[BioC] GEOquery and parsing SOFT files

[Wacek Kusnierczyk]

Wolfgang Huber wrote:
>
> Dear Wacek,
>
> thank you for the feedback and pointing this out. Two general remarks:

thank you for the response.

>
> 1. Please include a reproducible example (R script) for others to
> reproduce your experience, and subsequently the output of sessionInfo().

a reproducible (on my machine, at least) example is as follows:

    library(GEOquery)
    repeat {
       filename = getGEOfile('GSE13638')
       if (!is.null(filename)) break }
    system.time({gse13638 = getGEO(filename=filename)})
    # elapsed: 620

(so it was 'faster' this time, only 10 minutes...)

session info is as follows:

R version 2.10.0 Under development (unstable) (2009-05-25 r48607)
i686-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8   
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8  
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] GEOquery_2.9.0 RCurl_0.94-1   Biobase_2.5.2



>
> 2. Robert Gentleman's book "R Programming for Bioinformatics" (as well
> as many free sources on the web) describes how to profile R code in
> order to see in which functions the CPU time is spent. Based on this,
> you can investigate where to invest developer time for improving the
> code.

yes, i know;  but i thought someone could already have done this or have
a hint anyway, as this does not seem likely to be just my local
problem.  before i spend too much time on a potentially well-known
issue, it's surely fine to ask others, including the developer.

best regards,
vQ