[BioC] Install error affxparser for R 2.15

[Dan Tenenbaum]

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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