] "maNotes" [1] "maNotes" [1] "maNspots" [1] "maNspots" [1] "maNgr" [1] "maNgr" [1] "maNgc" [1] "maNgc" [1] "maNsr" [1] "maNsr" [1] "maNsc" [1] "maNsc" [1] "maSub" [1] "maSub" [1] "maPlate" [1] "maPlate" [1] "maControls" [1] "maControls" [1] "maNotes" [1] "maGridRow" [1] "maGridRow" [1] "maGridCol" [1] "maGridCol" [1] "maSpotRow" [1] "maSpotRow" [1] "maSpotCol" [1] "maSpotCol" [1] "maPrintTip" [1] "maPrintTip" [1] "maRf" [1] "maRf" [1] "maGf" [1] "maGf" [1] "maRb" [1] "maRb" [1] "maGb" [1] "maGb" [1] "maW" [1] "maW" [1] "maLR" [1] "maLR" [1] "maLG" [1] "maLG" [1] "maM" [1] "maM" [1] "maA" [1] "maA" [1] "maLayout" [1] "maLayout" [1] "maNspots" [1] "maNgr" [1] "maNgc" [1] "maNsr" [1] "maNsc" [1] "maGridRow" [1] "maGridCol" [1] "maSpotRow" [1] "maSpotCol" [1] "maPrintTip" [1] "maSub" [1] "maPlate" [1] "maControls" [1] "maNsamples" [1] "maNsamples" [1] "maGnames" [1] "maGnames" [1] "maTargets" [1] "maTargets" [1] "maNotes" [1] "maA" [1] "maM" [1] "maMloc" [1] "maMloc" [1] "maMscale" [1] "maMscale" [1] "maW" [1] "maLR" [1] "maLG" [1] "maLayout" [1] "maNspots" [1] "maNgr" [1] "maNgc" [1] "maNsr" [1] "maNsc" [1] "maGridRow" [1] "maGridCol" [1] "maSpotRow" [1] "maSpotCol" [1] "maPrintTip" [1] "maSub" [1] "maPlate" [1] "maControls" [1] "maNsamples" [1] "maGnames" [1] "maTargets" [1] "maNotes" [1] "maNormCall" [1] "maNormCall" [1] "maLabels<-" [1] "maLabels<-" [1] "maLabels<-" [1] "maInfo<-" [1] "maInfo<-" [1] "maNgr<-" [1] "maNgr<-" [1] "maNgr<-" [1] "maNgr<-" [1] "maNgc<-" [1] "maNgc<-" [1] "maNgc<-" [1] "maNgc<-" [1] "maNsr<-" [1] "maNsr<-" [1] "maNsr<-" [1] "maNsr<-" [1] "maNsc<-" [1] "maNsc<-" [1] "maNsc<-" [1] "maNsc<-" [1] "maNspots<-" [1] "maNspots<-" [1] "maNspots<-" [1] "maNspots<-" [1] "maSub<-" [1] "maSub<-" [1] "maSub<-" [1] "maSub<-" [1] "maSub<-" [1] "maPlate<-" [1] "maPlate<-" [1] "maPlate<-" [1] "maPlate<-" [1] "maControls<-" [1] "maControls<-" [1] "maControls<-" [1] "maControls<-" [1] "maLayout<-" [1] "maLayout<-" [1] "maLayout<-" [1] "maGnames<-" [1] "maGnames<-" [1] "maGnames<-" [1] "maTargets<-" [1] "maTargets<-" [1] "maTargets<-" [1] "maW<-" [1] "maW<-" [1] "maW<-" [1] "maGf<-" [1] "maGf<-" [1] "maRf<-" [1] "maRf<-" [1] "maGb<-" [1] "maGb<-" [1] "maGb<-" [1] "maRb<-" [1] "maRb<-" [1] "maRb<-" [1] "maA<-" [1] "maA<-" [1] "maM<-" [1] "maM<-" [1] "maMloc<-" [1] "maMloc<-" [1] "maMscale<-" [1] "maMscale<-" [1] "maNotes<-" [1] "maNotes<-" [1] "maNotes<-" [1] "maNotes<-" [1] "maNotes<-" [1] "summary" [1] "summary" [1] "summary" [1] "summary" [1] "summary" [1] "ShowLargeObject" [1] "show" [1] "[" [1] "[" [1] "[" [1] "[" [1] "boxplot" [1] "boxplot" [1] "boxplot" [1] "image" [1] "image" [1] "image" [1] "points" [1] "points" [1] "points" [1] "text" [1] "text" [1] "text" [1] "lines" [1] "lines" [1] "lines" ** help >>> Building/Updating help pages for package 'marray' Formats: text html latex example [-methods text html latex boxplot text html latex example cbind text html latex example coerce-methods text html latex dim text html latex example findID text html latex example htmlPage text html latex example image text html latex example ma2D text html latex example maBoxplot text html latex example maColorBar text html latex example maCompCoord text html latex example maCompInd text html latex example maCompLayout text html latex example maCompNormA text html latex example maCompPlate text html latex example maCoord2Ind text html latex example maDefaultPar text html latex example maDotsDefaults text html latex example maDotsMatch text html latex example maGenControls text html latex example maGeneTable text html latex example maImage text html latex example maImage.func text html latex example maInd2Coord text html latex example maLegendLines text html latex example maLoess text html latex example maLoessLines text html latex example maMAD text html latex example maMed text html latex example maNA text html latex maNorm text html latex example maNorm2D text html latex example maNormLoess text html latex example maNormMAD text html latex example maNormMain text html latex example maNormMed text html latex example maNormScale text html latex example maNum2Logic text html latex example maPalette text html latex example maPlot text html latex example maPlot.func text html latex example maSelectGnames text html latex example maText text html latex example maTop text html latex example maTwoSamples text html latex mapGeneInfo text html latex example marray-internal text html latex marrayInfo-class text html latex example marrayLayout-class text html latex example marrayNorm-class text html latex example marrayRaw-class text html latex example opVersionID text html latex example plotMA text html latex example print-methods text html latex read.Galfile text html latex example read.marrayInfo text html latex example read.marrayLayout text html latex example read.marrayRaw text html latex example rm.na text html latex example showLargeObject text html latex example stat.confband.text text html latex example stat.gnames text html latex example swirl text html latex write.list text html latex example write.marray text html latex example write.xls text html latex example Warning in load(zfile, envir = envir) : no input is available * DONE (marray) [1] "Installation complete" [1] "Attempting to download vsn from http://www.bioconductor.org/repository/devel/package/Source" [1] "Download complete." [1] "Installing vsn" * Installing *source* package 'vsn' ... ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c vsn.c -o vsn.o gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o vsn.so vsn.o -lcc_dynamic -framework R ld: warning multiple definitions of symbol _xerbla_ /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_ /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of _xerbla_ ld: warning multiple definitions of symbol _crc32 /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32 /usr/lib/libz.1.dylib(crc32.o) definition of _crc32 ld: warning multiple definitions of symbol _get_crc_table /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table ld: warning multiple definitions of symbol _deflate /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate /usr/lib/libz.1.dylib(deflate.o) definition of _deflate ld: warning multiple definitions of symbol _deflateCopy /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy ld: warning multiple definitions of symbol _deflateReset /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateReset /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset ld: warning multiple definitions of symbol _deflateSetDictionary /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateSetDictionary /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary ld: warning multiple definitions of symbol _deflateInit2_ /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateInit2_ /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_ ld: warning multiple definitions of symbol _deflateEnd /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd ld: warning multiple definitions of symbol _deflateParams /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateParams /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams ld: warning multiple definitions of symbol _deflateInit_ /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateInit_ /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_ ld: warning multiple definitions of symbol _zError /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError /usr/lib/libz.1.dylib(zutil.o) definition of _zError ld: warning multiple definitions of symbol _zlibVersion /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion ld: warning multiple definitions of symbol _inflateEnd /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd ld: warning multiple definitions of symbol _inflateSync /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync ld: warning multiple definitions of symbol _inflateSyncPoint /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSyncPoint /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint ld: warning multiple definitions of symbol _inflate /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate /usr/lib/libz.1.dylib(inflate.o) definition of _inflate ld: warning multiple definitions of symbol _inflateSetDictionary /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSetDictionary /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary ld: warning multiple definitions of symbol _inflateInit2_ /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateInit2_ /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_ ld: warning multiple definitions of symbol _inflateReset /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateReset /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset ld: warning multiple definitions of symbol _inflateInit_ /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateInit_ /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_ ld: warning multiple definitions of symbol _adler32 /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32 /usr/lib/libz.1.dylib(adler32.o) definition of _adler32 ld: warning multiple definitions of symbol _BC /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ libreadline.4.3.dylibterminal.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.dylibterminal.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.dylibterminal.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) >

On Thu, Oct 28, 2004 at 10:33:36AM -0500, Rahul Kakkar wrote: > This posting is regarding 2 problems, but all dealing with trying to > run Bioconductor on MacOS 10.3.x. > Hi, sorry you are having trouble. One problem you seem to be having is that you do not have tcl/tk installed. Many developers use this so you might want to install it. Information is in the R FAQ for OS X (or use the email archive for pointers). capabilities() #in R should tell you. l> capabilities() jpeg png tcltk X11 http/ftp sockets libxml fifo TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE cledit IEEE754 TRUE TRUE Second, there is some chance that you tried to do this just when we updated the repository, and so for that 1 or 2 minutes it is in an inconsistent state. You might try again, for example I use OS X (and the unstable R, but I have no trouble updating these packages). both install.packages2("annotate", develOK=T) install.packages2("genefilter", develOK=T) seem to work for me. Are you sure you are getting R 2.0.0 (as some of these errors could happen if downloading recent versions of these packages into R 1.9.1). Could you please try just one of these two now and see what happens? Robert > I initially tried to download and install Rv2.0.0 / Bioconductor. I > included X11 upgrade during the installation. I used > > source("http://www.bioconductor.org/getBioC.R") > >getBioC("affy", develOK=TRUE) > I installed into my user directory rather than the system dir. > Please see the paste at the end of this email for the output and > numerous errors. In brief, the errors included numerous slot class > errors, inability to locate the library "annotate" in any know > repository (and subsequently unable to execute packages which depend > upon it such as annaffy and geneplotter) and inability to compile > certain packages (genefilter, SparseM, Ruuid). Note that MacOS X > Developer Tools is installed. > > "affy" loaded fine, but ReadAffy gave an error: > > library(affy) > Loading required package: Biobase > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > > data<-ReadAffy(widget=TRUE) > Loading required package: tkWidgets > Loading required package: widgetTools > Loading required package: tcltk > Error in fun(...) : this isn't a Tk applicationcouldn't connect to > display ":0" > Error: .onLoad failed in loadNamespace for 'tcltk' > Error in fun(...) : Package tcltk not able to be loaded! > Error: .onLoad failed in loadNamespace for 'widgetTools' > Error: package 'widgetTools' could not be loaded > > > > "genefilter" could not be loaded of course: > > library(genefilter) > Loading required package: survival > Loading required package: splines > Error in library.dynam(lib, package, package.lib) : > shared library 'genefilter' not found > In addition: Warning message: > Package 'genefilter' contains no R code in: loadNamespace(package, > c(which.lib.loc, lib.loc)) > Error in library(genefilter) : package/namespace load failed for > 'genefilter' > > > > Trying to install genefilter via a different means gave the following: > > install.packages2("genefilter", develOK=TRUE) > Warning message: > Failed to read repdatadesc at > http://www.bioconductor.org/repository/devel/package in: > loadRepDD(repURL, rddFile, method = method) > Error in repURL(replisting(object), pos) : > subscript out of bounds > > > > Given the numerous errors, I completely uninstalled Rv2 and tried > Rv1.9.1 / Biocondcutor. Downloaded and installed as per some very > helpful previous posts > (http://files.protsuggest.org/biocond/html/3612.html). This included > installing Bioconductor packages via the "Affy bundle" script under the > "Packages" menu in R as well as installing MacOS X developer tools . > > Came across an issue with the function ReadAffy(widget=TRUE): > > > data<-ReadAffy(widget=TRUE) > Error in fileBrowser(textToShow = "Choose CEL files", testFun = > hasSuffix("[cC][eE][lL]")) : > couldn't find function "tktoplevel" > Error in end() : couldn't find function "tkgrab.release" > > data<-ReadAffy(widget=TRUE) > Error in fileBrowser(textToShow = "Choose CEL files", testFun = > hasSuffix("[cC][eE][lL]")) : > couldn't find function "tktoplevel" > Error in end() : couldn't find function "tkgrab.release" > > > > Note widgetTools (1.4.2) and tkWidgets (1.5.10) are installed. I > suspect this has something to do with X Windows, but I'm not > knowledgeable enough to figure this one out. I did install the X11 > app, but Im not sure how to use it to run the widget function if this > is indeed the issue. > > I would appreciate any assistance in getting R / Bioconductor, either > version, to work on my macintosh. > > Obliged, > > -Rahul > > > > Rahul Kakkar M.D. > Post-Doctoral Fellow > > Elizabeth M. McNally Laboratory > Department of Medicine > University of Chicago Hospitals > MC 6088 > 5841 S. Maryland Avenue > Chicago, IL 60637 > > P: (773) 702-2684 F: (773) 702-2681 E: rkakkar@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@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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.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.dylibterminal.so) definition of _PC > /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC > ** R > ** data > ** inst > ** save image > [1] TRUE > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > Loading required package: reposTools > [1] TRUE > [1] TRUE > [1] "Cdf" > [1] "name.levels" > [1] "name.levels" > [1] "name.levels<-" > [1] "name.levels<-" > [1] "pbase" > [1] "pbase" > [1] "pbase<-" > [1] "pbase<-" > [1] "pbase.levels" > [1] "pbase.levels" > [1] "pbase.levels<-" > [1] "pbase.levels<-" > [1] "tbase" > [1] "tbase" > [1] "tbase<-" > [1] "tbase<-" > [1] "tbase.levels" > [1] "tbase.levels" > [1] "tbase.levels<-" > [1] "tbase.levels<-" > [1] "show" > > ** help > >>> Building/Updating help pages for package 'makecdfenv' > Formats: text html latex example > Cdf-class text html latex > getInfoInAffyFile text html latex > make.cdf.env text html latex example > make.cdf.package text html latex example > pmormm text html latex > read.cdffile text html latex example > * DONE (makecdfenv) > [1] "Installation complete" > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: Package XML not found in any known repository. > Note: Package annotate not found in any known repository. > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download Ruuid from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing Ruuid" > * Installing *source* package 'Ruuid' ... > creating cache ./config.cache > checking for glib-config... no > checking how to run the C preprocessor... cc -E > checking for /usr/include/unistd.h... yes > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include > -fno-common -g -O2 -c Rinit.c -o Rinit.o > In file included from Ruuid.h:5, > from Rinit.c:1: > uuidP.h:24:18: glib.h: No such file or directory > In file included from Ruuid.h:5, > from Rinit.c:1: > uuidP.h:36: error: parse error before "guint32" > uuidP.h:36: warning: no semicolon at end of struct or union > uuidP.h:37: warning: data definition has no type or storage class > uuidP.h:38: error: parse error before "time_hi_and_version" > uuidP.h:38: warning: data definition has no type or storage class > uuidP.h:39: error: parse error before "clock_seq" > uuidP.h:39: warning: data definition has no type or storage class > uuidP.h:40: error: parse error before "node" > uuidP.h:40: warning: data definition has no type or storage class > uuidP.h:41: error: parse error before '}' token > make: *** [Rinit.o] Error 1 > ERROR: compilation failed for package 'Ruuid' > Note: Package Ruuid not found in any known repository. > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download SparseM from > http://www.bioconductor.org//CRANrepository" > [1] "Download complete." > [1] "Installing SparseM" > * Installing *source* package 'SparseM' ... > ** libs > g77 -fno-common -g -O2 -c bckslv.f -o bckslv.o > make: g77: Command not found > make: *** [bckslv.o] Error 127 > ERROR: compilation failed for package 'SparseM' > Note: Package SparseM not found in any known repository. > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: Package XML not found in any known repository. > Note: Package graph not found in any known repository. > Note: Package Rgraphviz not found in any known repository. > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download fibroEset from > http://www.bioconductor.org/data/experimental/repos/" > [1] "Download complete." > [1] "Installing fibroEset" > * Installing *source* package 'fibroEset' ... > ** R > ** data > ** help > >>> Building/Updating help pages for package 'fibroEset' > Formats: text html latex example > fibroEset text html latex example > * DONE (fibroEset) > [1] "Installation complete" > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download hu6800 from > http://www.bioconductor.org/data/metaData-devel/" > [1] "Download complete." > [1] "Installing hu6800" > * Installing *source* package 'hu6800' ... > ** R > ** data > ** preparing package for lazy loading > > ** help > >>> Building/Updating help pages for package 'hu6800' > Formats: text html latex example > hu6800 text html latex > hu6800ACCNUM text html latex example > hu6800CHR text html latex example > hu6800CHRLENGTHS text html latex example > hu6800CHRLOC text html latex example > hu6800ENZYME text html latex example > hu6800ENZYME2PROBE text html latex example > hu6800GENENAME text html latex example > hu6800GO text html latex example > hu6800GO2ALLPROBES text html latex example > hu6800GO2PROBE text html latex example > hu6800GRIF text html latex example > hu6800LOCUSID text html latex example > hu6800MAP text html latex example > hu6800OMIM text html latex example > hu6800ORGANISM text html latex example > hu6800PATH text html latex example > hu6800PATH2PROBE text html latex example > hu6800PMID text html latex example > hu6800PMID2PROBE text html latex example > hu6800QC text html latex > hu6800REFSEQ text html latex example > hu6800SUMFUNC text html latex example > hu6800SYMBOL text html latex example > hu6800UNIGENE text html latex example > * DONE (hu6800) > [1] "Installation complete" > [1] "Attempting to download geneplotter from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing geneplotter" > * Installing *source* package 'geneplotter' ... > ** R > ** data > ** inst > ** save image > [1] TRUE > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > [1] TRUE > Loading required package: annotate > Error: geneplotter requires annotate > In addition: Warning message: > There is no package called 'annotate' in: library(package, > character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, > Execution halted > /Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1: 7714 > Broken pipe cat > "/Users/rkakkar/Library/R/library/geneplotter/R/geneplotter" > ERROR: execution of package source for 'geneplotter' failed > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download golubEsets from > http://www.bioconductor.org/data/experimental/repos/" > [1] "Download complete." > [1] "Installing golubEsets" > * Installing *source* package 'golubEsets' ... > ** R > ** data > ** help > >>> Building/Updating help pages for package 'golubEsets' > Formats: text html latex example > golubMerge text html latex example > golubTest text html latex example > golubTrain text html latex example > [1] "Installation complete" > * DONE (golubEsets) > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download xtable from > http://www.bioconductor.org//CRANrepository" > [1] "Download complete." > [1] "Installing xtable" > * Installing *source* package 'xtable' ... > ** R > ** data > ** help > >>> Building/Updating help pages for package 'xtable' > Formats: text html latex example > print.xtable text html latex > string text html latex > table.attributes text html latex > tli text html latex > xtable text html latex example > * DONE (xtable) > [1] "Installation complete" > [1] "Attempting to download edd from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing edd" > * Installing *source* package 'edd' ... > ** R > ** inst > ** save image > [1] TRUE > Loading required package: golubEsets > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > Loading required package: Biobase > Loading required package: class > Loading required package: nnet > Loading required package: xtable > [1] "eddDist" > [1] "stub" > [1] "stub" > [1] "plotlim" > [1] "plotlim" > [1] "tag" > [1] "tag" > [1] "latexTag" > [1] "latexTag" > [1] "parms" > [1] "parms" > [1] "med" > [1] "med" > [1] "Mad" > [1] "Mad" > [1] "CDFname" > [1] "CDFname" > [1] "qfName" > [1] "qfName" > [1] "qfun" > [1] "qfun" > [1] "genName" > [1][1] "Installation complete" > "genName" > [1] "testVec" > [1] "testVec" > > ** help > >>> Building/Updating help pages for package 'edd' > Formats: text html latex example > centerScale text html latex example > edd text html latex example > eddDist-class text html latex example > eddObsolete text html latex example > flatQQNorm text html latex example > latEDtable text html latex example > makeCandmat.raw text html latex example > maxKSp text html latex example > plotED text html latex example > * DONE (edd) > [1] "Attempting to download ROC from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing ROC" > * Installing *source* package 'ROC' ... > ** R > ** inst > ** save image > [1] TRUE > [1] TRUE > [1] "rocc" > [1] "plot" > [1] "plot" > > ** help > >>> Building/Updating help pages for package 'ROC' > Formats: text html latex example > AUC text html latex example > plot-methods text html latex example > rocc-class text html latex example > rocdemo.sca text html latex example > trapezint text html latex example > [1] "Installation complete" > * DONE (ROC) > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download statmod from > http://www.bioconductor.org//CRANrepository" > [1] "Download complete." > [1] "Installing statmod" > * Installing *source* package 'statmod' ... > ** R > ** data > ** preparing package for lazy loading > > ** help > >>> Building/Updating help pages for package 'statmod' > Formats: text html latex example > 1Introduction text html latex > digammaf text html latex example > gauss.quad text html latex example > gauss.quad.prob text html latex example > glmgam text html latex example > growthcurve text html latex example > hommel.test text html latex example > invgauss text html latex example > logmdigamma text html latex example > matvec text html latex example > meanT text html latex example > power text html latex example > qresiduals text html latex example > ranblock text html latex example > remlscor text html latex example > remlscorgamma text html latex example > sage.test text html latex example > tweedie text html latex example > welding text html latex > * DONE (statmod) > [1] "Installation complete" > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download sma from > http://www.bioconductor.org//CRANrepository" > [1] "Download