[Bioc-devel] os x binary

[Dan Tenenbaum]

On Thu, Nov 17, 2011 at 3:53 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> 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.

Maybe we should clarify which R binary we are talking about? On our
build system for release we use R 2.14.0 installed from this package:

http://cran.r-project.org/bin/macosx/R-2.14.0.pkg

"curl -I" reports that this file has not been changed since October 31.

So I'm not clear on what Simon actually rebuilt. I looked on R-sig-mac
and the only reference he makes to rebuilding (that I could find) is
something to do with R.app, and whatever binary he rebuilt is probably
on his att.com site, because it's not on CRAN.



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

That would be great. He said he built from source, but it would be
great to see sessionInfo(), etc.

>> 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.
>

Thanks
Dan

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