[BioC] parseGEO stack at first.entity <- findFirstEntity(con)

[rcaloger]

Hi,
I am using quite a lot the GEOquery libray.
Recently I found out that the link to the GSE repository changed on GEO 
therefore the getGEOfile function fails to download the file.Since there 
is not the possibility to change the download path in the getGEOfile it 
will be nice if the mantainers of GEOquery could add a parameter to the 
function to allow it.

Therefore, actually I am downloading locally the GSEXXX_family.soft.gz
and I use the parseGEO function to reformat the GSE data.
Yesterday, I tryed to parse the GSE3294_family.soft.gz:
library(GEOquery)
gse3294<-parseGEO("GSE3294_family.soft.gz")
since after few hours nothing came out. I debugged the function and find out that  
the function freeze at the first line.
first.entity <- findFirstEntity(con)

The problem was encoutered with GEOquery 1.6.0, running Bioconductor 1.8 on 
windowXP centrino 2GHz, 1.5GB RAM on the GSE3294
Cheers
Raf

-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705420
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Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
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