complete." > [1] "Installing sma" > * Installing *source* package 'sma' ... > ** R > ** data > [1] "Installation complete" > ** preparing package for lazy loading > > ** help > >>> Building/Updating help pages for package 'sma' > Formats: text html latex example > MouseArray text html latex > id2image text html latex example > init.addinfo text html latex example > init.ctl.index text html latex example > init.data text html latex example > init.grid text html latex example > init.names text html latex example > init.read.exp text html latex example > is.odd text html latex example > na text html latex > plot.bayesian text html latex example > plot.confband.lines text html latex example > plot.confband.points text html latex example > plot.confband.text text html latex example > plot.cor text html latex > plot.mat text html latex example > plot.mva text html latex example > plot.print.tip.lowess text html latex example > plot.qq text html latex example > plot.qqline text html latex example > plot.scale.box text html latex example > plot.single.slide text html latex example > plot.smooth.line text html latex example > plot.spatial text html latex example > plot.svb text html latex example > plot.t2 text html latex example > read.genepix text html latex > read.spot text html latex example > rgcolors.func text html latex example > sma-internal text html latex > stat.Chen text html latex example > stat.ChurSap text html latex example > stat.Newton text html latex example > stat.bay.est text html latex example > stat.bayesian text html latex example > stat.bwss text html latex > stat.diag.da text html latex > stat.gnames text html latex example > stat.ma text html latex example > stat.norm.exp text html latex example > stat.t2 text html latex example > write.spot text html latex example > * DONE (sma) > [1] "Attempting to download limma from > http://www.bioconductor.org//CRANrepository" > [1] "Download complete." > [1] "Installing limma" > * Installing *source* package 'limma' ... > ** R > ** inst > ** preparing package for lazy loading > > ** help > >>> Building/Updating help pages for package 'limma' > Formats: text html latex example > 1introduction text html latex > 2classes text html latex > 3reading text html latex > 4normalization text html latex > 5linearmodels text html latex > 6SingleChannel text html latex > 7diagnostics text html latex > 8Other text html latex > LargeDataObject text html latex example > PrintLayout text html latex example > TestResults text html latex > anova-method text html latex > asmalist text html latex > auROC text html latex example > backgroundcorrect text html latex example > blockDiag text html latex example > bwss text html latex > bwss.matrix text html latex > cbind text html latex example > changelog text html latex > channel2M text html latex example > classifytests-deprecated text html latex > classifytests text html latex example > contrasts.fit text html latex example > controlStatus text html latex example > decideTests text html latex > designMatrix-deprecated text html latex > dim text html latex example > dimnames text html latex > dupcor text html latex example > ebayes text html latex example > exprset2 text html latex > fitfdist text html latex > fitnormexp text html latex example > geneSetTest text html latex example > getSpacing text html latex example > getlayout text html latex example > gls.series text html latex example > gridspotrc text html latex > heatdiagram text html latex example > helpMethods text html latex example > imageplot text html latex example > imageplot3by2 text html latex > intraspotCorrelation text html latex example > isfullrank text html latex example > isnumeric text html latex example > kooperberg text html latex example > limmaguideURL text html latex > lm.series text html latex example > lmFit text html latex > lmscFit text html latex example > loessfit text html latex example > m.spot text html latex > m2logliknormexp text html latex > ma3x3 text html latex example > makeContrasts text html latex example > makeunique text html latex example > malist text html latex > marraylm text html latex > matvec text html latex example > merge text html latex example > modelMatrix text html latex example > modifyWeights text html latex example > normalizeRobustSpline text html latex example > normalizeWithinArrays text html latex example > normalizebetweenarrays text html latex example > normalizeprintorder text html latex example > normalizequantiles text html latex > normalizescale text html latex example > plotDensities text html latex example > plotma text html latex example > plotma3by2 text html latex > plotprinttiploess text html latex > poolvar text html latex example > printHead text html latex > printorder text html latex example > protectMetachar text html latex example > qqt text html latex example > qualwt text html latex example > read.maimages text html latex example > read.matrix text html latex > read.series text html latex > readGPRHeader text html latex > readImaGeneHeader text html latex > readSpotTypes text html latex > readTargets text html latex > readgal text html latex example > removeext text html latex example > rg.genepix text html latex > rg.quantarray text html latex > rg.series.spot text html latex > rg.spot text html latex > rglist text html latex > rlm.series text html latex example > signalnormexp text html latex > splitName text html latex example > squeezeVar text html latex example > subsetting text html latex example > summary text html latex > targetsA2C text html latex example > tmixture text html latex > toptable text html latex example > trigammainverse text html latex example > trimWhiteSpace text html latex example > uniquegenelist text html latex example > unwrapdups text html latex example > venn text html latex example > writefit text html latex > zscore text html latex example > * DONE (limma) > [1] "Installation complete" > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > [1] "Attempting to download marray from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing