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

Dan Tenenbaum dtenenba at fhcrc.org
Tue Nov 8 21:04:16 CET 2011 

Hi Henrik,

On Mon, Nov 7, 2011 at 2:41 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
> 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
>

I am able to reproduce the problem:

> library(digest)
> library(affxparser)
> pathname <- "~/Downloads/250k_nsp_libraryfile_rev4.zip"
> fi <- file.info(pathname)
> rownames(fi) <- NULL
> print(fi)
      size isdir mode               mtime               ctime
1 45043262 FALSE  644 2011-11-08 11:48:45 2011-11-08 11:48:45
                atime uid gid    uname grname
1 2011-11-08 11:54:09 502  20 dtenenba  staff
> print(digest(file=pathname))
[1] "cf10a53b36108315542276875d43c24a"
> 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] affxparser_1.26.1   digest_0.5.1        BiocInstaller_1.2.0

loaded via a namespace (and not attached):
[1] tools_2.14.0
> hdr <- readCdfHeader(pathname)
Abort trap: 6

It happens in 32-bit R as well.

That's on a Lion machine. On Leopard, I get a different error:

> library(affxparser)
> pathname <- "~/Downloads/250k_nsp_libraryfile_rev4.zip"
> hdr <- readCdfHeader(pathname)
Failed to read the CDF file header for:
/Users/biocbuild/Downloads/250k_nsp_libraryfile_rev4.zip
Error in basename(res$chiptype) : a character vector argument expected
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII

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

other attached packages:
[1] affxparser_1.26.1   BiocInstaller_1.2.0

loaded via a namespace (and not attached):
[1] tools_2.14.0
> library(digest)
> fi <- file.info(pathname)
> rownames(fi) <- NULL
> fi
      size isdir mode               mtime               ctime
1 45043262 FALSE  644 2011-11-08 11:58:53 2011-11-08 11:58:53
                atime uid gid     uname grname
1 2011-11-08 12:01:17 502  20 biocbuild  staff
> digest(file=pathname)
[1] "cf10a53b36108315542276875d43c24a"


Dan



> 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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