[Bioc-devel] os x binary

[Dan Tenenbaum]

Hi Kasper,

On Thu, Nov 17, 2011 at 1:47 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> Hi Dan
>
> I am on snow leopard.  We have not made any changes to the C code in
> affxparser in over a year I think, and it works on a wide variety of
> systems.  Everyone who has reported this problem seems to be able to
> fix it by re-installing the CRAN binary and rebuilding affxparser from
> source.  I am not sure that this includes anyone on Lion.
>
> Have you manually rebuild affxparser?  We have not bumped the version
> number since we have made no changes to the package, so according to
> my understanding of the build system it will not get rebuild
> automatically.

I bumped the version number yesterday to 1.26.2, and that is what was
built by our build system and is now available via biocLite().

If I build affxparser from source on my Lion machine, readCdfHeader() works.

Dan


>
> Kasper
>
> On Thu, Nov 17, 2011 at 4:01 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> 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
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>
>