[BioC] Rv1.91 or v2.0.0 on MacOS 10.3.5
Rahul Kakkar
rkakkar at uchicago.edu
Thu Oct 28 17:33:36 CEST 2004
This posting is regarding 2 problems, but all dealing with trying to
run Bioconductor on MacOS 10.3.x.
I initially tried to download and install Rv2.0.0 / Bioconductor. I
included X11 upgrade during the installation. I used
> source("http://www.bioconductor.org/getBioC.R")
>getBioC("affy", develOK=TRUE)
I installed into my user directory rather than the system dir.
Please see the paste at the end of this email for the output and
numerous errors. In brief, the errors included numerous slot class
errors, inability to locate the library "annotate" in any know
repository (and subsequently unable to execute packages which depend
upon it such as annaffy and geneplotter) and inability to compile
certain packages (genefilter, SparseM, Ruuid). Note that MacOS X
Developer Tools is installed.
"affy" loaded fine, but ReadAffy gave an error:
> library(affy)
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
> data<-ReadAffy(widget=TRUE)
Loading required package: tkWidgets
Loading required package: widgetTools
Loading required package: tcltk
Error in fun(...) : this isn't a Tk applicationcouldn't connect to
display ":0"
Error: .onLoad failed in loadNamespace for 'tcltk'
Error in fun(...) : Package tcltk not able to be loaded!
Error: .onLoad failed in loadNamespace for 'widgetTools'
Error: package 'widgetTools' could not be loaded
>
"genefilter" could not be loaded of course:
> library(genefilter)
Loading required package: survival
Loading required package: splines
Error in library.dynam(lib, package, package.lib) :
shared library 'genefilter' not found
In addition: Warning message:
Package 'genefilter' contains no R code in: loadNamespace(package,
c(which.lib.loc, lib.loc))
Error in library(genefilter) : package/namespace load failed for
'genefilter'
>
Trying to install genefilter via a different means gave the following:
> install.packages2("genefilter", develOK=TRUE)
Warning message:
Failed to read repdatadesc at
http://www.bioconductor.org/repository/devel/package in:
loadRepDD(repURL, rddFile, method = method)
Error in repURL(replisting(object), pos) :
subscript out of bounds
>
Given the numerous errors, I completely uninstalled Rv2 and tried
Rv1.9.1 / Biocondcutor. Downloaded and installed as per some very
helpful previous posts
(http://files.protsuggest.org/biocond/html/3612.html). This included
installing Bioconductor packages via the "Affy bundle" script under the
"Packages" menu in R as well as installing MacOS X developer tools .
Came across an issue with the function ReadAffy(widget=TRUE):
> data<-ReadAffy(widget=TRUE)
Error in fileBrowser(textToShow = "Choose CEL files", testFun =
hasSuffix("[cC][eE][lL]")) :
couldn't find function "tktoplevel"
Error in end() : couldn't find function "tkgrab.release"
> data<-ReadAffy(widget=TRUE)
Error in fileBrowser(textToShow = "Choose CEL files", testFun =
hasSuffix("[cC][eE][lL]")) :
couldn't find function "tktoplevel"
Error in end() : couldn't find function "tkgrab.release"
>
Note widgetTools (1.4.2) and tkWidgets (1.5.10) are installed. I
suspect this has something to do with X Windows, but I'm not
knowledgeable enough to figure this one out. I did install the X11
app, but Im not sure how to use it to run the widget function if this
is indeed the issue.
I would appreciate any assistance in getting R / Bioconductor, either
version, to work on my macintosh.
Obliged,
-Rahul
Rahul Kakkar M.D.
Post-Doctoral Fellow
Elizabeth M. McNally Laboratory
Department of Medicine
University of Chicago Hospitals
MC 6088
5841 S. Maryland Avenue
Chicago, IL 60637
P: (773) 702-2684 F: (773) 702-2681 E: rkakkar at uchicago.edu
OUTPUT FROM >getBioC("affy", develOK=TRUE) COMMAND IN Rv2.0.0:
R : Copyright 2004, The R Foundation for Statistical Computing
Version 2.0.0 (2004-10-04), ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.
> source("http://www.bioconductor.org/getBioC.R")
> getBioC("affy", develOK=TRUE)
Running getBioC version 1.2.66....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R
Please direct any concerns or questions to
bioconductor at stat.math.ethz.ch.
Please select an installation directory:
1:/Users/rkakkar/Library/R/library
2:/Library/Frameworks/R.framework/Resources/library
Selection: 1
[1] "Installing reposTools ..."
* Installing *source* package 'reposTools' ...
** R
** data
** inst
** save image
[1] TRUE
Loading required package: tools
[1] "replisting"
[1] "replisting"
[1] "repURL"
Creating a new generic function for "summary" in "reposTools"
[1] "summary"
[1] "repReleaseLevel"
[1] "repReleaseLevel"
[1] "show"
[1] "replisting"
[1] "repURL"
[1] "numSubReps"
[1] "numSubReps"
[1] "repdatadesc"
[1] "repdatadesc"
[1] "repdatadesc"
[1] "summary"
[1] "depends"
[1] "depends"
[1] "suggests"
[1] "suggests"
[1] "imports"
[1] "imports"
[1] "keywords"
[1] "keywords"
[1] "show"
[1] "ReposList"
[1] "repList"
[1] "repList"
[1] "repList<-"
[1] "repList<-"
[1] "numReps"
[1] "numReps"
[1] "getRepEntry"
[1] "getRepEntry"
[1] "repPkgs"
[1] "repPkgs"
[1] "repPkgInfoList"
[1] "repPkgInfoList"
[1] "repNames"
[1] "repNames"
[1] "repURLs"
[1] "repURLs"
[1] "show"
[1] "ReposEntry"
[1] "repType"
[1] "repName"
[1] "reposThemes"
[1] "reposThemes"
[1] "repType"
[1] "replisting"
[1] "repdatadesc"
[1] "repName"
[1] "repURL"
[1] "repdataframe"
[1] "repdataframe"
[1] "numSubReps"
[1] "getSubRep"
[1] "getSubRep"
[1] "getSubRepList"
[1] "getSubRepList"
[1] "depends"
[1] "suggests"
[1] "imports"
[1] "keywords"
[1] "hasFiles"
[1] "hasFiles"
[1] "pkgRVersion"
[1] "pkgRVersion"
[1] "repPkgs"
[1] "repObjects"
[1] "repObjects"
[1] "repPkgInfos"
[1] "repPkgInfos"
[1] "downloadFile"
[1] "downloadFile"
[1] "repReleaseLevel"
[1] "summary"
[1] "show"
[1] "pkgListing"
[1] "pkgList"
[1] "pkgList"
[1] "repList"
[1] "repListing"
[1] "repListing"
[1] "getRepEntry"
[1] "getRepURL"
[1] "getRepURL"
[1] "packages"
[1] "packages"
[1] "pkgVersionList"
[1] "pkgVersionList"
[1] "summary"
[1] "show"
[1] "reposTheme"
[1] "repThemeName"
[1] "repThemeName"
[1] "repThemePkgs"
[1] "repThemePkgs"
[1] "repThemeDesc"
[1] "repThemeDesc"
[1] "repThemeRepos"
[1] "repThemeRepos"
[1] "show"
[1] "VersionNumber"
[1] "stringRep"
[1] "major"
[1] "minor"
[1] "revision"
[1] "stringRep"
[1] "major"
[1] "minor"
[1] "revision"
[1] "show"
[1] "as.character"
[1] "pkgInfo"
[1] "pkgName"
[1] "pkgVersion"
[1] "pkgRelLevel"
[1] "pkgPath"
[1] "pkgContains"
[1] "pkgRelLevel"
[1] "pkgName"
[1] "pkgVersion"
[1] "pkgPath"
[1] "pkgContains"
[1] "=="
[1] "show"
[1] "localPkg"
[1] "Package"
[1] "Package"
[1] "PkgVersion"
[1] "PkgVersion"
[1] "Keywords"
[1] "Keywords"
[1] "Depends"
[1] "Depends"
[1] "Suggests"
[1] "Suggests"
[1] "Imports"
[1] "Imports"
[1] "Repos"
[1] "Repos"
[1] "Bundle"
[1] "Bundle"
[1] "pkgStatusList"
[1] "show"
[1] "statusList"
[1] "statusList"
[1] "statusList<-"
[1] "statusList<-"
[1] "matchesList"
[1] "matchesList"
[1] "matchesList<-"
[1] "matchesList<-"
[1] "packages"
[1] "found"
[1] "found"
[1] "notFound"
[1] "notFound"
[1] "updated"
[1] "updated"
[1] "notUpdated"
[1] "notUpdated"
[1] "urls"
[1] "urls"
[1] "pkgVersions"
[1] "pkgVersions"
[1] "foundPkgs"
[1] "foundPkgs"
[1] "notFoundPkgs"
[1] "notFoundPkgs"
[1] "updatedPkgs"
[1] "updatedPkgs"
[1] "getPackage"
[1] "getPackage"
[1] "getFound"
[1] "getFound"
[1] "getUpdated"
[1] "getUpdated"
[1] "getUrl"
[1] "getUrl"
[1] "getPkgVersion"
[1] "getPkgVersion"
[1] "pkgStatus"
[1] "package"
[1] "package"
[1] "found"
[1] "updated"
[1] "URL"
[1] "URL"
[1] "pkgVersion"
[1] "show"
** help
>>> Building/Updating help pages for package 'reposTools'
Formats: text html latex example
ReposEntry-class text html latex example
ReposList-class text html latex example
VersionNumber-class text html latex example
buildPkgInfo text html latex example
buildReposEntry text html latex example
buildVersionNumber text html latex example
checkVers text html latex example
closeLocLib text html latex example
download.packages2 text html latex example
genRepos text html latex example
genReposHtml text html latex example
getDependings text html latex example
getLocalPkgs text html latex example
getMaxVersion text html latex example
getOptReposList text html latex example
getPkgVers text html latex example
getReplisting text html latex example
getReposEntry text html latex example
getReposList text html latex example
getReposOption text html latex example
getRversion text html latex example
initVersionNumber text html latex
install.packages2 text html latex example
load.locLib text html latex example
loadDepends text html latex example
loadRepDD text html latex example
localPkg-class text html latex example
note text html latex example
parseThemesXML text html latex example
pkgInfo-class text html latex example
pkgListing-class text html latex example
pkgStatus-class text html latex example
pkgStatusList-class text html latex example
repdatadesc-class text html latex example
replisting-class text html latex example
reposTheme-class text html latex example
reposToolsLibPaths text html latex example
repositories text html latex example
resolve.depends text html latex example
save.locLib text html latex example
saveDfRda text html latex example
splitDFstrings text html latex example
syncLocalLibList text html latex example
themes text html latex example
unpackExtractPkgDESC text html latex example
userQuery text html latex example
winConvertSourceRepos text html latex example
writeThemesXML text html latex example
* DONE (reposTools)
Loading required package: reposTools
Loading required package: tools
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download widgetTools from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing widgetTools"
* Installing *source* package 'widgetTools' ...
