Problem installing Biobase on Solaris
Hi I forgot to paste the compiler output: gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c anyMissing.c -o anyMissing.o anyMissing.c: In function `anyMissing': anyMissing.c:33: warning: implicit declaration of function `__builtin_isnan' gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c envir.c -o envir.o gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c matchpt.c -o matchpt.o gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c Rinit.c -o Rinit.o gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c rowMedians.c -o rowMedians.o gcc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/include -I/usr/local/ssl/include -I/usr/local/pgsql/include -I/usr/local/include/ncurses -I/usr/local/BerkeleyDB.4.2/include -I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include -fPIC -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib -I/usr/local/rrdtool-1.2.19/include -c sublist_extract.c -o sublist_extract.o gcc -std=gnu99 -G -L/usr/local/lib -R/usr/local/lib -R/usr/lib -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib -L/usr/lib -R/usr/openwin/lib -L/usr/openwin/lib -L/usr/local/ssl/lib -R/usr/local/ssl/lib -L/usr/local/BerkeleyDB.4.2/lib -R/usr/local/BerkeleyDB.4.2/lib -L/usr/X11R6/lib -R/usr/X11R6/lib -o Biobase.so anyMissing.o envir.o matchpt.o Rinit.o rowMedians.o sublist_extract.o Thanks Paulo
Prof Brian Ripley wrote:
What compiler is this? This is a compiler issue, not an R one. My guess is that you are mixing gcc (which has __builtin_isnan) and cc (which does not). On Fri, 5 Sep 2008, 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 The machine I am using is a Sun SPARC Victoria Falls SunOS 5.10 Generic_127111-11 sun4v sparc SUNW,T5140 I posted this message to the BioC list and it was suggested that I tried installing any R package that needed compilation. I installed the XML package with no problems. Any help is appreciated. Thanks in advance Paulo
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