EMBOSS 1.4.2 installation

Staffan Bergh staffan at sgibest.sto.se.pnu.com
Wed Aug 30 17:07:14 UTC 2000

OK, got it all installed, but here are some things that I had to hack
in the configuration/compilation. Somewhat vague at points since I'm
an extremely bad note-keeper, but it may help someone ...

first: # uname -a 
       IRIX64 wille 6.5 07151432 IP27

So this is IRIX 6.5, and I want to compile -n32 ... I have z, png, gd
libraries (-n32) in /usr/global/lib32 [for historical reasons, NOT in
/usr/local -- SGI had this annoying habit of putting their own stuff
into /usr/local so you could never be sure that a OS upgrade wouldn't
squat on your painfully installed stuff ... They've stopped doing that
but it'd be a real pain unravelling everything now :-(]

I'm not using gcc, but SGI's own cc.

First hurdle: the configure script checks for a working C++ compiler
... unnecessarily, it seems. We have something wrong with the license
or installation or something, so our c++ compiler doesn't work ->
configure stops. You can comment out the check for C++ with no harm
done! Comment out everything between lines 1503 and 1608,
inclusive. (You'll need to do the same thing for the EMBASSY apps,

Second hurdle: configure does something strange when trying to check
the versions of the graphics libraries. It seems it has this fixed
path ALT_HOME (set to /usr/local with a fallback to /usr) that it uses
to set LD_FLAGS and CPP_FLAGS for the test of zlib/png/gd. Since I
don't have the libraries in /usr/local/lib, configure fails to find
zlib et al. So you need to check ALT_HOME and possibly the other
two. This is lines 4644 and 4662-3. (this also affects the TOPO

Third hurdle: libtool seems to drop the '-n32' passed in via setenv
CFLAGS '-n32'. Easy fix, setenv CC 'cc -n32' will do it.

Fourth hurdle: libtool does some fancy stuff with version strings,
calculating version variables for ld. However, there is at least one
library that breaks this - libplplot.so.5.99 will make libtool produce
an extremely long string that causes ld32 to dump core with a bus
error [this is probably a bug in SGI's linker ...] The work-round for
this is tricky: 

     1. run make until ld32 coredumps

     2. edit libtool:

	look for 

	     case "$version_type" in
	     none) ;;


	and edit the while loop test (a few lines down) to

	    while test $loop != 90; do

     3. run make again and watch the output until it gets to 

     mv -f .libs/hsregsub.lo hsregsub.o
     ln -s hsregsub.o hsregsub.lo
	/bin/sh ../libtool --mode=link cc -n32  \
	  -O -L/usr/global/lib32 -o libajax.la -rpath /usr/local/lib \
	  -version-info 1:0:1 ajacd.lo [etc]

	libtool will hang here, never testing true on the while loop!
	So control-C out of the compile, edit libtool back to having 0
	in the loop test.

     4. run make again. Now it goes to the end!

There must be a simpler and better way of fixing this, but my shell
programming skills are too feeble :-)

Having said that, it installed relatively painlessly! Less pain than
compiling blast, at least ...

So now we start weaning users from GCG ... Next on the agenda is a web

Cheers /staffan


Staffan Bergh
Pharmacia, P14:5, SE-112 87 Stockholm, Sweden

email:  Staffan.Bergh at eu.pnu.com + Don't let that horse eat that violin
phone:  (int+46)  08 695 9884    +               cried Chagall's mother
fax:    (int+46)  08 695 4084    + but he kept right on painting
mobile: (int+46) 070 698 8829    +             -- Lawrence Ferlinghetti

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