[BioC] Problem installing Biobase on Solaris

Paulo Nuin nuin at genedrift.org
Thu Sep 4 23:37:58 CEST 2008

Hi Herve

Thanks. Just tried installing XML (Matrix requires some graphical 
libraries) and it worked fine. I am starting to think that the Biobase 
problem might be related to the GCC version I am using, 3.4.3. I might 
need to upgrade it and test.

Thanks a lot.


Herve Pages wrote:
> Hi Paulo,
> The C code in Biobase makes no direct reference to the __builtin_isnan 
> symbol
> so your problem doesn't seem to be specific to the Biobase package and 
> will
> most likely happen with other packages containing native code.
> Try to install the XML or Matrix or whatever package with C code from the
> CRAN repository. If it doesn't work then you might try to report the 
> problem
> on the R-devel mailing list (more audience there so more chance that 
> someone
> will have access to a Solaris machine). Don't forget to report your
> sessionInfo() + exact version of Solaris + arch + compiler that you 
> are using.
> Good luck!
> H.
> Paulo Nuin wrote:
>> Hi everyone
>> This is my first post to the list. I had experience installing and 
>> using Bioconductor on Linux and Windows systems but I am encountering 
>> problems installing Biobase on Solaris running on Sparc. The package 
>> compilation works fine, with only a warning
>> warning: implicit declaration of function `__builtin_isnan'
>> the help files are generated but in the end it fails with an error 
>> also related __builtin_isnan
>> ** building package indices ...
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared library 
>> '/usr/local/lib/R/library/Biobase/libs/Biobase.so':
>>  ld.so.1: R: fatal: relocation error: file 
>> /usr/local/lib/R/library/Biobase/libs/Biobase.so: symbol 
>> __builtin_isnan: referenced symbol not found
>> Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> 
>> <Anonymous>
>> Execution halted
>> ERROR: installing package indices failed
>> Any help is appreciated. Thanks in advance
>> Paulo
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