** R
** inst
** preparing package for lazy loading
Warning message:
Undefined slot classes in definition of "widgetView": winid (class "
tkwin ") in: .completeClassSlots(ClassDef, where)
** help
>>> Building/Updating help pages for package 'widgetTools'
Formats: text html latex example
basicPW-class text html latex example
button text html latex example
dropdownList text html latex example
makeViewer text html latex example
oneVScrList text html latex example
safeFileOpen text html latex example
tooltip text html latex example
widget-class text html latex example
widgetView-class text html latex example
writeText text html latex example
* DONE (widgetTools)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download DynDoc from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing DynDoc"
* Installing *source* package 'DynDoc' ...
** R
** save image
[1] TRUE
Loading required package: tools
[1] "DynDoc"
Warning message:
Undefined slot classes in definition of "DynDoc": codeChunks (class "
chunkList ") in: .completeClassSlots(ClassDef, where)
[1] "indexEntry"
[1] "indexEntry"
[1] "path"
[1] "path"
[1] "pdfPath"
[1] "pdfPath"
[1] "getDepends"
[1] "getDepends"
[1] "getRequires"
[1] "getRequires"
[1] "getSuggests"
[1] "getSuggests"
[1] "getKeywords"
[1] "getKeywords"
[1] "codeChunks"
[1] "codeChunks"
[1] "chunks"
[1] "chunks"
[1] "setChunk<-"
[1] "setChunk<-"
[1] "numChunks"
[1] "numChunks"
[1] "getChunk"
[1] "getChunk"
[1] "evalChunk"
[1] "evalChunk"
Creating a new generic function for "summary" in "DynDoc"
[1] "summary"
[1] "show"
[1] "SweaveOptions"
[1] "SweaveOptions"
[1] "getOptions"
[1] "getOptions"
[1] "numOptions"
[1] "numOptions"
[1] "show"
[1] "codeChunk"
[1] "codeChunk"
[1] "chunk"
[1] "chunk"
[1] "chunk<-"
[1] "chunk<-"
[1] "chunkName"
[1] "chunkName"
[1] "SweaveOptions"
[1] "getOptions"
[1] "evalChunk"
[1] "show"
[1] "chunkList"
[1] "chunkList"
[1] "chunks"
[1] "numChunks"
[1] "evalEnv"
[1] "evalEnv"
[1] "summary"
[1] "show"
[1] "getChunk"
[1] "setChunk<-"
[1] "getAllCodeChunks"
[1] "getAllCodeChunks"
[1] "evalChunk"
[1] "Vignette"
Warning message:
Undefined slot classes in definition of "Vignette": vigPkgVersion
(class " VersionNumber ") in: .completeClassSlots(ClassDef, where)
[1] "vigPkgVersion"
[1] "vigPkgVersion"
[1] "vignetteCode"
[1] "path"
[1] "getDepends"
[1] "chunks"
[1] "chunkList"
[1] "setChunk<-"
[1] "evalEnv"
[1] "numChunks"
[1] "getChunk"
[1] "evalChunk"
[1] "summary"
[1] "show"
** help
>>> Building/Updating help pages for package 'DynDoc'
Formats: text html latex example
DynDoc-class text html latex example
SweaveOptions-class text html latex example
Vignette-class text html latex example
chunkList-class text html latex example
codeChunk-class text html latex example
getPkgVigList text html latex example
getVignette text html latex example
getVignetteCode text html latex example
getVignetteHeader text html latex example
tangleToR text html latex example
vignetteCode-class text html latex example
* DONE (DynDoc)
[1] "Installation complete"
[1] "Attempting to download tkWidgets from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing tkWidgets"
* Installing *source* package 'tkWidgets' ...
** R
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'tkWidgets'
Formats: text html latex example
DPExplorer text html latex example
WName text html latex example
appendSepDir text html latex example
args2XML text html latex example
argsWidget text html latex example
colInfo-class text html latex example
dataViewer text html latex example
dbArgsWidget text html latex example
eExplorer text html latex example
fileBrowser text html latex example
fileWizard text html latex example
getLightTW text html latex example
getWvalues text html latex example
guess.sep text html latex example
hasChar text html latex example
importPhenoData text html latex example
importWizard text html latex example
listSelect text html latex example
objNameToList text html latex example
objViewer text html latex example
objectBrowser text html latex example
pExplorer text html latex example
pickFiles text html latex example
pickItems text html latex example
pickObjs text html latex example
setArgsList text html latex example
stdType text html latex example
tkMIAME text html latex
tkSampleNames text html latex
tkphenoData text html latex
vExplorer text html latex example
values.Widget text html latex example
widgetRender text html latex example
* DONE (tkWidgets)
[1] "Installation complete"
[1] "Attempting to download Biobase from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing Biobase"
* Installing *source* package 'Biobase' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c Rinit.c -o Rinit.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c envir.c -o envir.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
Biobase.so Rinit.o envir.o -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** data
** inst
** save image
[1] TRUE
Loading required package: tools
[1] "aggregator"
[1] "aggenv"
[1] "aggenv"
[1] "initfun"
[1] "initfun"
[1] "aggfun"
[1] "aggfun"
[1] "container"
[1] "content"
[1] "content"
[1] "locked"
[1] "locked"
[1] "[[<-"
[1] "[["
[1] "length"
[1] "show"
[1] "["
[1] "phenoData"
[1] "pData"
[1] "pData"
[1] "varLabels"
[1] "varLabels"
[1] "["
[1] "[["
[1] "[[<-"
[1] "show"
[1] "MIAME"
[1] "show"
[1] "abstract"
[1] "abstract"
[1] "samples"
[1] "samples"
[1] "hybridizations"
[1] "hybridizations"
[1] "normControls"
[1] "normControls"
[1] "preproc"
[1] "preproc"
[1] "otherInfo"
[1] "otherInfo"
[1] "expinfo"
[1] "expinfo"
[1] "characterORMIAME"
[1] "exprMatrix"
[1] "exprSet"
[1] "update2MIAME"
[1] "update2MIAME"
[1] "exprs"
[1] "exprs"
[1] "se.exprs"
[1] "se.exprs"
[1] "exprs<-"
[1] "exprs<-"
[1] "se.exprs<-"
[1] "se.exprs<-"
[1] "notes"
[1] "notes"
[1] "notes<-"
[1] "notes<-"
[1] "description"
[1] "description"
[1] "description<-"
[1] "description<-"
[1] "abstract"
[1] "phenoData"
[1] "phenoData"
[1] "phenoData<-"
[1] "phenoData<-"
[1] "pData"
[1] "pData<-"
[1] "pData<-"
[1] "[[<-"
[1] "[["
[1] "pData<-"
[1] "sampleNames"
[1] "sampleNames"
[1] "sampleNames<-"
[1] "sampleNames<-"
[1] "geneNames"
[1] "geneNames"
[1] "geneNames<-"
[1] "geneNames<-"
[1] "varLabels"
[1] "annotation"
[1] "annotation"
[1] "annotation<-"
[1] "annotation<-"
[1] "["
[1] "show"
[1] "iter"
[1] "iter"
[1] "iter"
[1] "iter"
[1] "split"
[1] "split"
[1] "split"
[1] "split"
[1] "write.exprs"
[1] "write.exprs"
[1] "exprs2excel"
[1] "exprs2excel"
[1] "exprList"
[1] "eSet"
[1] "eList"
[1] "eList"
[1] "eList<-"
[1] "eList<-"
[1] "eList<-"
[1] "eList<-"
[1] "getExpData"
[1] "getExpData"
[1] "exprs"
[1] "["
[1] "show"
[1] "phenoData"
[1] "phenoData<-"
[1] "pData"
[1] "pData<-"
[1] "combine"
[1] "combine"
[1] "combine"
[1] "combine"
[1] "combine"
** help
>>> Building/Updating help pages for package 'Biobase'
Formats: text html latex example
Aggregate text html latex example
aaMap text html latex example
addVig2Menu text html latex example
aggregator-class text html latex
as.data.frame.exprSet text html latex example
characterORmiame-class text html latex
combine text html latex example
container-class text html latex example
contents text html latex example
copyEnv text html latex example
copySubstitute text html latex example
createPackage text html latex example
dumpPackTxt text html latex example
eSet-class text html latex example
esApply text html latex example
eset text html latex example
exprList-class text html latex example
exprMatrix-class text html latex
exprSet-class text html latex example
geneData text html latex example
getPkgVigs text html latex example
iter-methods text html latex
miame-class text html latex
multiassign text html latex example
openPDF text html latex example
openVignette text html latex example
package.version text html latex example
phenoData-class text html latex
read.MIAME text html latex example
read.exprSet text html latex example
read.phenoData text html latex example
testBioCConnection text html latex example
* DONE (Biobase)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download hgu95av2cdf from
http://www.bioconductor.org/data/cdfenvs/repos/"
[1] "Download complete."
