OSX 10.6 & 10.7 users: Workaround for faulty BioC build of affxparser v1.26.2

[Henrik Bengtsson]

Hi, this message only applies users of OSX 10.6 ("Snow Leopard") or
OSX 10.7 ("Lion") running R v2.14.0 or newer.

It has been reported that if one (i) on R v2.14.0, (ii) on OSX 10.6 or
10.7, (iii) install the *binary* build of affxparser v1.26.2 by
Bioconductor, then affxparser causes R to crash completely:

https://stat.ethz.ch/pipermail/bioc-devel/2011-November/002969.html

Kasper Hansen has provided a binary build of affxparser v1.26.2 for
OSX 10.6 (and possibly also OSX 10.7*). You can install that one by:

source("http://www.braju.com/R/hbLite.R");
hbBiocLite("affxparser");

It will detect whether you need this specially patch or not, and
install the proper version for you. If you have already installed the
fault version from Bioconductor, just uninstall by
remove.packages("affxparser") and retry. You can verify that you have
the patched version installed by:

> packageDescription("affxparser")$Packaged
[1] "2011-11-20 16:44:36 UTC; khansen"

Cheers,

Henrik

(*) If you have access to OSX 10.7 ("Lion"), could you please check
whether the patched version of affxparser on OSX or not, and report
back? Try the following:

library("affxparser");
readCdfHeader("annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf");

It should not crash R, but return a list of CDF attributes. The above
CDF can be downloaded from:

http://www.aroma-project.org/data/annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf.gz

[Jorge Melendez]

Hi Henrik

worked ok

> library("affxparser");

> readCdfHeader("annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf");

$ncols

[1] 2560

$nrows

[1] 2560

$nunits

[1] 262338

$nqcunits

[1] 6

$refseq

[1] ""

$chiptype

[1] "Mapping250K_Nsp"

$filename

[1] "annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf"

$rows

[1] 2560

$cols

[1] 2560

$probesets

[1] 262338

$qcprobesets

[1] 6

$reference

[1] ""

> sessionInfo()

R version 2.14.2 (2012-02-29)

Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

Thank you!

::::::::::::::::::::::::::::::::::::::::::::::::::

[Henrik Bengtsson]

Hi, sorry about the affxparser mess.

See if the following

source("http://aroma-project.org/affxparser.R");
installAffxparser();

solves your problems. The above will run tests to make sure
everything works fine and if it says that is the case, you're read to
rock'n'roll.

Please report back and let me know if it works, because then I'll
include the above as part of the default installation.

/Henrik

On Wed, Sep 26, 2012 at 7:12 AM, Martina Dori <martin...@gmail.com> wrote:
> Hi Henrik,
> I'm working on OS X 10.8.2 and
>
>> sessionInfo()
>
> R version 2.15.0 (2012-03-30)
>
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
>
> I followed the instruction you gave and uninstalled the affxparser I had and
> re-installed the previous version.
> It gave me this warning:
>
> Warning messages:
>
> 1: In packageDescription(pkg) : no package 'affxparser' was found
>
> 2: package ‘R.utils’ was built under R version 2.15.1
>
> 3: package ‘R.oo’ was built under R version 2.15.1
>
> 4: package ‘R.methodsS3’ was built under R version 2.15.1
>
>
> So I checked if it was installed

>
>> packageDescription("affxparser")$Packaged
>
> [1] "2011-11-20 16:44:36 UTC; khansen"
>
>

> Because it seemed to be installed, I tried to check my CDF file
> (GenomeWideSNP_6,Full.cdf) as you mentioned as test but it returned me as
> follows
>
> *** caught segfault ***
>
> address 0xfffffffc, cause 'memory not mapped'
>
>
> Traceback:
>
> 1: .Call("R_affx_get_cdf_file_header", filename, PACKAGE = "affxparser")
>
> 2:
> readCdfHeader("annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf")
>
>
> Possible actions:
>
> 1: abort (with core dump, if enabled)
>
> 2: normal R exit
>
> 3: exit R without saving workspace
>
> 4: exit R saving workspace
>
> R(2155,0xacadaa28) malloc: *** error for object 0xbfffe730: pointer being
> freed was not allocated
>
> *** set a breakpoint in malloc_error_break to debug
>
>
> I loaded the aroma.affymetrix library and because it didn't find the
> affxparser R automatically installed the latest version.
>
> What should I do?
>
> Thank you very much for any help
>
> Martina

> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
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[Martina Dori]

It worked!!!!!!!  :)

Thank you very much! 

Martina