[Bioc-devel] affxparser: Core dump with R 2.14.x on OSX [take #2]
dtenenba at fhcrc.org
Fri Jan 20 22:44:02 CET 2012
On Fri, Jan 20, 2012 at 10:33 AM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote:
> 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
> became cluttered with mistakes, I'm starting a new thread on the same
> 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:
> which should return a named header. (Download CDF file:
> ; 2.2Mb). Another example is
> CURRENT WORKAROUNDS:
> - Install affxparser from source
> - 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
> 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
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
BTW, the trace is:
Hope this helps. If I can be of assistance in further debugging this,
please let me know.
> Bioc-devel at r-project.org mailing list
More information about the Bioc-devel