[BioC] Install error affxparser for R 2.15

[David Ruau]

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.

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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