marray" > * Installing *source* package 'marray' ... > ** R > ** data > ** inst > ** save image > [1] TRUE > [1] TRUE > [1] "marrayInfo" > [1] "marrayLayout" > [1] "marrayRaw" > [1] "marrayNorm" > [1] "maLabels" > [1] "maLabels" > [1] "maInfo" > [1] "maInfo" > [1] "maNotes" > [1] "maNotes" > [1] "maNspots" > [1] "maNspots" > [1] "maNgr" > [1] "maNgr" > [1] "maNgc" > [1] "maNgc" > [1] "maNsr" > [1] "maNsr" > [1] "maNsc" > [1] "maNsc" > [1] "maSub" > [1] "maSub" > [1] "maPlate" > [1] "maPlate" > [1] "maControls" > [1] "maControls" > [1] "maNotes" > [1] "maGridRow" > [1] "maGridRow" > [1] "maGridCol" > [1] "maGridCol" > [1] "maSpotRow" > [1] "maSpotRow" > [1] "maSpotCol" > [1] "maSpotCol" > [1] "maPrintTip" > [1] "maPrintTip" > [1] "maRf" > [1] "maRf" > [1] "maGf" > [1] "maGf" > [1] "maRb" > [1] "maRb" > [1] "maGb" > [1] "maGb" > [1] "maW" > [1] "maW" > [1] "maLR" > [1] "maLR" > [1] "maLG" > [1] "maLG" > [1] "maM" > [1] "maM" > [1] "maA" > [1] "maA" > [1] "maLayout" > [1] "maLayout" > [1] "maNspots" > [1] "maNgr" > [1] "maNgc" > [1] "maNsr" > [1] "maNsc" > [1] "maGridRow" > [1] "maGridCol" > [1] "maSpotRow" > [1] "maSpotCol" > [1] "maPrintTip" > [1] "maSub" > [1] "maPlate" > [1] "maControls" > [1] "maNsamples" > [1] "maNsamples" > [1] "maGnames" > [1] "maGnames" > [1] "maTargets" > [1] "maTargets" > [1] "maNotes" > [1] "maA" > [1] "maM" > [1] "maMloc" > [1] "maMloc" > [1] "maMscale" > [1] "maMscale" > [1] "maW" > [1] "maLR" > [1] "maLG" > [1] "maLayout" > [1] "maNspots" > [1] "maNgr" > [1] "maNgc" > [1] "maNsr" > [1] "maNsc" > [1] "maGridRow" > [1] "maGridCol" > [1] "maSpotRow" > [1] "maSpotCol" > [1] "maPrintTip" > [1] "maSub" > [1] "maPlate" > [1] "maControls" > [1] "maNsamples" > [1] "maGnames" > [1] "maTargets" > [1] "maNotes" > [1] "maNormCall" > [1] "maNormCall" > [1] "maLabels<-" > [1] "maLabels<-" > [1] "maLabels<-" > [1] "maInfo<-" > [1] "maInfo<-" > [1] "maNgr<-" > [1] "maNgr<-" > [1] "maNgr<-" > [1] "maNgr<-" > [1] "maNgc<-" > [1] "maNgc<-" > [1] "maNgc<-" > [1] "maNgc<-" > [1] "maNsr<-" > [1] "maNsr<-" > [1] "maNsr<-" > [1] "maNsr<-" > [1] "maNsc<-" > [1] "maNsc<-" > [1] "maNsc<-" > [1] "maNsc<-" > [1] "maNspots<-" > [1] "maNspots<-" > [1] "maNspots<-" > [1] "maNspots<-" > [1] "maSub<-" > [1] "maSub<-" > [1] "maSub<-" > [1] "maSub<-" > [1] "maSub<-" > [1] "maPlate<-" > [1] "maPlate<-" > [1] "maPlate<-" > [1] "maPlate<-" > [1] "maControls<-" > [1] "maControls<-" > [1] "maControls<-" > [1] "maControls<-" > [1] "maLayout<-" > [1] "maLayout<-" > [1] "maLayout<-" > [1] "maGnames<-" > [1] "maGnames<-" > [1] "maGnames<-" > [1] "maTargets<-" > [1] "maTargets<-" > [1] "maTargets<-" > [1] "maW<-" > [1] "maW<-" > [1] "maW<-" > [1] "maGf<-" > [1] "maGf<-" > [1] "maRf<-" > [1] "maRf<-" > [1] "maGb<-" > [1] "maGb<-" > [1] "maGb<-" > [1] "maRb<-" > [1] "maRb<-" > [1] "maRb<-" > [1] "maA<-" > [1] "maA<-" > [1] "maM<-" > [1] "maM<-" > [1] "maMloc<-" > [1] "maMloc<-" > [1] "maMscale<-" > [1] "maMscale<-" > [1] "maNotes<-" > [1] "maNotes<-" > [1] "maNotes<-" > [1] "maNotes<-" > [1] "maNotes<-" > [1] "summary" > [1] "summary" > [1] "summary" > [1] "summary" > [1] "summary" > [1] "ShowLargeObject" > [1] "show" > [1] "[" > [1] "[" > [1] "[" > [1] "[" > [1] "boxplot" > [1] "boxplot" > [1] "boxplot" > [1] "image" > [1] "image" > [1] "image" > [1] "points" > [1] "points" > [1] "points" > [1] "text" > [1] "text" > [1] "text" > [1] "lines" > [1] "lines" > [1] "lines" > > ** help > >>> Building/Updating help pages for package 'marray' > Formats: text html latex example > [-methods text html latex > boxplot text html latex example > cbind text html latex example > coerce-methods text html latex > dim text html latex example > findID text html latex example > htmlPage text html latex example > image text html latex example > ma2D text html latex example > maBoxplot text html latex example > maColorBar text html latex example > maCompCoord text html latex example > maCompInd text html latex example > maCompLayout text html latex example > maCompNormA text html latex example > maCompPlate text html latex example > maCoord2Ind text html latex example > maDefaultPar text html latex example > maDotsDefaults text html latex example > maDotsMatch text html latex example > maGenControls text html latex example > maGeneTable text html latex example > maImage text html latex example > maImage.func text html latex example > maInd2Coord text html latex example > maLegendLines text html latex example > maLoess text html latex example > maLoessLines text html latex example > maMAD text html latex example > maMed text html latex example > maNA text html latex > maNorm text html latex example > maNorm2D text html latex example > maNormLoess text html latex example > maNormMAD text html latex example > maNormMain text html latex example > maNormMed text html latex example > maNormScale text html latex example > maNum2Logic text html latex example > maPalette text html latex example > maPlot text html latex example > maPlot.func text html latex example > maSelectGnames text html latex example > maText text html latex example > maTop text html latex example > maTwoSamples text html latex > mapGeneInfo text html latex example > marray-internal text html latex > marrayInfo-class text html latex example > marrayLayout-class text html latex example > marrayNorm-class text html latex example > marrayRaw-class text html latex example > opVersionID text html latex example > plotMA text html latex example > print-methods text html latex > read.Galfile text html latex example > read.marrayInfo text html latex example > read.marrayLayout text html latex example > read.marrayRaw text html latex example > rm.na text html latex example > showLargeObject text html latex example > stat.confband.text text html latex example > stat.gnames text html latex example > swirl text html latex > write.list text html latex example > write.marray text html latex example > write.xls text html latex example > Warning in load(zfile, envir = envir) : no input is available > * DONE (marray) > [1] "Installation complete" > [1] "Attempting