[BioC] RBGL compile error

[Li.Long at isb-sib.ch]

>From the msgs, it seems that

(1) you invoked libg2c (Fortran to C) somehow, RBGL doesn't have any
Fortran codes, so it's something else that leads the compiler into
thinking Fortran;

(2) the compiler seems trying to make an executable instead of making a
shared lib;

You probably have the same issue when installing other libs, and the
problem may not be RBGL-specific.

A simple way to make a shared lib for RBGL is:
    c++ -shared -L/usr/local/lib -o RBGL.so <...all the .o files>
Your line has a lot more other options.

I suggest that you look into how those options come into play.

Best,

Li

> bash-2.05b# R CMD INSTALL ~ygc/R_packages/BioC1.8/RBGL_1.8.1.tar.gz
> * Installing *source* package 'RBGL' ...
> untarring boost include tree...
> ** libs
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> bbc.cpp -o bbc.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> cliques.cpp -o cliques.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> hcs.cpp -o hcs.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> incrConnComp.cpp -o incrConnComp.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> interfaces.cpp -o interfaces.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> layout.cpp -o layout.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> minST.cpp -o minST.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> mincut.cpp -o mincut.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> ordering.cpp -o ordering.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> shortestPath.cpp -o shortestPath.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> sna.cpp -o sna.o
> c++ -I/usr/pkg/lib/R/include  -DPNG_NO_ASSEMBLER_CODE -I/usr/pkg/include
> -I/usr/include  -IboostIncl   -O2 -I/usr/pkg/include -I/usr/include -c
> wavefront.cpp -o wavefront.o
> c++  -L/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -Wl,-R/usr/pkg/lib
> -L/usr/X11R6/lib -Wl,-R/usr/X11R6/lib -o RBGL.so bbc.o cliques.o hcs.o
> incrConnComp.o interfaces.o layout.o minST.o mincut.o ordering.o
> shortestPath.o sna.o wavefront.o   -L/usr/pkg/lib/R/lib -lR
> /usr/lib/libg2c.so.2: warning: warning: mktemp() possibly used unsafely,
> use
> mkstemp() or mkdtemp()
> /usr/lib/crt0.o(.text+0xd0): In function `_start':
> : undefined reference to `main'
> *** Error code 1
>
> Stop.
> make: stopped in /tmp/R.INSTALL.03454a/RBGL/src
> ERROR: compilation failed for package 'RBGL'
> ** Removing '/usr/pkg/lib/R/library/RBGL'
>
>
>
> this is the RBGL compile output.I don't know what's wrong.Did anyone know
> what's wrong and tell me how to solve this problem.
>
> Thanks anyway.....
> --
>
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