[Bioc-devel] affxparser: Core dump with R 2.14.x on OSX [take #2]

[Dan Tenenbaum]

On Fri, Jan 20, 2012 at 1:44 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> Hi Henrik,
>
>
> On Fri, Jan 20, 2012 at 10:33 AM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
>> Hi,
>>
>> this is a kind request for the BioC team to have another look at
>> fixing the binary affxparser builds.  Quite a few OSX users on R
>> v2.14.0 have R crashing because of this problem.
>
> Thanks for the prompt and the detailed problem report.
>
>
>>
>> Since thread 'Re: [Bioc-devel] affxparser: Core dump with R 2.14.0 on
>> OSX' on Nov 7, 2011
>> [https://stat.ethz.ch/pipermail/bioc-devel/2011-November/002969.html]
>> became cluttered with mistakes, I'm starting a new thread on the same
>> topic.
>>
>> PROBLEM:
>> The binary build of affxparser v1.26.2 for OSX provided by
>> Bioconductor is broken and causes R v2.14.0 to crash ("core dump",
>> "abort trap", ...) on OSX 10.6 ("Snow Leopard") and (I assume; someone
>> please confirm) OSX 10.7 ("Lion"),
>
> I can confirm that it happens on Lion too.
>
>> but not OSX 10.5 ("Leopard").  A
>> reproducible example is:
>>
>> library("affxparser");
>> readCdfHeader("Mapping10K_Xba142.cdf");
>>
>> which should return a named header. (Download CDF file:
>> http://www.aroma-project.org/data/annotationData/chipTypes/Mapping10K_Xba142/Mapping10K_Xba142.CDF.gz
>> ; 2.2Mb).  Another example is
>> [http://www.aroma-project.org/data/annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf.gz]:
>>
>> library("affxparser");
>> readCdfHeader("Mapping250K_Nsp.cdf");
>>
>>
>> CURRENT WORKAROUNDS:
>> - Install affxparser from source
>> [http://bioconductor.org/packages/2.9/bioc/src/contrib/affxparser_1.26.2.tar.gz].
>> - Install Kasper Hansen's binary build (not universal?)
>> [http://www.braju.com/R/repos/osx_10.6/affxparser_1.26.2.tgz] that
>> works on (at least) OSX 10.6.8.
>>
>> See also aroma.affymetrix thread 'OSX 10.6 & 10.7 users: Workaround
>> for faulty BioC build of affxparser v1.26.2' on Jan 14, 2012
>> [https://groups.google.com/forum/#!topic/aroma-affymetrix/lEfDanThLEA/discussion]
>>
>>
>> TROUBLESHOOTING:
>> I can confirm that installing from source, works on an OSX 10.6.8
>> machine with R v2.14.1
>> (http://cran.r-project.org/bin/macosx/R-2.14.1.pkg).  Installing
>> Kasper's binary build also works.  I've a limited understanding on the
>> different types of OSX package binaries, only access to OSX 10.6.8,
>> making it hard for me to do any more troubleshooting, but as far as I
>> understand there is something wrong with the way affxparser is build
>> on the Bioconductor servers.
>>
>
>
> An important fact to bear in mind is that the BioC Mac build servers
> are running Leopard (OS X 10.5.8).
>
> It's a bit tricky to debug since it works fine on the platform it's
> built on...but using primitive means (Rprintf() statements), I was
> able to narrow down the problem to the
> FileHeaderReader::ReadMagicNumber()
> function in
> affxparser/src/fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp
>
> In that function, the expression
> if (fileMagicNumber != DATA_FILE_MAGIC_NUMBER)
> evaluates to true, and therefore an
> affymetrix_calvin_exceptions::InvalidFileTypeException is thrown.
>
> I don't really know why the magic number is wrong, or would vary
> between operating systems, but perhaps this gives you something to go
> on?
>
> BTW, the trace is:
> R: readCdfHeader()
> C++:
> R_affx_get_cdf_file_header()
> FusionCDFData::ReadHeader()
> FusionCDFData::CreateObject()
> FusionCDFData::IsCalvinCompatibleFile()
> GenericFileReader::ReadFileHeaderNoDataGroupHeader()
> FileHeaderReader::Read()
> FileHeaderReader::ReadMagicNumber()
>
> Hope this helps. If I can be of assistance in further debugging this,
> please let me know.

I should also have mentioned that in the ReadMagicNumber() function,
fileMagicNumber == 67
with the file Mapping10K_Xba142.cdf, and the expected magic number is 59.

Dan

> Thanks,
> Dan
>
>
>> Thanks
>>
>> Henrik
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel