[CWB] Installing from svn on ubuntu 11.10

[Giovanni Marco Dall'Olio]

2011/10/26 "Andrés Chandía" <andres at chandia.net>

> Perfect, I did it this way:
>
> :~/$ sudo rm -rf cwb-perl/CWB-CQI
> :~/$ sudo svn co https://cwb.svn.sourceforge.net/svnroot/cwb/perl/trunkcwb-perl
>

Don't call svn as a super user, it's dangerous and you don't need it.

You can just do:

:~/$ sudo rm -rf cwb-perl/CWB-CQI
:~/$ svn co https://cwb.svn.sourceforge.net/svnroot/cwb/perl/trunk cwb-perl
:~$ cd cwb-perl/CWB-CQI/
:~/cwb-perl/CWB-CQI$ sudo perl Makefile.PL  --config
/usr/local/cwb-3.4.0/bin/cwb-config



Checking if your kit is complete...
> Looks good
>
> Writing Makefile for CWB::CQI
>
> :~/cwb-perl/CWB-CQI$ sudo make
> cp lib/CWB/CQI.pm blib/lib/CWB/CQI.pm
> cp lib/CWB/CQI/Server.pm blib/lib/CWB/CQI/Server.pm
> cp lib/CWB/CQI/IOClient.pm blib/lib/CWB/CQI/IOClient.pm
> cp lib/CWB/CQI/Client.pm blib/lib/CWB/CQI/Client.pm
> Manifying blib/man3/CWB::CQI::IOClient.3pm
> Manifying blib/man3/CWB::CQI::Server.3pm
> Manifying blib/man3/CWB::CQI::Client.3pm
>
> :~/cwb-perl/CWB-CQI$ sudo make test
>
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/00_load.t ........... ok
> t/01_load_ioclient.t .. ok
> t/10_vss.t ............ 1/31 # CQP query: "small"%c (","? [pos="JJ.*"])*
> [pos="NN.*"]
> t/10_vss.t ............ ok
> t/11_vss_ioclient.t ... ok
> All tests successful.
> Files=4, Tests=66,  1 wallclock secs ( 0.04 usr  0.00 sys +  0.24 cusr
> 0.04 csys =  0.32 CPU)
> Result: PASS
>
> :~/cwb-perl/CWB-CQI$ sudo make install
> Installing /usr/local/share/perl/5.12.4/CWB/CQI/Server.pm
> Installing /usr/local/man/man3/CWB::CQI::Server.3pm
> Installing /usr/local/man/man3/CWB::CQI::IOClient.3pm
> Installing /usr/local/man/man3/CWB::CQI::Client.3pm
> Appending installation info to /usr/local/lib/perl/5.12.4/perllocal.pod
>
>
>
> _______________________
>             andrés chandía
> [image: chandia.net] <http://www.chandia.net>
> P No imprima innecesariamente. ¡Cuide el medio ambiente!
>
> On Tue, October 25, 2011 7:21 pm, Stefan Evert wrote:
> ->
> ->> Now, at the CWB-CQI installation in make test i got some error but make
> install went well,
> ->> is this something to worry about?
> ->
> -> Only if you want to use the CQi interface ...
> ->
> -> That's actually a buglet in the CWB::CQI::Server module, which expects
> the cqpserver binary to
> -> be in the standard search path (so it can be invoked with system
> "cqpserver ..." from Perl).
> -> This should really be pulled from the configuration information in the
> CWB module, but that
> -> hasn't been implemented yet because CWB-CQI doesn't depend on the basic
> CWB/Perl package.
> ->
> -> If you need CWB-CQI to work, there are two possible workarounds:
> ->
> -> 1) Add /usr/local/cwb-3.4.0/bin to your path
> ->
> -> 2) Check out the latest SVN copy, where I've fixed the bug (not tested
> thoroughly, so I'd be
> -> interested to hear if this fixes the problem for you)
> ->
> -> Cheers,
> -> Stefan
> ->
> -> _______________________________________________
> -> CWB mailing list
> -> CWB at sslmit.unibo.it
> -> http://devel.sslmit.unibo.it/mailman/listinfo/cwb
> ->
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>
>


-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it
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