[Bioc-devel] os x binary

[Kasper Daniel Hansen]

On Thu, Nov 17, 2011 at 5:27 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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).

Well, actually my statement is not based on my own testing.  But this
is what I have told people who had problems and it seems that made the
problem go away.  I am building R from source myself, so I am not
using the binary.

Perhaps Oliver can say exactly what he did to get his problem solved?

> 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.

On its way.

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