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

[Henrik Bengtsson]

Hi,

over at the aroma.affymetrix mailing list, a user (cc:ed) reports that
affxparser v1.26.1 core dumps when trying to read a CDF file.  I'm
moving it to BioC-devel, and asks if others can reproduce this.  I
don't have access to R v2.14.0 on OSX.  It does not core dump on
Windows 7 with the same setup and versions.  The OP says he got the
problems after updated to R v2.14.0.  The CDF file
(Mapping250K_Nsp.cdf) is available in (34Mb download after login):

  http://www.affymetrix.com/Auth/support/downloads/library_files/250k_nsp_libraryfile_rev4.zip

More details below.

BTW, Peter, could you please check if you have issues with any other
CDF files, such as the Mapping10K_Xba142.cdf?

/Henrik

On Mon, Nov 7, 2011 at 2:27 PM, Peter Kang wrote:
> 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.

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