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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