to download vsn from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing vsn" > * Installing *source* package 'vsn' ... > ** libs > gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/usr/local/include -fno-common -g -O2 -c vsn.c -o vsn.o > gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o > vsn.so vsn.o -lcc_dynamic -framework R > ld: warning multiple definitions of symbol _xerbla_ > /Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_ > /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ > vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of > _xerbla_ > ld: warning multiple definitions of symbol _crc32 > /Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32 > /usr/lib/libz.1.dylib(crc32.o) definition of _crc32 > ld: warning multiple definitions of symbol _get_crc_table > /Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table > /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table > ld: warning multiple definitions of symbol _deflate > /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate > /usr/lib/libz.1.dylib(deflate.o) definition of _deflate > ld: warning multiple definitions of symbol _deflateCopy > /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy > ld: warning multiple definitions of symbol _deflateReset > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateReset > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset > ld: warning multiple definitions of symbol _deflateSetDictionary > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateSetDictionary > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary > ld: warning multiple definitions of symbol _deflateInit2_ > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateInit2_ > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_ > ld: warning multiple definitions of symbol _deflateEnd > /Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd > ld: warning multiple definitions of symbol _deflateParams > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateParams > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams > ld: warning multiple definitions of symbol _deflateInit_ > /Library/Frameworks/R.framework/R(deflate.lo) definition of > _deflateInit_ > /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_ > ld: warning multiple definitions of symbol _zError > /Library/Frameworks/R.framework/R(zutil.lo) definition of _zError > /usr/lib/libz.1.dylib(zutil.o) definition of _zError > ld: warning multiple definitions of symbol _zlibVersion > /Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion > /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion > ld: warning multiple definitions of symbol _inflateEnd > /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd > ld: warning multiple definitions of symbol _inflateSync > /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync > ld: warning multiple definitions of symbol _inflateSyncPoint > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateSyncPoint > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint > ld: warning multiple definitions of symbol _inflate > /Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate > /usr/lib/libz.1.dylib(inflate.o) definition of _inflate > ld: warning multiple definitions of symbol _inflateSetDictionary > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateSetDictionary > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary > ld: warning multiple definitions of symbol _inflateInit2_ > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateInit2_ > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_ > ld: warning multiple definitions of symbol _inflateReset > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateReset > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset > ld: warning multiple definitions of symbol _inflateInit_ > /Library/Frameworks/R.framework/R(inflate.lo) definition of > _inflateInit_ > /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_ > ld: warning multiple definitions of symbol _adler32 > /Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32 > /usr/lib/libz.1.dylib(adler32.o) definition of _adler32 > ld: warning multiple definitions of symbol _BC > /Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/ > libreadline.4.3.dylibterminal.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.dylibterminal.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.dylibterminal.so) definition of _PC > /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC > ld: warning multiple definitions of symbol _gzeof > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof > /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof > ld: warning multiple definitions of symbol _gzclose > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose > /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose > ld: warning multiple definitions of symbol _gzdopen > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen > /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen > ld: warning multiple definitions of symbol _gzerror > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror > /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror > ld: warning multiple definitions of symbol _gzflush > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush > /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush > ld: warning multiple definitions of symbol _gzgetc > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc > /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc > ld: warning multiple definitions of symbol _gzgets > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets > /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets > ld: warning multiple definitions of symbol _gzopen > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen > /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen > ld: warning multiple definitions of symbol _gzprintf > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf > /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf > ld: warning multiple definitions of symbol _gzputc > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc > /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc > ld: warning multiple definitions of symbol _gzputs > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs > /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs > ld: warning multiple definitions of symbol _gzread > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread > /usr/lib/libz.1.dylib(gzio.o) definition of _gzread > ld: warning multiple definitions of symbol _gzrewind > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind > /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind > ld: warning multiple definitions of symbol _gzseek > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek > /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek > ld: warning multiple definitions of symbol _gzsetparams > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams > /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams > ld: warning multiple definitions of symbol _gztell > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell > /usr/lib/libz.1.dylib(gzio.o) definition of _gztell > ld: warning multiple definitions of symbol _gzwrite > /Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite > /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite > ** R > ** data > ** inst > ** save image > Loading required package: Biobase > Loading required package: tools > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > > ** help > >>> Building/Updating help pages for package 'vsn' > Formats: text html latex example > getIntensityMatrix text html latex example > kidney text html latex example > log.na text html latex example > lymphoma text html latex example > meanSdPlot text html latex example > nchoosek text html latex example > normalize.AffyBatch.vsn text html latex example > rowSds text html latex example > sagmbSimulateData text html latex example > sqr text html latex example > vsn text html latex example > vsnPlotPar text html latex example > vsnh text html latex example > * DONE (vsn) > [1] "Installation complete" > [1] "Attempting to download globaltest from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing globaltest" > * Installing *source* package 'globaltest' ... > ** R > ** data > ** inst > ** preparing package for lazy loading > Creating a new generic function for "names" in "globaltest" > Creating a new generic function for "names<-" in "globaltest" > Creating a new generic function for "scale" in "globaltest" > Creating a new generic function for "plot" in "globaltest" > > ** help > >>> Building/Updating help pages for package 'globaltest' > Formats: text html latex example > checkerboard text html latex example > exampleX text html latex > exampleY text html latex > geneplot text html latex example > globaltest text html latex example > gt.barplot-class text html latex > gt.result-class text html latex > permutations text html latex example > regressionplot text html latex example > sampleplot text html latex example > sampling text html latex example > * DONE (globaltest) > [1] "Installation complete" > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: Package SJava not found in any known repository. > [1] "Attempting to download RMAGEML from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing RMAGEML" > > gzip: /tmp/Rtmp553/RMAGEML_2.1.0.tar.gz: not in gzip format > ERROR: cannot extract package from '/tmp/Rtmp553/RMAGEML_2.1.0.tar.gz' > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: You did not specify a download type. Using a default value of: > Source > This will be fine for almost all users > > Note: Package XML not found in any known repository. > Note: Package annotate not found in any known repository. > [1] "Attempting to download siggenes from > http://www.bioconductor.org/repository/devel/package/Source" > [1] "Download complete." > [1] "Installing siggenes" > > gzip: /tmp/Rtmp553/siggenes_1.2.10.tar.gz: not in gzip format > ERROR: cannot extract package from '/tmp/Rtmp553/siggenes_1.2.10.tar.gz' > [1] "Attempting to download pamr from > http://www.bioconductor.org//CRANrepository" > [1] "Download complete." > [1] "Installing pamr" > * Installing *source* package 'pamr' ... > ** libs > gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include > -I/usr/local/include -fno-common -g -O2 -c cox_func.c -o cox_func.o > g77 -fno-common -g -O2 -c knnimpute.f -o knnimpute.o > make: g77: Command not found > make: *** [knnimpute.o] Error 127 > ERROR: compilation failed for package 'pamr' > From URL: http://www.bioconductor.org/repository/devel/package/Source > widgetTools version 1.4.7 > DynDoc version 1.4.1 > tkWidgets version 1.5.19 > Biobase version 1.4.22 > affydata version 1.4.0 > affy version 1.5.8 > affyPLM version 1.2.2 > genefilter version 1.4.5 > Biostrings version 1.0.0 > matchprobes version 1.0.12 > multtest version 1.5.2 > annaffy version 1.0.11 > gcrma version 1.1.1 > makecdfenv version 1.4.8 > Ruuid version 1.4.5 > geneplotter version 1.4.2 > edd version 1.4.2 > ROC version 1.0.12 > marray version 1.5.21 > vsn version 1.5.0 > globaltest version 3.0.1 > RMAGEML version 2.1.0 > siggenes version 1.2.10 > > From URL: http://www.bioconductor.org/data/cdfenvs/repos/ > hgu95av2cdf version 1.4.3 > hgu133acdf version 1.4.3 > hu6800cdf version 1.4.3 > > From URL: http://www.bioconductor.org/data/metaData-devel/ > GO version 1.6.5 > KEGG version 1.6.5 > hgu95av2 version 1.6.5 > rae230a version 1.6.5 > hu6800 version 1.6.5 > > From URL: http://www.bioconductor.org/data/probes/Packages/ > hgu95av2probe version 1.0 > hu6800probe version 1.0 > rae230aprobe version 1.0 > > From URL: http://www.bioconductor.org//CRANrepository > SparseM version 0.52 > xtable version 1.2-4 > statmod version 1.1.0 > sma version 0.5.14 > limma version 1.8.1 > pamr version 1.22 > > From URL: http://www.bioconductor.org/data/experimental/repos/ > fibroEset version 1.0 > golubEsets version 1.0 > > Packages that were not updated: > annotate > graph > Rgraphviz > > There were 13 warnings (use warnings() to see them) > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+