[Bioc-devel] affxparser: Core dump with R 2.14.0 on OSX

Henrik,
Thanks for your advice. This is what I get:

library("affxparser");
library("digest");

pathname <-
"annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf";
fi <- file.info (pathname);
rownames(fi) <- NULL;
print(fi);

? ? ? ?size isdir mode ? ? ? ? ? ? ? mtime ? ? ? ? ? ? ? ctime
1 194455495 FALSE ?755 2005-08-24 16:01:42 2011-11-07 09:53:41
? ? ? ? ? ? ? ? atime uid gid ?uname grname
1 2011-11-07 11:47:58 503 ?20 hpkang ?staff

print(digest(file=pathname));

[1] "59ae263311a2cf63b8d1b9b4cc7d663b"

print(sessionInfo());

R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
other attached packages:
[1] digest_0.5.1 ? ? ?affxparser_1.26.1

hdr <- readCdfHeader(pathname);

zsh: abort (core dumped) ?R

On Mon, Nov 7, 2011 at 12:35 PM, Henrik Bengtsson wrote:

Hi,

you can still do sessionInfo() just before you call the core-dumping
method; sessionInfo() is so key to solving problems, especially core
dumps so we cannot be without them. ?What do you get when you do:

library("affxparser");
library("digest");

pathname <-
"annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf";
fi <- file.info(pathname);
rownames(fi) <- NULL;
print(fi);
print(digest(file=pathname));

print(sessionInfo());
hdr <- readCdfHeader(pathname);
str(hdr);

Also, if you get some core dump messages, what are they?

After you reply here, I'm most likely going to move this to the
Bioconductor devel mailing list, because that is most likely where the
real help will come from.

/Henrik

On Mon, Nov 7, 2011 at 11:54 AM, Peter Kang wrote:

Sorry, I couldn't do sessionInfo() or traceback() because of the core
dump.
The core dump was with all of the latest packages in R 2.14.0. The funny
thing is it worked perfectly well before I upgraded R and reinstalled
aroma.
I tried Henrik's suggestion, and get the 'core dumped' error after
hdr <- readCdfHeader(pathname);
I also redownloaded the cdf files from the Affy website, no difference.
Thank you.

On Mon, Nov 7, 2011 at 11:19 AM, Henrik Bengtsson
<henrik.bengtsson at aroma-project.org> wrote:

On Mon, Nov 7, 2011 at 9:35 AM, Pierre Neuvial wrote:

What is your sessionInfo() ?

Perhaps you need to upgrade aroma.affymetrix instead, although I
don't
see why you would get this core dump.

Yes, sessionInfo() and showing that you've tried with the latest
version speeds up troubleshooting and response time.

I the past, basically all core dumps have been attributed to the
affxparser package *and* almost all of those have been due to corrupt
Affymetrix files. ? I suspect that affxparser is the player here to,
and maybe even a corrupt file. ?So, in a fresh R session try with:

library("affxparser");
pathname <-
"annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf";
hdr <- readCdfHeader(pathname);
str(hdr);
cdfList <- readCdf(pathname);
str(cdfList);

Core dump?

/Henrik

Pierre

On Mon, Nov 7, 2011 at 6:20 PM, Peter Kang wrote:

I just upgraded to 2.14.0 (Mac OSX), and I'm getting a 'core dumped'
error when trying to access the cdf file.

cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
print(cdf)

zsh: abort (core dumped) ?R

Do I need to downgrade R?

Thank you.