[EMBOSS] Failure to build on Ubuntu 11.04

[Sylvain Foisy Ph. D.]

Hi,

On 2011-09-07, at 7:04 AM, ajb at ebi.ac.uk wrote:

> Regarding the oddity: having had a look, the Ubuntu people have
> decided to put some libraries in different locations from
> most other linux distributions. I've modified the script
> which should now , at least, fix that problem. You can download it from:
> 
>    http://www.ebi.ac.uk/~ajb/test/install-jemboss-server.sh
> 
> (you may need to "chmod 755" it after download).

Ah, Linux distros... I tried the new script, with default choices, with a clean d/l of EMBOSS and EMBASSY apps and I got this:

ajjava.c:122:31: fatal error: security/pam_appl.h: No such file or directory
compilation terminated.
make[3]: *** [ajjava.lo] Error 1
make[3]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax/core'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax/core'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/ajax'
make: *** [all-recursive] Error 1

Let me guess: 

% apt-get install libpam0g-dev

Right? Must be because compilation did work a-ok with the script after this install.

> Wrt crypt: the above script works for me using PAM authentication
> (requires libpam0g-dev installation). I can't guarantee it'll
> work with other authentication methods on Ubuntu yet, given
> their library organisation, but feel free to test it and let me
> know. Before you do that though, please send me your
> jemboss/utils/install.record file (produced automatically after you ran
> the installation script - edit it to replace any sensitive info
> with 'x's first) so I can see what options you had chosen to
> give before the compilation failed (in order to try to
> reproduce the original failure). We do, however, recommend PAM
> authentication for servers on those distributions that
> support PAM.

I had selected shadow, which might explain this error. I actually never use jemboss in a client-server setup but rather as a local standalone resource on the server for the users to use locally via the Xfce4 GUI. BTW, the script is not using axis2c yet? It only recognized axis-1_4.

Thanks for the help

Sylvain