[1] "Installing hgu95av2cdf"
* Installing *source* package 'hgu95av2cdf' ...
** R
** data
** help
>>> Building/Updating help pages for package 'hgu95av2cdf'
Formats: text html latex example
geometry text html latex example
hgu95av2cdf text html latex
* DONE (hgu95av2cdf)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download hgu133acdf from
http://www.bioconductor.org/data/cdfenvs/repos/"
[1] "Download complete."
[1] "Installing hgu133acdf"
* Installing *source* package 'hgu133acdf' ...
** R
** data
** help
>>> Building/Updating help pages for package 'hgu133acdf'
Formats: text html latex example
geometry text html latex example
hgu133acdf text html latex
* DONE (hgu133acdf)
[1] "Installation complete"
[1] "Attempting to download affydata from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing affydata"
* Installing *source* package 'affydata' ...
** R
** data
** inst
** help
>>> Building/Updating help pages for package 'affydata'
Formats: text html latex example
Dilution text html latex
missing link(s): AffyBatch AffyBatch
* DONE (affydata)
[1] "Installation complete"
[1] "Attempting to download affy from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing affy"
* Installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c
chipbackground.c -o chipbackground.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c
getall_locations.c -o getall_locations.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c
mas5calls.c -o mas5calls.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c qnorm.c -o
qnorm.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c
read_abatch.c -o read_abatch.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c rma2.c -o
rma2.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c
rma_background2.c -o rma_background2.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c
rma_common.c -o rma_common.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o
read_abatch.o rma2.o rma_background2.o rma_common.o -lz -lcc_dynamic
-framework R
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
ld: warning multiple definitions of symbol _crc32
/usr/lib/libz.dylib(crc32.o) definition of _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/usr/lib/libz.dylib(crc32.o) definition of _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflateInit_
/usr/lib/libz.dylib(deflate.o) definition of _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
ld: warning multiple definitions of symbol _deflateCopy
/usr/lib/libz.dylib(deflate.o) definition of _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateParams
/usr/lib/libz.dylib(deflate.o) definition of _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
ld: warning multiple definitions of symbol _deflateReset
/usr/lib/libz.dylib(deflate.o) definition of _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/usr/lib/libz.dylib(deflate.o) definition of _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
ld: warning multiple definitions of symbol _deflateEnd
/usr/lib/libz.dylib(deflate.o) definition of _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflate
/usr/lib/libz.dylib(deflate.o) definition of _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
ld: warning multiple definitions of symbol _deflateInit2_
/usr/lib/libz.dylib(deflate.o) definition of _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
ld: warning multiple definitions of symbol _gzwrite
/usr/lib/libz.dylib(gzio.o) definition of _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
ld: warning multiple definitions of symbol _gztell
/usr/lib/libz.dylib(gzio.o) definition of _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
ld: warning multiple definitions of symbol _gzseek
/usr/lib/libz.dylib(gzio.o) definition of _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
ld: warning multiple definitions of symbol _gzread
/usr/lib/libz.dylib(gzio.o) definition of _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
ld: warning multiple definitions of symbol _gzopen
/usr/lib/libz.dylib(gzio.o) definition of _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
ld: warning multiple definitions of symbol _gzgetc
/usr/lib/libz.dylib(gzio.o) definition of _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
ld: warning multiple definitions of symbol _gzeof
/usr/lib/libz.dylib(gzio.o) definition of _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/usr/lib/libz.dylib(gzio.o) definition of _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/usr/lib/libz.dylib(gzio.o) definition of _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/usr/lib/libz.dylib(gzio.o) definition of _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/usr/lib/libz.dylib(gzio.o) definition of _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
ld: warning multiple definitions of symbol _gzgets
/usr/lib/libz.dylib(gzio.o) definition of _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
ld: warning multiple definitions of symbol _gzprintf
/usr/lib/libz.dylib(gzio.o) definition of _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/usr/lib/libz.dylib(gzio.o) definition of _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/usr/lib/libz.dylib(gzio.o) definition of _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
ld: warning multiple definitions of symbol _gzrewind
/usr/lib/libz.dylib(gzio.o) definition of _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
ld: warning multiple definitions of symbol _gzsetparams
/usr/lib/libz.dylib(gzio.o) definition of _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
ld: warning multiple definitions of symbol _inflateSyncPoint
/usr/lib/libz.dylib(inflate.o) definition of _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/usr/lib/libz.dylib(inflate.o) definition of _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
ld: warning multiple definitions of symbol _inflateInit2_
/usr/lib/libz.dylib(inflate.o) definition of _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
ld: warning multiple definitions of symbol _inflateEnd
/usr/lib/libz.dylib(inflate.o) definition of _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateReset
/usr/lib/libz.dylib(inflate.o) definition of _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/usr/lib/libz.dylib(inflate.o) definition of _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
ld: warning multiple definitions of symbol _inflateSetDictionary
/usr/lib/libz.dylib(inflate.o) definition of _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
ld: warning multiple definitions of symbol _inflateSync
/usr/lib/libz.dylib(inflate.o) definition of _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
ld: warning multiple definitions of symbol _adler32
/usr/lib/libz.dylib(adler32.o) definition of _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
ld: warning multiple definitions of symbol _zError
/usr/lib/libz.dylib(zutil.o) definition of _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/usr/lib/libz.dylib(zutil.o) definition of _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
** R
** data
** demo
** inst
** save image
[1] TRUE
[1] TRUE
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
[1] TRUE
Loading required package: reposTools
[1] "ProgressBarText"
[1] "initialize"
[1] "open"
[1] "open"
[1] "update"
[1] "update"
[1] "close"
[1] "close"
[1] "AffyBatch"
[1] "cdfName"
[1] "cdfName"
[1] "intensity"
[1] "intensity"
[1] "intensity<-"
[1] "intensity<-"
[1] "length"
[1] "ncol"
[1] "ncol"
[1] "nrow"
[1] "nrow"
[1] "geneNames"
[1] "geneNames<-"
[1] "show"
[1] "indexProbes"
[1] "indexProbes"
[1] "pmindex"
[1] "pmindex"
[1] "mmindex"
[1] "mmindex"
[1] "probeNames"
[1] "probeNames"
[1] "probes"
[1] "probes"
[1] "pm"
[1] "pm"
[1] "pm<-"
[1] "pm<-"
[1] "mm"
[1] "mm"
[1] "mm<-"
[1] "mm<-"
[1] "probeset"
[1] "probeset"
[1] "["
[1] "[<-"
[1] "bg.correct"
[1] "bg.correct"
[1] "normalize.methods"
[1] "normalize.methods"
[1] "normalize"
[1] "normalize"
[1] "computeExprSet"
[1] "computeExprSet"
[1] "image"
[1] "image"
[1] "boxplot"
[1] "boxplot"
[1] "hist"
[1] "hist"
[1] "mas5calls"
[1] "mas5calls"
[1] "Mbox"
[1] "Mbox"
[1] "MAplot"
[1] "MAplot"
[1] "ProbeSet"
[1] "show"
[1] "colnames"
[1] "sampleNames"
[1] "colnames"
[1] "pm"
[1] "pm<-"
[1] "mm"
[1] "mm<-"
[1] "express.summary.stat"
[1] "express.summary.stat"
[1] "barplot"
[1] "barplot"
[1] "mas5calls"
** help
>>> Building/Updating help pages for package 'affy'
Formats: text html latex example
.setAffyOptions text html latex example
AffyBatch-class text html latex example
AffyRNAdeg text html latex example
MAplot text html latex example
ProbeSet-class text html latex example
ProgressBarText-class text html latex example
SpikeIn text html latex
affy-options text html latex example
affy.scalevalue.exprSet text html latex
affybatch.example text html latex
barplot.ProbeSet text html latex example
bg.adjust text html latex
bgc text html latex example
cdfFromBioC text html latex example
cdfenv.example text html latex
cleancdfname text html latex example
debug.affy123 text html latex
expresso text html latex example
expressoWidget text html latex example
fit.li.wong text html latex example
generateExprSet-methods text html latex example
generateExprVal-methods text html latex example
generateExprVal.method.avgdiff text html latex example
generateExprVal.method.playerout text html latex
hlog text html latex
justrma text html latex example
missing link(s): read.celfile
list.celfiles text html latex example
loess.normalize text html latex
maffy.normalise text html latex example
maffy.subset text html latex example
mas5 text html latex example
mas5calls text html latex example
merge.AffyBatch text html latex example
multiloess text html latex
mva.pairs text html latex example
normalize-methods text html latex example
normalize text html latex
normalize.constant text html latex
normalize.contrast text html latex example
normalize.invariantset text html latex
normalize.loess text html latex example
normalize.qspline text html latex
normalize.quantiles text html latex
normalize.quantiles.robust text html latex
pairs.AffyBatch text html latex example
plot.ProbeSet text html latex example
plot.density text html latex example
plotLocation text html latex example
pmcorrect text html latex example
ppsetApply text html latex example
probeMatch-methods text html latex
probeNames-methods text html latex
read.affybatch text html latex example
read.probematrix text html latex example
rma text html latex example
simplemultiLoess text html latex
summary text html latex
tukey.biweight text html latex
whatcdf text html latex
xy2indices text html latex example
* DONE (affy)
[1] "Installation complete"
[1] "Attempting to download affyPLM from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing affyPLM"
* Installing *source* package 'affyPLM' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c LESN.c -o LESN.o
LESN.c:190: warning: static declaration for `log2' follows non-static
