[Bioc-devel] os x binary

[Dan Tenenbaum]

Hi Kasper,

On Mon, Nov 14, 2011 at 1:24 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> On Mon, Nov 14, 2011 at 12:57 PM, Kasper Daniel Hansen
> <kasperdanielhansen at gmail.com> wrote:
>> Some problems with the CRAN binary for OS X has been reported on
>> r-sig-mac.  Oliver (cc'ed) reported a problem with affxparser
>> segfaulting that we solved by
>> (1) installing an updated R binary
>> (2) recompiling affxparser from source
>>
>> It was not enough to do (1) and the reinstall using biocLite and type
>> = "mac.binary".
>>
>> The building team might already be aware of this, but in case they are
>> not I would suggest re-installing the R binary and rebuilding
>> packages.
>>
>
> Thanks, I will update the R on pitt (Mac machine used for release
> builds) as soon as it is finished with the builds it's running now.
>

The new affxparser produced by the latest R binary is now available,
and on my machine (running Lion) it still produces the same segfault:

R --vanilla -q -e 'library(affxparser);sessionInfo(); h <-
readCdfHeader("Mapping250K_Nsp.cdf")'
> library(affxparser);sessionInfo(); h <- readCdfHeader("Mapping250K_Nsp.cdf")
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affxparser_1.26.2
Abort trap: 6



On a different machine (running Leopard) it works:

compbio$ R --vanilla -q -e 'library(affxparser);sessionInfo(>
> library(affxparser);sessionInfo(); h <- readCdfHeader("Mapping250K_Nsp.cdf")
R version 2.14.0 (2011-10-31)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] affxparser_1.26.2
>
>

So I think there may still be a problem.
Dan




> Dan
>
>
>> Kasper
>>
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>>
>