[BioC] Install error affxparser for R 2.15

[David Ruau]

Yes, I do build R from source. I use the macport package manager.
It's strange I always had a problems with affxparser and rgl.
For rgl I could download the binary version and install it with R CMD INSTALL but today I could not download the binary version of affxparser from bioconductor.org.

Thanks for your help!
David

On Apr 9, 2012, at 12:37 PM, Dan Tenenbaum wrote:

> On Mon, Apr 9, 2012 at 12:35 PM, David Ruau <druau at stanford.edu> wrote:
>> Thanks, it worked.
>> 
> 
> Great. I'm guessing you built R from source and that is why
> getOption("pkgType")
> returns "source".
> So biocLite() will always try to install from source unless you pass
> type="mac.binary.leopard"
> 
> If you want, you can put
> options("pkgType" = "mac.binary.leopard")
> in your ~/.Rprofile
> and biocLite will always do a binary install.
> Or
> options("pkgType" = "both")
> will cause it to install binary unless a newer source package is available.
> 
> Dan
> 
> 
> 
>> David
>> 
>> On Apr 9, 2012, at 12:25 PM, Dan Tenenbaum wrote:
>> 
>>> On Mon, Apr 9, 2012 at 12:23 PM, David Ruau <druau at stanford.edu> wrote:
>>>> Hi Dan,
>>>> 
>>>> I pasted the output here http://pastebin.com/Lnt79kC5
>>>> biocLite() tries to install affxparser, fails and ask you if you want to update it (at the same time as other packages). And then fails again.
>>>> 
>>> OK, what if you do this:
>>> biocLite("affxparser", type="mac.binary.leopard")
>>> 
>>> ?
>>> Dan
>>> 
>>> 
>>>> Thanks,
>>>> David
>>>> 
>>>> On Apr 9, 2012, at 11:47 AM, Dan Tenenbaum wrote:
>>>> 
>>>>> Hi David,
>>>>> 
>>>>> On Mon, Apr 9, 2012 at 11:33 AM, David Ruau <druau at stanford.edu> wrote:
>>>>>> Hello,
>>>>>> 
>>>>>> I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8)
>>>>>> I cannot install from source and the binary version that is not available from Mac OSX snow leopard.
>>>>> 
>>>>> 
>>>>> Can you show the output of
>>>>> biocLite("affxparser")
>>>>> 
>>>>> without type="source"?
>>>>> 
>>>>> It works on my lion system with R 2.15.0 and BiocInstaller 1.4.3.
>>>>> 
>>>>> Dan
>>>>> 
>>>>> 
>>>>>> Below are the relevant lines of the install process.
>>>>>> 
>>>>>> ---
>>>>>>> biocLite("affxparser", type='source')
>>>>>> BioC_mirror: http://bioconductor.org
>>>>>> Using R version 2.15, BiocInstaller version 1.4.3.
>>>>>> Installing package(s) 'affxparser'
>>>>>> trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/affxparser_1.28.0.tar.gz'
>>>>>> 
>>>>>> [snip...]
>>>>>> 
>>>>>> /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include    -fPIC  -pipe -O2 -m64  -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o
>>>>>> In file included from fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.h:30:0,
>>>>>>                 from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24:
>>>>>> fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring
>>>>>> fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset
>>>>>> make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1
>>>>>> ERROR: compilation failed for package ‘affxparser’
>>>>>> * removing ‘/opt/local/lib/R/library/affxparser’
>>>>>> * restoring previous ‘/opt/local/lib/R/library/affxparser’
>>>>>> 
>>>>>> The downloaded source packages are in
>>>>>>        ‘/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tmp-/Rtmpn4Zczi/downloaded_packages’
>>>>>> Updating HTML index of packages in '.Library'
>>>>>> Making packages.html  ... done
>>>>>> Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1'
>>>>>> Update all/some/none? [a/s/n]: n
>>>>>> Warning message:
>>>>>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>>>>>>  installation of package ‘affxparser’ had non-zero exit status
>>>>>> 
>>>>>>> sessionInfo()
>>>>>> R version 2.15.0 (2012-03-30)
>>>>>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
>>>>>> 
>>>>>> locale:
>>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C
>>>>>> 
>>>>>> attached base packages:
>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>> 
>>>>>> other attached packages:
>>>>>> [1] BiocInstaller_1.4.3
>>>>>> 
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] inline_0.3.8 Rcpp_0.9.10  tools_2.15.0
>>>>>> 
>>>>>> 
>>>>>> Thanks,
>>>>>> David
>>>>>> 
>>>>>> _______________________________________________
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>>>> 
>>