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c SCAB.c -o SCAB.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c avg_log.c -o avg_log.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c biweight.c -o biweight.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c chipbackground.c -o
chipbackground.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c do_PLMrlm.c -o
do_PLMrlm.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c do_PLMrma.c -o
do_PLMrma.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c do_PLMthreestep.c -o
do_PLMthreestep.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c idealmismatch.c -o
idealmismatch.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c lm.c -o lm.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c lm_threestep.c -o
lm_threestep.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c log_avg.c -o log_avg.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c matrix_functions.c -o
matrix_functions.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c medianPM.c -o medianPM.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c median_logPM.c -o
median_logPM.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c medianpolish.c -o
medianpolish.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c nthLargestPM.c -o
nthLargestPM.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c preprocess.c -o
preprocess.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c psi_fns.c -o psi_fns.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c qnorm.c -o qnorm.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c qnorm_probeset.c -o
qnorm_probeset.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rlm.c -o rlm.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rlm_PLM.c -o rlm_PLM.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rlm_anova.c -o
rlm_anova.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rlm_se.c -o rlm_se.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rlm_threestep.c -o
rlm_threestep.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rmaPLM_pseudo.c -o
rmaPLM_pseudo.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rma_PLM.c -o rma_PLM.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rma_background2.c -o
rma_background2.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c rma_common.c -o
rma_common.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c scaling.c -o scaling.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c threestep.c -o
threestep.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c threestep_PLM.c -o
threestep_PLM.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c threestep_common.c -o
threestep_common.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c threestep_summary.c -o
threestep_summary.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c
threestep_summary_methods.c -o threestep_summary_methods.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c weightedkerneldensity.c
-o weightedkerneldensity.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
affyPLM.so LESN.o SCAB.o avg_log.o biweight.o chipbackground.o
do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm.o
lm_threestep.o log_avg.o matrix_functions.o medianPM.o median_logPM.o
medianpolish.o nthLargestPM.o preprocess.o psi_fns.o qnorm.o
qnorm_probeset.o rlm.o rlm_PLM.o rlm_anova.o rlm_se.o rlm_threestep.o
rmaPLM_pseudo.o rma_PLM.o rma_background2.o rma_common.o scaling.o
threestep.o threestep_PLM.o threestep_common.o threestep_summary.o
threestep_summary_methods.o weightedkerneldensity.o -framework vecLib
-lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** inst
** save image
[1] TRUE
[1] TRUE
[1] TRUE
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
[1] TRUE
Loading required package: reposTools
[1] TRUE
[1] TRUE
[1] "PLMset"
[1] "cdfName"
Creating a new generic function for "weights" in "affyPLM"
[1] "weights"
[1] "weights<-"
[1] "weights<-"
[1] "coefs"
[1] "coefs"
[1] "coefs<-"
[1] "coefs<-"
[1] "coefs.probe"
[1] "coefs.probe"
[1] "se"
[1] "se"
[1] "se.probe"
[1] "se.probe"
[1] "se<-"
[1] "se<-"
[1] "indexProbes"
[1] "indexProbesProcessed"
[1] "indexProbesProcessed"
[1] "image"
[1] "boxplot"
[1] "show"
[1] "coefs.const"
[1] "coefs.const"
[1] "se.const"
[1] "se.const"
[1] "summary"
[1] "Mbox"
[1] "resid<-"
[1] "resid<-"
Creating a new generic function for "resid" in "affyPLM"
[1] "resid"
[1] "residuals<-"
[1] "residuals<-"
Creating a new generic function for "residuals" in "affyPLM"
[1] "residuals"
[1] "normvec"
[1] "normvec"
[1] "varcov"
[1] "varcov"
[1] "residSE"
[1] "residSE"
[1] "sampleNames<-"
[1] "model.description"
[1] "model.description"
[1] "MAplot"
** help
>>> Building/Updating help pages for package 'affyPLM'
Formats: text html latex example
MAplot text html latex
PLMset-class text html latex example
PLMset2exprSet text html latex example
affyPLM-internal text html latex
bg.correct.LESN text html latex example
fitPLM text html latex example
normalize.exprSet text html latex example
normalize.quantiles.probeset text html latex
normalize.scaling text html latex example
pseudo text html latex example
rmaPLM text html latex example
threestep text html latex example
threestepPLM text html latex example
* DONE (affyPLM)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download GO from
http://www.bioconductor.org/data/metaData-devel/"
[1] "Download complete."
[1] "Installing GO"
* Installing *source* package 'GO' ...
** R
** data
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'GO'
Formats: text html latex example
GO text html latex
GOALLLOCUSID text html latex example
GOBPANCESTOR text html latex example
GOBPCHILDREN text html latex example
GOBPOFFSPRING text html latex example
GOBPPARENTS text html latex example
GOCCANCESTOR text html latex example
GOCCCHILDREN text html latex example
GOCCOFFSPRING text html latex example
GOCCPARENTS text html latex example
GOLOCUSID text html latex example
GOLOCUSID2ALLGO text html latex example
GOLOCUSID2GO text html latex example
GOMFANCESTOR text html latex example
GOMFCHILDREN text html latex example
GOMFOFFSPRING text html latex example
GOMFPARENTS text html latex example
GOQC text html latex
GOTERM text html latex example
* DONE (GO)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download KEGG from
http://www.bioconductor.org/data/metaData-devel/"
[1] "Download complete."
[1] "Installing KEGG"
* Installing *source* package 'KEGG' ...
** R
** data
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'KEGG'
Formats: text html latex example
KEGG text html latex
KEGGENZYMEID2GO text html latex example
KEGGEXTID2PATHID text html latex example
KEGGGO2ENZYMEID text html latex example
KEGGPATHID2EXTID text html latex example
KEGGPATHID2NAME text html latex example
KEGGPATHNAME2ID text html latex example
KEGGQC text html latex
* DONE (KEGG)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download hgu95av2 from
http://www.bioconductor.org/data/metaData-devel/"
[1] "Download complete."
[1] "Installing hgu95av2"
* Installing *source* package 'hgu95av2' ...
** R
** data
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'hgu95av2'
Formats: text html latex example
hgu95av2 text html latex
hgu95av2ACCNUM text html latex example
hgu95av2CHR text html latex example
hgu95av2CHRLENGTHS text html latex example
hgu95av2CHRLOC text html latex example
hgu95av2ENZYME text html latex example
hgu95av2ENZYME2PROBE text html latex example
hgu95av2GENENAME text html latex example
hgu95av2GO text html latex example
hgu95av2GO2ALLPROBES text html latex example
hgu95av2GO2PROBE text html latex example
hgu95av2GRIF text html latex example
hgu95av2LOCUSID text html latex example
hgu95av2MAP text html latex example
hgu95av2OMIM text html latex example
hgu95av2ORGANISM text html latex example
hgu95av2PATH text html latex example
hgu95av2PATH2PROBE text html latex example
hgu95av2PMID text html latex example
hgu95av2PMID2PROBE text html latex example
hgu95av2QC text html latex
hgu95av2REFSEQ text html latex example
hgu95av2SUMFUNC text html latex example
hgu95av2SYMBOL text html latex example
hgu95av2UNIGENE text html latex example
* DONE (hgu95av2)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download genefilter from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing genefilter"
* Installing *source* package 'genefilter' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c genedist.c -o genedist.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c init.c -o init.o
g77 -fno-common -g -O2 -c ttest.f -o ttest.o
make: g77: Command not found
make: *** [ttest.o] Error 127
ERROR: compilation failed for package 'genefilter'
Note: Package genefilter not found in any known repository.
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download Biostrings from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing Biostrings"
* Installing *source* package 'Biostrings' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c biostring.c -o
biostring.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
Biostrings.so biostring.o -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** data
** save image
[1] "BioAlphabet"
[1] "gapletter<-"
[1] "gapletter<-"
[1] "initialize"
[1] "NucleotideAlphabet"
[1] "initialize"
[1] "AminoAcidAlphabet"
[1] "BioPatternAlphabet"
[1] "gapletter<-"
[1] "initialize"
[1] "BioString"
Creating a new generic function for "as.matrix" in "Biostrings"
[1] "as.matrix"
[1] "BioStringNewValues"
[1] "BioStringNewValues"
[1] "BioStringNewValues"
[1] "BioStringNewValues"
[1] "initialize"
[1] "length"
[1] "["
[1] "[["
Creating a new generic function for "substr" in "Biostrings"
[1] "substr"
Creating a new generic function for "substring" in "Biostrings"
[1] "substring"
[1] "as.character"
Creating a new generic function for "nchar" in "Biostrings"
[1] "nchar"
[1] "show"
[1] "matchDNAPattern"
[1] "matchDNAPattern"
[1] "matchDNAPattern"
[1] "matchDNAPattern"
[1] "allSameLetter"
[1] "allSameLetter"
[1] "allSameLetter"
[1] "allSameLetter"
[1] "anySameLetter"
[1] "anySameLetter"
[1] "anySameLetter"
[1] "anySameLetter"
[1] "LongestCommonPrefix"
[1] "["
** help
>>> Building/Updating help pages for package 'Biostrings'
Formats: text html latex example
AminoAcidAlphabet-class text html latex
BioAlphabet-class text html latex example
BioPatternAlphabet-class text html latex example
BioString-class text html latex example
BioStringNewValues text html latex example
DNAAlphabet text html latex example
DNAPatternAlphabet text html latex example
DNASuffixArray text html latex example
LongestCommonPrefix-class text html latex example
LongestCommonPrefix text html latex example
NucleotideAlphabet-class text html latex example
NucleotideString text html latex example
allSameLetter text html latex example
alphabetFrequency text html latex example
anySameLetter text html latex example
gapletterReplace text html latex example
matchDNAPattern text html latex example
reverseComplement text html latex example
sortDNAString text html latex example
yeastSEQCHR1 text html latex example
* DONE (Biostrings)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download rae230a from
http://www.bioconductor.org/data/metaData-devel/"
[1] "Download complete."
