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

[Henrik Bengtsson]

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.

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"), 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.

Thanks

Henrik