From nuin at genedrift.org  Fri Sep  5 17:52:31 2008
From: nuin at genedrift.org (Paulo Nuin)
Date: Fri, 05 Sep 2008 11:52:31 -0400
Subject: [Rd] Problem installing Biobase on Solaris
In-Reply-To: <alpine.LFD.1.10.0809051526520.20807@gannet.stats.ox.ac.uk>
References: <48C13C3A.1040503@genedrift.org>
	<alpine.LFD.1.10.0809051526520.20807@gannet.stats.ox.ac.uk>
Message-ID: <48C155BF.9040705@genedrift.org>

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
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>



[Rd] Problem installing Biobase on Solaris
Paulo Nuin