[BioC] (no subject)

[Michael Benjamin]

Thoughts: 
 
XML installation is tough.  Try manually downloading the package source
.gz for as many versions as you can find, then install that.  Try
installing the R XML package (not just the Bioconductor XML package). 
 
Only the "devel" version of AnnBuilder, I think 1.3.5, installed for me.
 
Good luck,
Michael Benjamin, MD
Emory University
 
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Bronwyn
Carlisle
Sent: Tuesday, December 09, 2003 9:54 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] (no subject)
 
Hi, I've been trying to install a number of Bioconductor packages and
keep getting error messages. Can someone tell me a)what I'm doing wrong,
b)How to fix it. I'm using a Mac G4 and OS X 10.3, on which I have
installed RAqua. As I only installed it and the base Bioconductor
package yesterday I am assuming I have the latest Bioc.R thing - can't
figure out how to get it if not. On base install, XML and MAGEML did not
install properly.

Example of me trying to install the database package :
> getBioC(libName="database", relLevel="release", getAllDeps=TRUE)
Running getBioC version 1.2.46....
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:~/Library/RAqua/library 
2:/Applications/StartR.app/RAqua.app/Contents/library 
Selection: 2

Synching your local package management information ...
Packages which have been removed:
XML
MAGEML


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 XML from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing XML"
Warning message: 
Installation of package XML had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
[1] "Attempting to download AnnBuilder from
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing AnnBuilder"
Warning message: 
Installation of package AnnBuilder had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
[1] "Attempting to download SAGElyzer from
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing SAGElyzer"
[1] "Installation complete"
[1] "Attempting to download Rdbi from
http://www.bioconductor.org//CRANrepository"
[1] "Download complete."
[1] "Installing Rdbi"
[1] "Installation complete"
[1] "Attempting to download RdbiPgSQL from
http://www.bioconductor.org/repository/release1.3/package/Source"
[1] "Download complete."
[1] "Installing RdbiPgSQL"
Warning message: 
Installation of package RdbiPgSQL had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 
>From URL: http://www.bioconductor.org//CRANrepository
XML version 0.95-4
Rdbi version 0.1-2

>From URL:
http://www.bioconductor.org/repository/release1.3/package/Source
AnnBuilder version 1.3.3
SAGElyzer version 1.3.0
RdbiPgSQL version 1.0.2

Bronwyn Carlisle
Biochemistry Department
University of Otago
Dunedin
New Zealand

Tel 64 3 479 7704

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