Re: [EMBOSS] Failure to build on Ubuntu 11.04
Hi Sylvain, 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. The 'shadow' selection is a bug which could be worked around for now, if necessary, by typing: export LDFLAGS=-lcrypt (setenv LDFLAGS -lcrypt) before invoking the script. It'll be fixed in the next release. However, as mentioned, PAM is better anyway and doesn't require doing so. I'm not sure from your message whether you're aware that you don't need to invoke the server script if you just want a simple standalone Jemboss for your users. Any EMBOSS installation using make install will create a script in the 'bin' directory called 'runJemboss.csh'. If users invoke that script (possibly via a symlink of your choice) then, as long as you have java in your PATH, it will fire-up a pre-configured standalone jemboss. The results of any applications will be stored in a jemboss subdirectory in a users home directory. As far as I'm aware axis2c isn't used by Jemboss yet, though it can be optionally configured into EMBOSS itself as a means of accessing some servers. ATB Alan ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Failure to build on Ubuntu 11.04
Hi, On 2011-09-07, at 7:04 AM, a...@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 ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
[EMBOSS] Failure to build on Ubuntu 11.04
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 ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Failure to build on Ubuntu 11.04
Le Tue, Sep 06, 2011 at 01:27:20PM -0400, Sylvain Foisy Ph. D. a écrit : - 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. Dear Sylvain, perhaps you can try to pass the --enable-systemlibs option during configuration ? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