[1] "Installing rae230a"
* Installing *source* package 'rae230a' ...
** R
** data
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'rae230a'
Formats: text html latex example
rae230a text html latex
rae230aACCNUM text html latex example
rae230aCHR text html latex example
rae230aCHRLENGTHS text html latex example
rae230aCHRLOC text html latex example
rae230aENZYME text html latex example
rae230aENZYME2PROBE text html latex example
rae230aGENENAME text html latex example
rae230aGO text html latex example
rae230aGO2ALLPROBES text html latex example
rae230aGO2PROBE text html latex example
rae230aGRIF text html latex example
rae230aLOCUSID text html latex example
rae230aMAP text html latex example
rae230aOMIM text html latex example
rae230aORGANISM text html latex example
rae230aPATH text html latex example
rae230aPATH2PROBE text html latex example
rae230aPMID text html latex example
rae230aPMID2PROBE text html latex example
rae230aQC text html latex
rae230aREFSEQ text html latex example
rae230aSUMFUNC text html latex example
rae230aSYMBOL text html latex example
rae230aUNIGENE text html latex example
* DONE (rae230a)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download hgu95av2probe from
http://www.bioconductor.org/data/probes/Packages/"
[1] "Download complete."
[1] "Installing hgu95av2probe"
* Installing *source* package 'hgu95av2probe' ...
** R
** data
** help
>>> Building/Updating help pages for package 'hgu95av2probe'
Formats: text html latex example
hgu95av2probe text html latex example
* DONE (hgu95av2probe)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download hu6800cdf from
http://www.bioconductor.org/data/cdfenvs/repos/"
[1] "Download complete."
[1] "Installing hu6800cdf"
* Installing *source* package 'hu6800cdf' ...
** R
** data
** help
>>> Building/Updating help pages for package 'hu6800cdf'
Formats: text html latex example
geometry text html latex example
hu6800cdf text html latex
[1] "Installation complete"
* DONE (hu6800cdf)
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download hu6800probe from
http://www.bioconductor.org/data/probes/Packages/"
[1] "Download complete."
[1] "Installing hu6800probe"
* Installing *source* package 'hu6800probe' ...
** R
** data
** help
>>> Building/Updating help pages for package 'hu6800probe'
Formats: text html latex example
hu6800probe text html latex example
* DONE (hu6800probe)
[1] "Installation complete"
[1] "Attempting to download matchprobes from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing matchprobes"
* Installing *source* package 'matchprobes' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c main.c -o main.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c strutils.c -o strutils.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
matchprobes.so main.o strutils.o -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** data
** inst
** save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
[1] TRUE
** help
>>> Building/Updating help pages for package 'matchprobes'
Formats: text html latex example
basecontent text html latex example
combineAffyBatch text html latex example
complementSeq text html latex example
getProbeDataAffy text html latex example
makeProbePackage text html latex example
matchprobes text html latex example
print.probetable text html latex example
reverseSeq text html latex example
* DONE (matchprobes)
[1] "Installation complete"
[1] "Attempting to download rae230aprobe from
http://www.bioconductor.org/data/probes/Packages/"
[1] "Download complete."
[1] "Installing rae230aprobe"
* Installing *source* package 'rae230aprobe' ...
** R
** data
** help
>>> Building/Updating help pages for package 'rae230aprobe'
Formats: text html latex example
rae230aprobe text html latex example
* DONE (rae230aprobe)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: Package XML not found in any known repository.
Note: Package annotate not found in any known repository.
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download multtest from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing multtest"
* Installing *source* package 'multtest' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c Rpack.c -o
Rpack.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c
block_sampling_fixed.c -o block_sampling_fixed.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c bootloop.c
-o bootloop.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c mt.c -o
mt.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c
pairt_sampling.c -o pairt_sampling.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c
pairt_sampling_fixed.c -o pairt_sampling_fixed.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c random.c
-o random.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c sampling.c
-o sampling.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c
sampling_fixed.c -o sampling_fixed.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c
stat_func.c -o stat_func.o
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -O -DUSEDOUBLE -fno-common -g -O2 -c
stat_order.c -o stat_order.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
multtest.so Rpack.o block_sampling_fixed.o bootloop.o mt.o
pairt_sampling.o pairt_sampling_fixed.o random.o sampling.o
sampling_fixed.o stat_func.o stat_order.o -lm -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** data
** inst
** save image
[1] TRUE
[1] "MTP"
Creating a new generic function for "print" in "multtest"
[1] "print"
Creating a new generic function for "plot" in "multtest"
[1] "plot"
Creating a new generic function for "summary" in "multtest"
[1] "summary"
[1] "["
Creating a new generic function for "as.list" in "multtest"
[1] "as.list"
** help
>>> Building/Updating help pages for package 'multtest'
Formats: text html latex example
MTP-class text html latex example
MTP-methods text html latex
MTP text html latex example
boot.resample text html latex example
fwer2gfwer text html latex example
get.index text html latex example
golub text html latex
meanX text html latex example
mt.internal text html latex
mt.maxT text html latex example
mt.plot text html latex example
mt.rawp2adjp text html latex example
mt.reject text html latex example
mt.sample.teststat text html latex example
mt.teststat text html latex example
ss.maxT text html latex example
wapply text html latex example
* DONE (multtest)
[1] "Installation complete"
[1] "Attempting to download annaffy from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing annaffy"
* Installing *source* package 'annaffy' ...
** R
** data
** inst
** save image
[1] TRUE
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Loading required package: GO
Loading required package: KEGG
Error: package 'annotate' required by 'annaffy' could not be found
Execution halted
cat: stdout: Broken pipe
ERROR: execution of package source for 'annaffy' failed
[1] "Attempting to download gcrma from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing gcrma"
* Installing *source* package 'gcrma' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c computeAffinities.c -o
computeAffinities.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
gcrma.so computeAffinities.o -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** data
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'gcrma'
Formats: text html latex example
affinity.spline.coefs text html latex
bg.adjust.affinities text html latex
bg.parameters.ns text html latex
compute.affinities text html latex
fast.bkg text html latex
gcrma text html latex example
getCDF text html latex
justGCRMA text html latex example
* DONE (gcrma)
[1] "Installation complete"
[1] "Attempting to download makecdfenv from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing makecdfenv"
* Installing *source* package 'makecdfenv' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c
read_cdffile.c -o read_cdffile.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
makecdfenv.so read_cdffile.o -lz -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _crc32
/usr/lib/libz.dylib(crc32.o) definition of _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/usr/lib/libz.dylib(crc32.o) definition of _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflateInit_
/usr/lib/libz.dylib(deflate.o) definition of _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
ld: warning multiple definitions of symbol _deflateCopy
/usr/lib/libz.dylib(deflate.o) definition of _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateParams
/usr/lib/libz.dylib(deflate.o) definition of _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
ld: warning multiple definitions of symbol _deflateReset
/usr/lib/libz.dylib(deflate.o) definition of _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/usr/lib/libz.dylib(deflate.o) definition of _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
ld: warning multiple definitions of symbol _deflateEnd
/usr/lib/libz.dylib(deflate.o) definition of _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflate
/usr/lib/libz.dylib(deflate.o) definition of _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
ld: warning multiple definitions of symbol _deflateInit2_
/usr/lib/libz.dylib(deflate.o) definition of _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
ld: warning multiple definitions of symbol _gzwrite
/usr/lib/libz.dylib(gzio.o) definition of _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
ld: warning multiple definitions of symbol _gztell
/usr/lib/libz.dylib(gzio.o) definition of _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
ld: warning multiple definitions of symbol _gzseek
/usr/lib/libz.dylib(gzio.o) definition of _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
ld: warning multiple definitions of symbol _gzread
/usr/lib/libz.dylib(gzio.o) definition of _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
ld: warning multiple definitions of symbol _gzopen
/usr/lib/libz.dylib(gzio.o) definition of _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
ld: warning multiple definitions of symbol _gzgetc
/usr/lib/libz.dylib(gzio.o) definition of _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
ld: warning multiple definitions of symbol _gzeof
/usr/lib/libz.dylib(gzio.o) definition of _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/usr/lib/libz.dylib(gzio.o) definition of _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/usr/lib/libz.dylib(gzio.o) definition of _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/usr/lib/libz.dylib(gzio.o) definition of _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/usr/lib/libz.dylib(gzio.o) definition of _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
ld: warning multiple definitions of symbol _gzgets
/usr/lib/libz.dylib(gzio.o) definition of _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
ld: warning multiple definitions of symbol _gzprintf
/usr/lib/libz.dylib(gzio.o) definition of _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/usr/lib/libz.dylib(gzio.o) definition of _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/usr/lib/libz.dylib(gzio.o) definition of _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
ld: warning multiple definitions of symbol _gzrewind
/usr/lib/libz.dylib(gzio.o) definition of _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
ld: warning multiple definitions of symbol _gzsetparams
/usr/lib/libz.dylib(gzio.o) definition of _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
ld: warning multiple definitions of symbol _inflateSyncPoint
/usr/lib/libz.dylib(inflate.o) definition of _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/usr/lib/libz.dylib(inflate.o) definition of _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
ld: warning multiple definitions of symbol _inflateInit2_
/usr/lib/libz.dylib(inflate.o) definition of _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
ld: warning multiple definitions of symbol _inflateEnd
/usr/lib/libz.dylib(inflate.o) definition of _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateReset
/usr/lib/libz.dylib(inflate.o) definition of _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/usr/lib/libz.dylib(inflate.o) definition of _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
ld: warning multiple definitions of symbol _inflateSetDictionary
/usr/lib/libz.dylib(inflate.o) definition of _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
ld: warning multiple definitions of symbol _inflateSync
/usr/lib/libz.dylib(inflate.o) definition of _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
ld: warning multiple definitions of symbol _adler32
/usr/lib/libz.dylib(adler32.o) definition of _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
ld: warning multiple definitions of symbol _zError
/usr/lib/libz.dylib(zutil.o) definition of _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/usr/lib/libz.dylib(zutil.o) definition of _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
** R
** data
** inst
** save image
[1] TRUE
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Loading required package: reposTools
[1] TRUE
[1] TRUE
[1] "Cdf"
[1] "name.levels"
[1] "name.levels"
[1] "name.levels<-"
[1] "name.levels<-"
[1] "pbase"
[1] "pbase"
[1] "pbase<-"
[1] "pbase<-"
[1] "pbase.levels"
[1] "pbase.levels"
[1] "pbase.levels<-"
[1] "pbase.levels<-"
[1] "tbase"
[1] "tbase"
[1] "tbase<-"
[1] "tbase<-"
[1] "tbase.levels"
[1] "tbase.levels"
[1] "tbase.levels<-"
[1] "tbase.levels<-"
[1] "show"
** help
>>> Building/Updating help pages for package 'makecdfenv'
Formats: text html latex example
Cdf-class text html latex
getInfoInAffyFile text html latex
make.cdf.env text html latex example
make.cdf.package text html latex example
pmormm text html latex
read.cdffile text html latex example
* DONE (makecdfenv)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: Package XML not found in any known repository.
