quetsion about installing Jemboss on Alpha

[Guy Bottu]

from : BEN

	Dear developers,
	
I am trying to install Jemboss. My computer is a Compaq ES40 with 4 processors 
and CompaqTry64 5.1A. I did install the Java SDK 1.3.1. I tried to "make" 
EMBOSSS 2.3.1 with the commands :

./configure --prefix=/sw/emboss231 --with-pngdriver=/sw/png
   --with-java=/usr/opt/java131/include
   --with-javaos=/usr/opt/java131/include/alpha
make

but I get the error message :

In file included from ../ajax/ajjava.h:13,
                 from ../ajax/ajax.h:67,
                 from emboss.h:4,
                 from embaln.c:21:
/usr/opt/java131/include/jni.h:38:2: #error "Modules that interface with Java 
must be compiled and linked with the -pthread option"
*** Exit 1
Stop.
*** Exit 1
Stop.

If I add "manually" in .../emboss231/EMBOSS-2.3.1/ajax/Makefile
CPPFLAGS = ....     -pthread

the compilation goes beyond, but it gets stuck in nucleus. Is there a convenient 
way to precise that -pthread shoud be added whenever gcc must compile for 
Jemboss ? Or is it a sound idea of trying to disable the "error". The file
/usr/opt/java131/include/jni.h contains :
/* Compaq Java: Add following error to ensure that UNIX users specify threading 
options */
#if (defined(__alpha) && defined(__unix__) && !defined(_REENTRANT))
#ifdef __linux__
#error "Modules that interface with Java must be compiled with the -D_REENTRANT 
option"
#else
#error "Modules that interface with Java must be compiled and linked with the -p
thread option"
#endif
#endif


	Thanks in advance,
	Guy Bottu