[BioC] problems with pm.getabst

[Max_Kuhn at bd.com]

Robert,

Thanks for the reply. The internet connection was my first thought. The
fresh install I did after first noticing the problem was done through R via
install.packages and getBioC, so I'd be surprised if that's the issue (but
this is windows...). Without using the --internet2 flag, install.packaes
will fail with a message, but this seams like different behavior.

I don't usually hit NCBI databases and I can get to web pages via output
from other annotation functions.

Also, I did not get to the point where R prints that the XML package was
loaded. Given this, I just put a browser() into pubmed and it seems to
crash when

   return(.handleXML(query))

is executed. Given this, I'll cc the list on this message.

Max





|---------+---------------------------->
|         |           Robert Gentleman |
|         |           <rgentlem at jimmy.h|
|         |           arvard.edu>      |
|         |                            |
|         |           07/23/2004 09:18 |
|         |           AM               |
|         |                            |
|---------+---------------------------->
  >---------------------------------------------------------------------------------------------------------------|
  |                                                                                                               |
  |        To:      Max_Kuhn at bd.com                                                                               |
  |        cc:                                                                                                    |
  |        Subject: Re: [BioC] problems with pm.getabst                                                           |
  >---------------------------------------------------------------------------------------------------------------|




With a slightly newer version of all, I get:
>    absts <- pm.getabst(hoxa9, "hgu95av2")
Loading required package: XML
> absts
$"37809_at"
$"37809_at"[[1]]
An object of class 'pubMedAbst':
Title:   Aberrant expression of HOXA9, DEK, CBL and CSF1R in acute
myeloid leukemia.
PMID:    14738146
Authors: S Casas, B Nagy, E Elonen, A Avent
On, ML Larramendy, J Sierra, T Ruutu, S Knuutila
Journal: Leuk Lymphoma
Date:    Nov 2003


Are you sure you have an internet connection at all?
you could try downloading a package using install.packages to see.
Also, and if so, you may not be able to get stuff from NCBI - they do
ban IPs if they get too many requests

but I am reasonably sure your problems are due to internet
 connectivity (and you if fresh installing let me suggest a more
 recent version of R - I think 1.9.1 is the latest stable)
Robert

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| Robert Gentleman                 phone : (617) 632-5250
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| Associate Professor              fax:   (617)  632-2444
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| Department of Biostatistics      office: M1B20
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