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

Dan Tenenbaum dtenenba at fhcrc.org
Tue Nov 8 21:31:19 CET 2011 

On Tue, Nov 8, 2011 at 12:21 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> Reading Dan's error I realize I did something else: he points to the zip archive
>  pathname <- "~/Downloads/250k_nsp_libraryfile_rev4.zip"
> whereas I unzip the archive, and point it directly to the cdf file
> inside some subdirectory of the unpacked zip file.
>
> We do not expect that readCdfHeader on a zip archive works.  We are
> aware that reading "wrong" files may lead to a core dump which is
> rather bad and we should try to fix this.

Seems like there is stil a problem on Lion.
I unzipped the zip file and then:

> hdr <- readCdfHeader("CD_Mapping250K_Nsp_rev4/Full/Mapping250K_Nsp/LibFiles/Mapping250K_Nsp.cdf")
Abort trap: 6

It works on Leopard, though.

Dan

>
> Kasper
>
>
> On Tue, Nov 8, 2011 at 3:04 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> 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.
>>>
>>> [...]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>

More information about the Bioc-devel mailing list