[Bioc-devel] os x binary

[Dan Tenenbaum]

On Thu, Nov 17, 2011 at 2:18 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> 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?

Yes, your understanding is correct.

It does seem to tell us that there is a problem with the binaries, at
least the one produced on Leopard (which is what our build system
uses).

Earlier in this thread, you said installing the latest R 2.14.0 binary
from CRAN would solve this problem. It appears that it does not solve
it, at least for some machines (Lion may or may not be the deciding
factor).

If you want to send me (off-list) the .tgz file produced by
R CMD INSTALL --build affxparser
on your Snow Leopard system, I'll test if it works on my Lion system.

Dan



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