Note: Package annotate not found in any known repository.
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download Ruuid from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing Ruuid"
* Installing *source* package 'Ruuid' ...
creating cache ./config.cache
checking for glib-config... no
checking how to run the C preprocessor... cc -E
checking for /usr/include/unistd.h... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include/glib12 -DHAVE_UNISTD_H=1 -I/usr/local/include
-fno-common -g -O2 -c Rinit.c -o Rinit.o
In file included from Ruuid.h:5,
from Rinit.c:1:
uuidP.h:24:18: glib.h: No such file or directory
In file included from Ruuid.h:5,
from Rinit.c:1:
uuidP.h:36: error: parse error before "guint32"
uuidP.h:36: warning: no semicolon at end of struct or union
uuidP.h:37: warning: data definition has no type or storage class
uuidP.h:38: error: parse error before "time_hi_and_version"
uuidP.h:38: warning: data definition has no type or storage class
uuidP.h:39: error: parse error before "clock_seq"
uuidP.h:39: warning: data definition has no type or storage class
uuidP.h:40: error: parse error before "node"
uuidP.h:40: warning: data definition has no type or storage class
uuidP.h:41: error: parse error before '}' token
make: *** [Rinit.o] Error 1
ERROR: compilation failed for package 'Ruuid'
Note: Package Ruuid not found in any known repository.
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download SparseM from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing SparseM"
* Installing *source* package 'SparseM' ...
** libs
g77 -fno-common -g -O2 -c bckslv.f -o bckslv.o
make: g77: Command not found
make: *** [bckslv.o] Error 127
ERROR: compilation failed for package 'SparseM'
Note: Package SparseM not found in any known repository.
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: Package XML not found in any known repository.
Note: Package graph not found in any known repository.
Note: Package Rgraphviz not found in any known repository.
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download fibroEset from
http://www.bioconductor.org/data/experimental/repos/"
[1] "Download complete."
[1] "Installing fibroEset"
* Installing *source* package 'fibroEset' ...
** R
** data
** help
>>> Building/Updating help pages for package 'fibroEset'
Formats: text html latex example
fibroEset text html latex example
* DONE (fibroEset)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download hu6800 from
http://www.bioconductor.org/data/metaData-devel/"
[1] "Download complete."
[1] "Installing hu6800"
* Installing *source* package 'hu6800' ...
** R
** data
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'hu6800'
Formats: text html latex example
hu6800 text html latex
hu6800ACCNUM text html latex example
hu6800CHR text html latex example
hu6800CHRLENGTHS text html latex example
hu6800CHRLOC text html latex example
hu6800ENZYME text html latex example
hu6800ENZYME2PROBE text html latex example
hu6800GENENAME text html latex example
hu6800GO text html latex example
hu6800GO2ALLPROBES text html latex example
hu6800GO2PROBE text html latex example
hu6800GRIF text html latex example
hu6800LOCUSID text html latex example
hu6800MAP text html latex example
hu6800OMIM text html latex example
hu6800ORGANISM text html latex example
hu6800PATH text html latex example
hu6800PATH2PROBE text html latex example
hu6800PMID text html latex example
hu6800PMID2PROBE text html latex example
hu6800QC text html latex
hu6800REFSEQ text html latex example
hu6800SUMFUNC text html latex example
hu6800SYMBOL text html latex example
hu6800UNIGENE text html latex example
* DONE (hu6800)
[1] "Installation complete"
[1] "Attempting to download geneplotter from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing geneplotter"
* Installing *source* package 'geneplotter' ...
** R
** data
** inst
** save image
[1] TRUE
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
[1] TRUE
Loading required package: annotate
Error: geneplotter requires annotate
In addition: Warning message:
There is no package called 'annotate' in: library(package,
character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts,
Execution halted
/Library/Frameworks/R.framework/Resources/bin/INSTALL: line 1: 7714
Broken pipe cat
"/Users/rkakkar/Library/R/library/geneplotter/R/geneplotter"
ERROR: execution of package source for 'geneplotter' failed
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download golubEsets from
http://www.bioconductor.org/data/experimental/repos/"
[1] "Download complete."
[1] "Installing golubEsets"
* Installing *source* package 'golubEsets' ...
** R
** data
** help
>>> Building/Updating help pages for package 'golubEsets'
Formats: text html latex example
golubMerge text html latex example
golubTest text html latex example
golubTrain text html latex example
[1] "Installation complete"
* DONE (golubEsets)
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download xtable from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing xtable"
* Installing *source* package 'xtable' ...
** R
** data
** help
>>> Building/Updating help pages for package 'xtable'
Formats: text html latex example
print.xtable text html latex
string text html latex
table.attributes text html latex
tli text html latex
xtable text html latex example
* DONE (xtable)
[1] "Installation complete"
[1] "Attempting to download edd from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing edd"
* Installing *source* package 'edd' ...
** R
** inst
** save image
[1] TRUE
Loading required package: golubEsets
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
Loading required package: Biobase
Loading required package: class
Loading required package: nnet
Loading required package: xtable
[1] "eddDist"
[1] "stub"
[1] "stub"
[1] "plotlim"
[1] "plotlim"
[1] "tag"
[1] "tag"
[1] "latexTag"
[1] "latexTag"
[1] "parms"
[1] "parms"
[1] "med"
[1] "med"
[1] "Mad"
[1] "Mad"
[1] "CDFname"
[1] "CDFname"
[1] "qfName"
[1] "qfName"
[1] "qfun"
[1] "qfun"
[1] "genName"
[1][1] "Installation complete"
"genName"
[1] "testVec"
[1] "testVec"
** help
>>> Building/Updating help pages for package 'edd'
Formats: text html latex example
centerScale text html latex example
edd text html latex example
eddDist-class text html latex example
eddObsolete text html latex example
flatQQNorm text html latex example
latEDtable text html latex example
makeCandmat.raw text html latex example
maxKSp text html latex example
plotED text html latex example
* DONE (edd)
[1] "Attempting to download ROC from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing ROC"
* Installing *source* package 'ROC' ...
** R
** inst
** save image
[1] TRUE
[1] TRUE
[1] "rocc"
[1] "plot"
[1] "plot"
** help
>>> Building/Updating help pages for package 'ROC'
Formats: text html latex example
AUC text html latex example
plot-methods text html latex example
rocc-class text html latex example
rocdemo.sca text html latex example
trapezint text html latex example
[1] "Installation complete"
* DONE (ROC)
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download statmod from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing statmod"
* Installing *source* package 'statmod' ...
** R
** data
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'statmod'
Formats: text html latex example
1Introduction text html latex
digammaf text html latex example
gauss.quad text html latex example
gauss.quad.prob text html latex example
glmgam text html latex example
growthcurve text html latex example
hommel.test text html latex example
invgauss text html latex example
logmdigamma text html latex example
matvec text html latex example
meanT text html latex example
power text html latex example
qresiduals text html latex example
ranblock text html latex example
remlscor text html latex example
remlscorgamma text html latex example
sage.test text html latex example
tweedie text html latex example
welding text html latex
* DONE (statmod)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download sma from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing sma"
* Installing *source* package 'sma' ...
** R
** data
[1] "Installation complete"
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'sma'
Formats: text html latex example
MouseArray text html latex
id2image text html latex example
init.addinfo text html latex example
init.ctl.index text html latex example
init.data text html latex example
init.grid text html latex example
init.names text html latex example
init.read.exp text html latex example
is.odd text html latex example
na text html latex
plot.bayesian text html latex example
plot.confband.lines text html latex example
plot.confband.points text html latex example
plot.confband.text text html latex example
plot.cor text html latex
plot.mat text html latex example
plot.mva text html latex example
plot.print.tip.lowess text html latex example
plot.qq text html latex example
plot.qqline text html latex example
plot.scale.box text html latex example
plot.single.slide text html latex example
plot.smooth.line text html latex example
plot.spatial text html latex example
plot.svb text html latex example
plot.t2 text html latex example
read.genepix text html latex
read.spot text html latex example
rgcolors.func text html latex example
sma-internal text html latex
stat.Chen text html latex example
stat.ChurSap text html latex example
stat.Newton text html latex example
stat.bay.est text html latex example
stat.bayesian text html latex example
stat.bwss text html latex
stat.diag.da text html latex
stat.gnames text html latex example
stat.ma text html latex example
stat.norm.exp text html latex example
stat.t2 text html latex example
write.spot text html latex example
* DONE (sma)
[1] "Attempting to download limma from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing limma"
* Installing *source* package 'limma' ...
