[BioC] Install error affxparser for R 2.15

[Dan Tenenbaum]

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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>