Emboss 2.1.0 on Irix

[ableasby at hgmp.mrc.ac.uk]

Your problem mainly stems from your configure line:

build for EMBOSS ${EMB_VER}  shared" ; \
./configure --srcdir=/src/emboss/${EMB_VER}/EMBOSS-${EMB_VER}
--prefix=/tools/emboss${EMB_VER}\
 --with-x --with-pngdriver --with-java  ;


You specified --with-pngdriver and --with-java without giving a
directory hence their values are therefore set to "yes". For 
--with-pngdriver a trailing '/lib' is assumed and should not be
specified.

Also, you must also specify --withjavaos=dir if you specify --with-java=dir.

I've emailed Len privately about the library version report
and asked him to test something so I'll wait for his reply before
commenting on that.

Cheers
Alan