** R
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'limma'
Formats: text html latex example
1introduction text html latex
2classes text html latex
3reading text html latex
4normalization text html latex
5linearmodels text html latex
6SingleChannel text html latex
7diagnostics text html latex
8Other text html latex
LargeDataObject text html latex example
PrintLayout text html latex example
TestResults text html latex
anova-method text html latex
asmalist text html latex
auROC text html latex example
backgroundcorrect text html latex example
blockDiag text html latex example
bwss text html latex
bwss.matrix text html latex
cbind text html latex example
changelog text html latex
channel2M text html latex example
classifytests-deprecated text html latex
classifytests text html latex example
contrasts.fit text html latex example
controlStatus text html latex example
decideTests text html latex
designMatrix-deprecated text html latex
dim text html latex example
dimnames text html latex
dupcor text html latex example
ebayes text html latex example
exprset2 text html latex
fitfdist text html latex
fitnormexp text html latex example
geneSetTest text html latex example
getSpacing text html latex example
getlayout text html latex example
gls.series text html latex example
gridspotrc text html latex
heatdiagram text html latex example
helpMethods text html latex example
imageplot text html latex example
imageplot3by2 text html latex
intraspotCorrelation text html latex example
isfullrank text html latex example
isnumeric text html latex example
kooperberg text html latex example
limmaguideURL text html latex
lm.series text html latex example
lmFit text html latex
lmscFit text html latex example
loessfit text html latex example
m.spot text html latex
m2logliknormexp text html latex
ma3x3 text html latex example
makeContrasts text html latex example
makeunique text html latex example
malist text html latex
marraylm text html latex
matvec text html latex example
merge text html latex example
modelMatrix text html latex example
modifyWeights text html latex example
normalizeRobustSpline text html latex example
normalizeWithinArrays text html latex example
normalizebetweenarrays text html latex example
normalizeprintorder text html latex example
normalizequantiles text html latex
normalizescale text html latex example
plotDensities text html latex example
plotma text html latex example
plotma3by2 text html latex
plotprinttiploess text html latex
poolvar text html latex example
printHead text html latex
printorder text html latex example
protectMetachar text html latex example
qqt text html latex example
qualwt text html latex example
read.maimages text html latex example
read.matrix text html latex
read.series text html latex
readGPRHeader text html latex
readImaGeneHeader text html latex
readSpotTypes text html latex
readTargets text html latex
readgal text html latex example
removeext text html latex example
rg.genepix text html latex
rg.quantarray text html latex
rg.series.spot text html latex
rg.spot text html latex
rglist text html latex
rlm.series text html latex example
signalnormexp text html latex
splitName text html latex example
squeezeVar text html latex example
subsetting text html latex example
summary text html latex
targetsA2C text html latex example
tmixture text html latex
toptable text html latex example
trigammainverse text html latex example
trimWhiteSpace text html latex example
uniquegenelist text html latex example
unwrapdups text html latex example
venn text html latex example
writefit text html latex
zscore text html latex example
* DONE (limma)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
[1] "Attempting to download marray from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing marray"
* Installing *source* package 'marray' ...
** R
** data
** inst
** save image
[1] TRUE
[1] TRUE
[1] "marrayInfo"
[1] "marrayLayout"
[1] "marrayRaw"
[1] "marrayNorm"
[1] "maLabels"
[1] "maLabels"
[1] "maInfo"
[1] "maInfo"
[1] "maNotes"
[1] "maNotes"
[1] "maNspots"
[1] "maNspots"
[1] "maNgr"
[1] "maNgr"
[1] "maNgc"
[1] "maNgc"
[1] "maNsr"
[1] "maNsr"
[1] "maNsc"
[1] "maNsc"
[1] "maSub"
[1] "maSub"
[1] "maPlate"
[1] "maPlate"
[1] "maControls"
[1] "maControls"
[1] "maNotes"
[1] "maGridRow"
[1] "maGridRow"
[1] "maGridCol"
[1] "maGridCol"
[1] "maSpotRow"
[1] "maSpotRow"
[1] "maSpotCol"
[1] "maSpotCol"
[1] "maPrintTip"
[1] "maPrintTip"
[1] "maRf"
[1] "maRf"
[1] "maGf"
[1] "maGf"
[1] "maRb"
[1] "maRb"
[1] "maGb"
[1] "maGb"
[1] "maW"
[1] "maW"
[1] "maLR"
[1] "maLR"
[1] "maLG"
[1] "maLG"
[1] "maM"
[1] "maM"
[1] "maA"
[1] "maA"
[1] "maLayout"
[1] "maLayout"
[1] "maNspots"
[1] "maNgr"
[1] "maNgc"
[1] "maNsr"
[1] "maNsc"
[1] "maGridRow"
[1] "maGridCol"
[1] "maSpotRow"
[1] "maSpotCol"
[1] "maPrintTip"
[1] "maSub"
[1] "maPlate"
[1] "maControls"
[1] "maNsamples"
[1] "maNsamples"
[1] "maGnames"
[1] "maGnames"
[1] "maTargets"
[1] "maTargets"
[1] "maNotes"
[1] "maA"
[1] "maM"
[1] "maMloc"
[1] "maMloc"
[1] "maMscale"
[1] "maMscale"
[1] "maW"
[1] "maLR"
[1] "maLG"
[1] "maLayout"
[1] "maNspots"
[1] "maNgr"
[1] "maNgc"
[1] "maNsr"
[1] "maNsc"
[1] "maGridRow"
[1] "maGridCol"
[1] "maSpotRow"
[1] "maSpotCol"
[1] "maPrintTip"
[1] "maSub"
[1] "maPlate"
[1] "maControls"
[1] "maNsamples"
[1] "maGnames"
[1] "maTargets"
[1] "maNotes"
[1] "maNormCall"
[1] "maNormCall"
[1] "maLabels<-"
[1] "maLabels<-"
[1] "maLabels<-"
[1] "maInfo<-"
[1] "maInfo<-"
[1] "maNgr<-"
[1] "maNgr<-"
[1] "maNgr<-"
[1] "maNgr<-"
[1] "maNgc<-"
[1] "maNgc<-"
[1] "maNgc<-"
[1] "maNgc<-"
[1] "maNsr<-"
[1] "maNsr<-"
[1] "maNsr<-"
[1] "maNsr<-"
[1] "maNsc<-"
[1] "maNsc<-"
[1] "maNsc<-"
[1] "maNsc<-"
[1] "maNspots<-"
[1] "maNspots<-"
[1] "maNspots<-"
[1] "maNspots<-"
[1] "maSub<-"
[1] "maSub<-"
[1] "maSub<-"
[1] "maSub<-"
[1] "maSub<-"
[1] "maPlate<-"
[1] "maPlate<-"
[1] "maPlate<-"
[1] "maPlate<-"
[1] "maControls<-"
[1] "maControls<-"
[1] "maControls<-"
[1] "maControls<-"
[1] "maLayout<-"
[1] "maLayout<-"
[1] "maLayout<-"
[1] "maGnames<-"
[1] "maGnames<-"
[1] "maGnames<-"
[1] "maTargets<-"
[1] "maTargets<-"
[1] "maTargets<-"
[1] "maW<-"
[1] "maW<-"
[1] "maW<-"
[1] "maGf<-"
[1] "maGf<-"
[1] "maRf<-"
[1] "maRf<-"
[1] "maGb<-"
[1] "maGb<-"
[1] "maGb<-"
[1] "maRb<-"
[1] "maRb<-"
[1] "maRb<-"
[1] "maA<-"
[1] "maA<-"
[1] "maM<-"
[1] "maM<-"
[1] "maMloc<-"
[1] "maMloc<-"
[1] "maMscale<-"
[1] "maMscale<-"
[1] "maNotes<-"
[1] "maNotes<-"
[1] "maNotes<-"
[1] "maNotes<-"
[1] "maNotes<-"
[1] "summary"
[1] "summary"
[1] "summary"
[1] "summary"
[1] "summary"
[1] "ShowLargeObject"
[1] "show"
[1] "["
[1] "["
[1] "["
[1] "["
[1] "boxplot"
[1] "boxplot"
[1] "boxplot"
[1] "image"
[1] "image"
[1] "image"
[1] "points"
[1] "points"
[1] "points"
[1] "text"
[1] "text"
[1] "text"
[1] "lines"
[1] "lines"
[1] "lines"
** help
>>> Building/Updating help pages for package 'marray'
Formats: text html latex example
[-methods text html latex
boxplot text html latex example
cbind text html latex example
coerce-methods text html latex
dim text html latex example
findID text html latex example
htmlPage text html latex example
image text html latex example
ma2D text html latex example
maBoxplot text html latex example
maColorBar text html latex example
maCompCoord text html latex example
maCompInd text html latex example
maCompLayout text html latex example
maCompNormA text html latex example
maCompPlate text html latex example
maCoord2Ind text html latex example
maDefaultPar text html latex example
maDotsDefaults text html latex example
maDotsMatch text html latex example
maGenControls text html latex example
maGeneTable text html latex example
maImage text html latex example
maImage.func text html latex example
maInd2Coord text html latex example
maLegendLines text html latex example
maLoess text html latex example
maLoessLines text html latex example
maMAD text html latex example
maMed text html latex example
maNA text html latex
maNorm text html latex example
maNorm2D text html latex example
maNormLoess text html latex example
maNormMAD text html latex example
maNormMain text html latex example
maNormMed text html latex example
maNormScale text html latex example
maNum2Logic text html latex example
maPalette text html latex example
maPlot text html latex example
maPlot.func text html latex example
maSelectGnames text html latex example
maText text html latex example
maTop text html latex example
maTwoSamples text html latex
mapGeneInfo text html latex example
marray-internal text html latex
marrayInfo-class text html latex example
marrayLayout-class text html latex example
marrayNorm-class text html latex example
marrayRaw-class text html latex example
opVersionID text html latex example
plotMA text html latex example
print-methods text html latex
read.Galfile text html latex example
read.marrayInfo text html latex example
read.marrayLayout text html latex example
read.marrayRaw text html latex example
rm.na text html latex example
showLargeObject text html latex example
stat.confband.text text html latex example
stat.gnames text html latex example
swirl text html latex
write.list text html latex example
write.marray text html latex example
write.xls text html latex example
Warning in load(zfile, envir = envir) : no input is available
* DONE (marray)
[1] "Installation complete"
[1] "Attempting to download vsn from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing vsn"
* Installing *source* package 'vsn' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c vsn.c -o vsn.o
gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
vsn.so vsn.o -lcc_dynamic -framework R
ld: warning multiple definitions of symbol _xerbla_
/Library/Frameworks/R.framework/R(print.lo) definition of _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
_xerbla_
ld: warning multiple definitions of symbol _crc32
/Library/Frameworks/R.framework/R(crc32.lo) definition of _crc32
/usr/lib/libz.1.dylib(crc32.o) definition of _crc32
ld: warning multiple definitions of symbol _get_crc_table
/Library/Frameworks/R.framework/R(crc32.lo) definition of _get_crc_table
/usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
ld: warning multiple definitions of symbol _deflate
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflate
/usr/lib/libz.1.dylib(deflate.o) definition of _deflate
ld: warning multiple definitions of symbol _deflateCopy
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateCopy
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
ld: warning multiple definitions of symbol _deflateReset
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateReset
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
