[BioC] Install error affxparser for R 2.15

[David Ruau]

Thanks, it worked.

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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>>