[BioC] Install error affxparser for R 2.15

[Dan Tenenbaum]

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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
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>>>
>