[BioC] installation in MacOSX

[James MacDonald]

What version of BioC are you using? Those errors look like what you get if you are running R > 1.8.0 with BioC < 1.3. Did you use getBioC()?

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Edmundo Rodríguez <edmundo.rodriguez at ucr.edu> 12/12/03 02:52PM >>>
I am trying to install bioconductor in a R version for Mac os X.
It seems as been installed, but when i try to run Affy package i get:

 > library(affy)
Welcome to Bioconductor
	 Vignettes contain introductory material.  To view,
	 simply type: openVignette()
	 For details on reading vignettes, see
	 the openVignette help page.

Synching your local package management information ...
Error in file(file, "wb") : unable to open connection
In addition: Warning message:
cannot open file 
`/Applications/StartR.app/RAqua.app/Contents/library/liblisting.Rda'
Error in f(libname, pkgname) : Package reposTools required
In addition: Warning message:
package:reposTools is required by package:affy (still attached) in: 
detach(name = "package:reposTools")

Synching your local package management information ...
Warning message:
package:Biobase is required by package:affy (still attached) in: 
detach(name = "package:Biobase")
Error in file(file, "wb") : unable to open connection
In addition: Warning message:
cannot open file 
`/Applications/StartR.app/RAqua.app/Contents/library/liblisting.Rda'
Warning message:
package:reposTools is required by package:affy (still attached) in: 
detach(name = "package:reposTools")
 >

 > Data <- ReadAffy(widget=TRUE)
Loading required package: tkWidgets
Attaching package 'DynDoc':


	The following object(s) are masked from package:base :

	 vignette

Loading required package: tcltk
Error in fun(...) : this isn't a Tk applicationcouldn't connect to 
display ":0"
Error in runHook(".onLoad", env, package.lib, package) :
	.onLoad failed
Error in f(libname, pkgname) : Package tcltk not able to be loaded!
Error in fileBrowser(textToShow = "Choose CEL files", testFun = 
hasSuffix("[cC][eE][lL]")) :
	couldn't find function "tktoplevel"
In addition: Warning message:
package:widgetTools is required by package:tkWidgets (still attached) 
in: detach(name = "package:widgetTools")
Error in end() : couldn't find function "tkdestroy"
 >

Would somebody like to explain me what is wrong?
Sorry i am boring you with sure is a naive question, but i am new in R 
and bioconductor

Thanks

Edmundo R

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