[Bioc-devel] os x binary

[Kasper Daniel Hansen]

On Thu, Nov 17, 2011 at 5:02 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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.

So the binary version works on Leopard but not on Lion (if I
understand you correctly).  Building from source works on Lion.
Doesn't this tell us that there is something wrong with the binaries?

Kasper

>
> 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
>>>>>
>>>>
>>>
>>
>