[BioC] getBioC v1.2.22 & [R] v1.6.2

Fri Mar 28 16:46:45 MET 2003

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 at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of John Zhang
Sent: 28 March 2003 15:46
To: Charles.White at NA.AMEDD.ARMY.MIL; bioconductor at 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 at 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 at 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 at 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

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