[BioC] Problem installing Biobase on Solaris

Herve Pages hpages at fhcrc.org
Thu Sep 4 23:28:55 CEST 2008

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!


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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