[EMBOSS] Failure to build on Ubuntu 11.04

[ajb at ebi.ac.uk]

Hello Sylvain,

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).

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.

HTH

Alan



> HI,
>
> I've build EMBOSS on numerous vertsion of Ubuntu before but this one got
> me stumped... I am testing an EMBOSS 6.4.0 build on an Ubuntu 11.04 VM
> under VirtualBox, pretty much as I have done before and I end up with an
> oddity (may be the problem) and a make failure. First the oddity: running
> the install-jemboss-server.sh script,  I get this:
>
> ------------------------- WARNING ----------------------------
>
> The script cannot find zlib installed under /usr
> or /usr/local
>
> Download zlib from
>        http://www.info-zip.org/pub/infozip/zlib/
>
> For details see the EMBOSS admin guide:
> http://emboss.sourceforge.net/admin/
>
> To exit use Control C or press return to continue.
>
> --------------------------------------------------------------
>
> This is weird because I know that zlibc, zlib1g and zlib1g-dev packages
> are present. Ok, I press return and the configure/make dance started.
> After a few minutes, make crashes with this message:
>
> ../ajax/core/.libs/libajax.so: undefined reference to `crypt'
> collect2: ld returned 1 exit status
> make[2]: *** [aaindexextract] Error 1
> make[2]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/opt/bio/sources/EMBOSS-6.4.0/emboss'
> make: *** [all-recursive] Error 1
>
>
> Any clue on this? I couldn't find any lead looking at the mailing list
> archive...
>
> Best regards
>
> Sylvain
>
>
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