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

[Dan Tenenbaum]

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.
Thanks,
Dan


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