Problem installing Biobase on Solaris
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Paulo Nuin ▴ 200
@paulo-nuin-3012
Last seen 6.9 years ago
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
Biobase Biobase • 614 views
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@herve-pages-1542
Last seen 2 hours ago
Seattle, WA, United States
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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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. Paulo 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >