[BioC] affylmGUI segfault on "pd.ragene.1.0.st.v1"

Harry Mangalam harry.mangalam at uci.edu
Tue Jan 6 00:45:49 CET 2009

Hi All,

I've been trying to get affylmGUI to run on my laptop (3GB, Ubuntu 
8.04, R as below:
> sessionInfo()
R version 2.8.0 (2008-10-20)


attached base packages:
[1] tools     tcltk     stats     graphics  grDevices utils     
[8] methods   base

other attached packages:
[1] affylmGUI_1.16.0     affy_1.16.0          preprocessCore_1.0.0
[4] affyio_1.6.1         Biobase_2.2.1        limma_2.16.3
The commands to start affylmGUI are:
library("pd.ragene.1.0.st.v1") # the array set, from Matt Settles

when I try to load data, whether my own (or the estrogen data set), it 
segfaults at the same place:
After I select a working directory, and select the targets file 
(included below), [R churns for a few seconds], and give the new data 
set a name, I can see that the data is 'available' via the data tree 
in the left panel.

At the point where I try to view the RNA targets via Menu -> RNA 
Targets -> RNA Targets, and release the mouse button, it segfaults, 
leaving the traceback:


As I said above, this is the case if it's my data or the estrogen data 

If I try to bypass that step and go direct to normalization (with my 
data), it will eventually emit the error that I don't have the 
correct CDF environment:

==== Error message ====
Error in getCdfInfo(object): Could not obtain CDF environment, 
problems encountered: Specified environment does not contain 
RaGene-1_0-st-v1 Library - package ragene10stv1cdf not installed. 
Data for package affy did not contain ragene10stv1cdf Bioconductor - 
ragene10stv1cdf not available

This despite loading without error the correct (from Matt Settles) 
library beforehand. > library("pd.ragene.1.0.st.v1")
Does the spelling variant muck it up?  

Best wishes,

==== targets.txt (whitespaces are TABS) ====

Name    FileName        Target
AB.1    0908F-02_AB_1.CEL       AB_Only
AB.2    0908F-02_AB_2.CEL       AB_Only
AB.3    0908F-02_AB_3.CEL       AB_Only
CIQ.1   0908F-02_CIQ_1.CEL      CIQ_Only
CIQ.2   0908F-02_CIQ_2.CEL      CIQ_Only
CIQ.3   0908F-02_CIQ_3.CEL      CIQ_Only
CIQ+AB.1        0908F-02_CIQ_AB_1.CEL   CIQ_AB_CoTreatment
CIQ+AB.2        0908F-02_CIQ_AB_2.CEL   CIQ_AB_CoTreatment
CIQ+AB.3        0908F-02_CIQ_AB_3.CEL   CIQ_AB_CoTreatment
Untreated.1     0908F-02_Untreated_1.CEL        CONTROL
Untreated.2     0908F-02_Untreated_2.CEL        CONTROL
Untreated.3     0908F-02_Untreated_3.CEL        CONTROL

Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, 
UC Irvine 92697  949 824-0084(o), 949 285-4487(c)
Good judgment comes from experience; 
Experience comes from bad judgment. [F. Brooks.]

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