[BioC] problems intalling bioconductor on windows NT

[Justin Borevitz]

I had this problem last night and this morning but I just tried again and
its working now.

You can run in R

install.packages("Biobase",CRAN=getOption("BIOC"))

install.packages("genefilter",CRAN=getOption("BIOC"))

those were the ones that initially failed for me.

Justin


http://naturalvariation.org 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of martino barenco
Sent: Wednesday, June 18, 2003 3:12 AM
To: jgentry at jimmy.harvard.edu; jmacdon at med.umich.edu
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] problems intalling bioconductor on windows NT

 

I updated to R 1.7.1 and it now works better in the sense that something
gets downloaded. However, there are still some problems:

when I type 

>getBioC(libName = "exprs") (or libName= <mailto:libName=@all> "all")

I get:

Running getBioC version 1.2.34....
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] "Installing reposTools ..."

Synching your local package management information ...
Package Biobase version 1.3.22 requires package genefilter, would you like
to try to install this package? [yes/no] yes
Note: No specified download type, defaulting to Win32 
Note: Package genefilter not found in any known repository. 
[1] "Attempting to download Biobase from
http://www.bioconductor.org/repository/release1.2/package/Win32"
[1] "Download complete."
[1] "Installing Biobase"
Note: Running R version 1.7.1 and package Biobase was built for R version
1.7.0
 , installing anyway.
 
[1] "Installation complete"
>From URL:  http://www.bioconductor.org/repository/release1.2/package/Win32
        Biobase version 1.3.22

Packages that were not updated:
        annotate
        geneplotter
        edd
        ROC
        multtest
        tkWidgets
        widgetTools

So, it seems that Biobase is not installed because genefilter can not be
found. Indeed, when I type:

>library(affy)
I get:

Error in checkPkgDeps(pkgname) : You can not load package Biobase as
it requires you to have package genefilter which is not currently installed.
Error in checkPkgDeps(pkgname) : You can not load package Biobase as
it requires you to have package genefilter which is not currently installed.
Error in getClass(Class) : "MIAME" is not a defined class
Error in library(affy) : .First.lib failed

Thank you very much for your precious help.

Martino

CoMPLEX-University College London

>From: Jeff Gentry 

>To: James MacDonald 

>CC: m_barenco at hotmail.com, bioconductor at stat.math.ethz.ch 

>Subject: Re: [BioC] problems intalling bioconductor on windows NT 

>Date: Mon, 16 Jun 2003 11:29:48 -0400 (EDT) 

> 

> > I believe you need R 1.7.1beta because there are some bugs in 1.7.0 

> > http://www.stats.uwo.ca/faculty/murdoch/software/r-devel/rw1071beta.exe 

> 

>Actually, R-1.7.1 was released today so should be available from CRAN. 

> 

> > bioconductor at stat.math.ethz.ch. 

> > [1] "Installing reposTools ..." 

> > Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : 

> > Failed to install package reposTools 

> > In addition: Warning messages: 

> > 1: downloaded length 932996 != reported length 5348600 

> > 2: error 1 in extracting from zip file 

> 

>I have no idea what is going on here, but it looks to me like perhaps the 

>download failed halfway through (the zip file on the server is indeed 

>5.3MB but the user didn't even get 1MB?) 

> 

>-J 

> 


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