ld: warning multiple definitions of symbol _deflateSetDictionary
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateSetDictionary
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
ld: warning multiple definitions of symbol _deflateInit2_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit2_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
ld: warning multiple definitions of symbol _deflateEnd
/Library/Frameworks/R.framework/R(deflate.lo) definition of _deflateEnd
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
ld: warning multiple definitions of symbol _deflateParams
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateParams
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
ld: warning multiple definitions of symbol _deflateInit_
/Library/Frameworks/R.framework/R(deflate.lo) definition of
_deflateInit_
/usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
ld: warning multiple definitions of symbol _zError
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zError
/usr/lib/libz.1.dylib(zutil.o) definition of _zError
ld: warning multiple definitions of symbol _zlibVersion
/Library/Frameworks/R.framework/R(zutil.lo) definition of _zlibVersion
/usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
ld: warning multiple definitions of symbol _inflateEnd
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateEnd
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
ld: warning multiple definitions of symbol _inflateSync
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflateSync
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
ld: warning multiple definitions of symbol _inflateSyncPoint
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSyncPoint
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
ld: warning multiple definitions of symbol _inflate
/Library/Frameworks/R.framework/R(inflate.lo) definition of _inflate
/usr/lib/libz.1.dylib(inflate.o) definition of _inflate
ld: warning multiple definitions of symbol _inflateSetDictionary
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateSetDictionary
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
ld: warning multiple definitions of symbol _inflateInit2_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit2_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
ld: warning multiple definitions of symbol _inflateReset
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateReset
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
ld: warning multiple definitions of symbol _inflateInit_
/Library/Frameworks/R.framework/R(inflate.lo) definition of
_inflateInit_
/usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
ld: warning multiple definitions of symbol _adler32
/Library/Frameworks/R.framework/R(adler32.lo) definition of _adler32
/usr/lib/libz.1.dylib(adler32.o) definition of _adler32
ld: warning multiple definitions of symbol _BC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _BC
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
ld: warning multiple definitions of symbol _UP
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _UP
/usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
ld: warning multiple definitions of symbol _PC
/Library/Frameworks/R.framework/Versions/2.0.0/Resources/lib/
libreadline.4.3.dylib(terminal.so) definition of _PC
/usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
ld: warning multiple definitions of symbol _gzeof
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzeof
/usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
ld: warning multiple definitions of symbol _gzclose
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzclose
/usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
ld: warning multiple definitions of symbol _gzdopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzdopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
ld: warning multiple definitions of symbol _gzerror
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzerror
/usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
ld: warning multiple definitions of symbol _gzflush
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzflush
/usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
ld: warning multiple definitions of symbol _gzgetc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgetc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
ld: warning multiple definitions of symbol _gzgets
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzgets
/usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
ld: warning multiple definitions of symbol _gzopen
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzopen
/usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
ld: warning multiple definitions of symbol _gzprintf
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzprintf
/usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
ld: warning multiple definitions of symbol _gzputc
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputc
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
ld: warning multiple definitions of symbol _gzputs
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzputs
/usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
ld: warning multiple definitions of symbol _gzread
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzread
/usr/lib/libz.1.dylib(gzio.o) definition of _gzread
ld: warning multiple definitions of symbol _gzrewind
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzrewind
/usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
ld: warning multiple definitions of symbol _gzseek
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzseek
/usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
ld: warning multiple definitions of symbol _gzsetparams
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzsetparams
/usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
ld: warning multiple definitions of symbol _gztell
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gztell
/usr/lib/libz.1.dylib(gzio.o) definition of _gztell
ld: warning multiple definitions of symbol _gzwrite
/Library/Frameworks/R.framework/R(gzio.lo) definition of _gzwrite
/usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
** R
** data
** inst
** save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view,
simply type: openVignette()
For details on reading vignettes, see
the openVignette help page.
** help
>>> Building/Updating help pages for package 'vsn'
Formats: text html latex example
getIntensityMatrix text html latex example
kidney text html latex example
log.na text html latex example
lymphoma text html latex example
meanSdPlot text html latex example
nchoosek text html latex example
normalize.AffyBatch.vsn text html latex example
rowSds text html latex example
sagmbSimulateData text html latex example
sqr text html latex example
vsn text html latex example
vsnPlotPar text html latex example
vsnh text html latex example
* DONE (vsn)
[1] "Installation complete"
[1] "Attempting to download globaltest from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing globaltest"
* Installing *source* package 'globaltest' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "names" in "globaltest"
Creating a new generic function for "names<-" in "globaltest"
Creating a new generic function for "scale" in "globaltest"
Creating a new generic function for "plot" in "globaltest"
** help
>>> Building/Updating help pages for package 'globaltest'
Formats: text html latex example
checkerboard text html latex example
exampleX text html latex
exampleY text html latex
geneplot text html latex example
globaltest text html latex example
gt.barplot-class text html latex
gt.result-class text html latex
permutations text html latex example
regressionplot text html latex example
sampleplot text html latex example
sampling text html latex example
* DONE (globaltest)
[1] "Installation complete"
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: Package SJava not found in any known repository.
[1] "Attempting to download RMAGEML from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing RMAGEML"
gzip: /tmp/Rtmp553/RMAGEML_2.1.0.tar.gz: not in gzip format
ERROR: cannot extract package from '/tmp/Rtmp553/RMAGEML_2.1.0.tar.gz'
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: You did not specify a download type. Using a default value of:
Source
This will be fine for almost all users
Note: Package XML not found in any known repository.
Note: Package annotate not found in any known repository.
[1] "Attempting to download siggenes from
http://www.bioconductor.org/repository/devel/package/Source"
[1] "Download complete."
[1] "Installing siggenes"
gzip: /tmp/Rtmp553/siggenes_1.2.10.tar.gz: not in gzip format
ERROR: cannot extract package from '/tmp/Rtmp553/siggenes_1.2.10.tar.gz'
[1] "Attempting to download pamr from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing pamr"
* Installing *source* package 'pamr' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c cox_func.c -o cox_func.o
g77 -fno-common -g -O2 -c knnimpute.f -o knnimpute.o
make: g77: Command not found
make: *** [knnimpute.o] Error 127
ERROR: compilation failed for package 'pamr'
From URL: http://www.bioconductor.org/repository/devel/package/Source
widgetTools version 1.4.7
DynDoc version 1.4.1
tkWidgets version 1.5.19
Biobase version 1.4.22
affydata version 1.4.0
affy version 1.5.8
affyPLM version 1.2.2
genefilter version 1.4.5
Biostrings version 1.0.0
matchprobes version 1.0.12
multtest version 1.5.2
annaffy version 1.0.11
gcrma version 1.1.1
makecdfenv version 1.4.8
Ruuid version 1.4.5
geneplotter version 1.4.2
edd version 1.4.2
ROC version 1.0.12
marray version 1.5.21
vsn version 1.5.0
globaltest version 3.0.1
RMAGEML version 2.1.0
siggenes version 1.2.10
From URL: http://www.bioconductor.org/data/cdfenvs/repos/
hgu95av2cdf version 1.4.3
hgu133acdf version 1.4.3
hu6800cdf version 1.4.3
From URL: http://www.bioconductor.org/data/metaData-devel/
GO version 1.6.5
KEGG version 1.6.5
hgu95av2 version 1.6.5
rae230a version 1.6.5
hu6800 version 1.6.5
From URL: http://www.bioconductor.org/data/probes/Packages/
hgu95av2probe version 1.0
hu6800probe version 1.0
rae230aprobe version 1.0
From URL: http://www.bioconductor.org//CRANrepository
SparseM version 0.52
xtable version 1.2-4
statmod version 1.1.0
sma version 0.5.14
limma version 1.8.1
pamr version 1.22
From URL: http://www.bioconductor.org/data/experimental/repos/
fibroEset version 1.0
golubEsets version 1.0
Packages that were not updated:
annotate
graph
Rgraphviz
There were 13 warnings (use warnings() to see them)
>
More information about the Bioconductor
mailing list