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

Fri Mar 28 10:21:53 MET 2003

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.

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]]