All, I'm using R 1.9.0 in Win2000 with a fresh install of R and Bioconductor via getBioC. When I run the help file example for pm.getabst: library(annotate) library(hgu95av2) hoxa9 <- "37809_at" absts <- pm.getabst(hoxa9, "hgu95av2") it runs for a minute, then either stops R or indefinitely hangs (depending on which computer I use). I haven't seen any error messages. I have also make sure that I've started R using the --internet2 option. Any thoughts? Thanks, Max ----------------------------------------- This message is intended only for the designated recipient(s...{{dropped}}

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@jimmy.h| |="" |="" arvard.edu=""> | | | | | | 07/23/2004 09:18 | | | AM | | | | |---------+----------------------------> >------------------------------------------------------------------- --------------------------------------------| | | | To: Max_Kuhn@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 +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+ ----------------------------------------- This message is intended only for the designated recipient(s...{{dropped}}