Dear Charles There are a few bugs in the install script at the moment (re: XML, tcl8.3). I am sure they will be fixed very soon, but I have written up a short how to install bioconductor in the meantime. This file is attached. Aedin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of John Zhang Sent: 28 March 2003 15:46 To: Charles.White@NA.AMEDD.ARMY.MIL; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] getBioC v1.2.22 & [R] v1.6.2 >The first script failure occurred when attempting to download the XML >package. At that point, I used the R package installation function to >install XML and the script executed for a few more packages. The second >script failure occurred when attempting to download the RPgSQL package. >Maybe I don't know what I'm doing but I can't find that package on CRAN. >Help completing the Bioconductor install would be appreciated. I'd like to >get the software up and running before attending the class at ENAR on >Sunday. Thanks. RPgSQL is available through CRAN-Package Sources - Devel. > > > >Charles E. White, Biostatistician > >Walter Reed Army Institute of Research > >503 Robert Grant Ave., Room 1w102 > >Silver Spring, MD 20910-1557 > >301 319-9781 > >WRAIR Home Page: http://wrair-www.army.mil/ > > > >PS: The error log follows: > > > >getBioC(libName = "all") > >Running getBioC version 1.2.22.... > >If you encounter problems, first make sure that > >you are running the latest version of getBioC() > >which can be found at: www.bioconductor.org/getBioC.R > > > >Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. > > > >[1] "Getting/installing packages reposTools and Biobase" > >Loading required package: Biobase > >Welcome to Bioconductor > > To view some introductory material -- look at our vignettes > > Simply type: openVignette() > > to see the available vignettes > > To read a vignette see the openVignette help page for details > >Creating a new generic function for "summary" in package > >Biobase > > > >Attaching package `Biobase': > > > > > > The following object(s) are masked from package:base : > > > > split summary > > > >Package affy version 1.1.1 requires package tkWidgets, would you like to try >to install this package? [yes/no] y > >y is not a valid response, try again. > >Package affy version 1.1.1 requires package tkWidgets, would you like to try >to install this package? [yes/no] yes > >Note: No specified download type, defaulting to Win32 > >[1] "Attempting to download tkWidgets from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing tkWidgets" > >[1] "Installation complete" > >[1] "Attempting to download affy from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing affy" > >[1] "Installation complete" > >Package AnnBuilder version 1.0.2 requires package XML, would you like to try >to install this package? [yes/no] yes > >Note: No specified download type, defaulting to Win32 > >[1] "Attempting to download XML from >http://www.bioconductor.org//CRANrepository" > >[1] "Download complete." > >[1] "Installing XML" > >Error in paste(out, ", installing anyway.\n") : > > Object "out" not found > >> {a <- CRAN.packages() > >+ install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a)} > >trying URL `http://cran.r-project.org/bin/windows/contrib/PACKAGES' > >Content type `text/plain; charset=iso-8859-1' length 9475 bytes > >opened URL > >downloaded 9475 bytes > > > >trying URL `http://cran.r-project.org/bin/windows/contrib/XML.zip' > >Content type `application/zip' length 927911 bytes > >opened URL > >downloaded 906Kb > > > > > >Delete downloaded files (y/N)? y > > > >updating HTML package descriptions > >> getBioC(libName = "all") > >Running getBioC version 1.2.22.... > >If you encounter problems, first make sure that > >you are running the latest version of getBioC() > >which can be found at: www.bioconductor.org/getBioC.R > > > >Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. > > > >[1] "Getting/installing packages reposTools and Biobase" > >Package AnnBuilder version 1.0.2 requires package RPgSQL, would you like to >try to install this package? [yes/no] yes > >Note: No specified download type, defaulting to Win32 > >Package AnnBuilder version 1.0.2 requires package annotate, would you like >to try to install this package? [yes/no] yes > >Note: No specified download type, defaulting to Win32 > >Note: http://www.bioconductor.org/repository/release1.1/package/Source does >not seem to have a valid repository, skipping > >[1] "Attempting to download annotate from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing annotate" > >[1] "Installation complete" > >[1] "Attempting to download edd from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing edd" > >[1] "Installation complete" > >[1] "Attempting to download genefilter from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing genefilter" > >[1] "Installation complete" > >[1] "Attempting to download geneplotter from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing geneplotter" > >[1] "Installation complete" > >[1] "Attempting to download graph from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing graph" > >[1] "Installation complete" > >[1] "Attempting to download hexbin from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing hexbin" > >[1] "Installation complete" > >[1] "Attempting to download marrayClasses from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing marrayClasses" > >[1] "Installation complete" > >[1] "Attempting to download marrayInput from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing marrayInput" > >[1] "Installation complete" > >[1] "Attempting to download marrayNorm from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing marrayNorm" > >[1] "Installation complete" > >[1] "Attempting to download marrayPlots from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing marrayPlots" > >[1] "Installation complete" > >[1] "Attempting to download marrayTools from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing marrayTools" > >[1] "Installation complete" > >[1] "Attempting to download multtest from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing multtest" > >[1] "Installation complete" > >[1] "Attempting to download rhdf5 from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing rhdf5" > >[1] "Installation complete" > >[1] "Attempting to download ROC from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing ROC" > >[1] "Installation complete" > >[1] "Attempting to download vsn from >http://www.bioconductor.org/repository/release1.1/package/Win32" > >[1] "Download complete." > >[1] "Installing vsn" > >[1] "Installation complete" > >>From URL: http://www.bioconductor.org/repository/release1.1/package/Win32 > > annotate version 1.0.5 > > edd version 1.0 > > genefilter version 1.0.2 > > geneplotter version 1.0 > > graph version 1.0 > > hexbin version 1.0 > > marrayClasses version 1.1 > > marrayInput version 1.1 > > marrayNorm version 1.1.1 > > marrayPlots version 1.1.2 > > marrayTools version 1.0.4 > > multtest version 1.0 > > rhdf5 version 1.0.1 > > ROC version 1.0.1 > > vsn version 1.0.0 > > > >Packages that were not updated: > > affy > > AnnBuilder > > Biobase > > reposTools > > tkWidgets > > > >Warning message: > > > > Package AnnBuilder version 1.0.2 requires package RPgSQL > > in: resolve.depends(pkgInfo, repEntry, force, searchOptions = >searchOptions, > >> {a <- CRAN.packages() > >+ install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a)} > >trying URL `http://cran.r-project.org/bin/windows/contrib/PACKAGES' > >Content type `text/plain; charset=iso-8859-1' length 9475 bytes > >opened URL > >downloaded 9475 bytes > > > >> {a <- CRAN.packages() > >+ install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a)} > >trying URL `http://cran.r-project.org/bin/windows/contrib/PACKAGES' > >Content type `text/plain; charset=iso-8859-1' length 9475 bytes > >opened URL > >downloaded 9475 bytes > > > >> > > > [[alternate HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------- next part -------------- A non-text attachment was scrubbed... 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> I apologize if I am missing something really obvious but I have looked at > four U.S. mirror sites under package sources and I do not see this package. > Where do I look? Thanks. There is no Windows version of this package, but it is not necessary for the Windows version of AnnBuilder to properly function. As of the very latest version of getBioC (just put on the site a few minutes ago) - 1.2.23, you can now specify the option "force=TRUE", and it will download packages even if all dependencies are not met. -J