Sync clustalx 2.0.12-2 (multiverse) from Debian unstable (non-free)

[Stunts]

Binary package hint: clustalx

This package version is heavily outdated. You should consider updating it.

The newer version have better stability, (highly) improved speed and a much cleaner GUI.

The new version builds on Ubuntu 10.04, and is available here, together with the build logs:
https://launchpad.net/~plessy/+archive/plessy/+build/1472225

We are past feature Freeze, but, according to the guidelines:
The benefits of the latest version far out weight the "dangers" of a regression. This new version has been very tested and is much much improved relatively to the one available in the repositories;
The package builds, installs and upgrades, and no other packages depend on it, so it won't break anything downstream.
Nobody uses such an old version, since it is too slow for larger datasets, it only outputs data in a single format (as opposed to the new one that outputs to several format for different programs), and is generally "ugly" and unappealing to use.

Thanks you.

[Charles Plessy (plessy)]

Dear Stunts,

I just updated the clustalx package in Debian. You can contact MOTUs to request a sync.

Have a nice day,

--
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian/med
Tsurumi, Kanagawa, Japan.

[Stunts (f-pinamartins)]

Hello again, and thanks for your feedback Charles!
According to https://wiki.ubuntu.com/SyncRequestProcess here is the info that I must provide for the syncing to take effect:

# Source package name
ClustalX

# Source package version number to sync
2.0.12-1

# Where to sync from (e.g. 'Debian sid main', 'Debian experimental non-free')
Debian sid (unstable) non-free
(I'm not 100% sure this is the info I'm supposed to provide here, just to make sure, here's the link: http://packages.debian.org/sid/clustalx).

#If there are Ubuntu changes apart from debian/changelog or if FeatureFreeze is in effect:
No changes Required that I am aware of.

I hope it's still in time for Karmic!

[Fabrice Coutadeur (fabricesp)]

Hi,

As we are way past Feature Freeze, please follow the Feature Freeze exception process described at https://wiki.ubuntu.com/FreezeExceptionProcess.
Anyway, without a really good reason, it will be very complicated to have in Karmic: we are one week from release :-) Otherwise, it will be automatically synced when next development cycle begins.

I'll unsubscribe u-u-s for the moment: please feel free to subcribe u-u-s again when the FFe is approved.

Thank,s
Fabrice

[Stunts (f-pinamartins)]

Fair enough. I'll just resubscribe this as soon as development for Lucid Lynx starts.
It's not like it's a show stopper or anything. Better to have it up to date in the long term support release anyway.
Thanks for your feedback anyway.

[Fabrice Coutadeur (fabricesp)]

Hi,

For Lucid, we are syncing from Testing, and the new version has not yet entered there. You should check why, and see if it's worth keeping the actual version, or syncing from Unstable (with arguments :-) )

Thanks,
Fabrice

[Stunts (f-pinamartins)]

You really should sync this package from Unstable. The one currently in the repository have a very "clunky" interface and is simply unsuitable for large datasets, even on very fast machines.
Anything else I can do to help this getting into the repos?
Thank you.

[Fabrice Coutadeur (fabricesp)]

Hi,

When trying to build the version in unstable, I'm getting those errors:
g++ -c -pipe -O2 -Wall -W -D_REENTRANT -DOS_UNIX -DQT_NO_DEBUG -DQT_XML_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/share/qt4/mkspecs/linux-g++ -I. -I/usr/include/qt4/QtCore -I/usr/include/qt4/QtGui -I/usr/include/qt4/QtXml -I/usr/include/qt4 -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -I. -o moc_AlignmentFormatOptions.o moc_AlignmentFormatOptions.cpp
moc_AlignmentFormatOptions.cpp:14:2: error: #error "This file was generated using the moc from 4.5.0. It"
moc_AlignmentFormatOptions.cpp:15:2: error: #error "cannot be used with the include files from this version of Qt."
moc_AlignmentFormatOptions.cpp:16:2: error: #error "(The moc has changed too much.)"
make[1]: *** [moc_AlignmentFormatOptions.o] Error 1
make[1]: Leaving directory `/build/fabrice-clustalx_2.0.12-1-amd64-1y24j8/clustalx-2.0.12'
dh_auto_build: make -j1 returned exit code 2
make: *** [build-stamp] Error 2

It seems that the version is not compatible with the QT version in Ubuntu. That could also explain why this version is still in Unstable...

So for the moment, except if this error is fixed, it's not possible to sync the package from Debian.

Sorry,
Fabrice

[Stunts (f-pinamartins)]

I have successfully built clustalx directly from source (ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.0.12/clustalx-2.0.12.tar.gz) using ubuntu karmic.
I have installed the following packages in order to build it: qt4-dev-tools; build-essential; qt4-qmake.

I don't really know what the debian patches do, but are they still required?

[Charles Plessy (plessy)]

Hi Stunts and Fabrice,

Indeed, libqt4-dev and other packages in Lucid are already in version 4.6 and clustalx does not like this. I confirmed in a PPA that clustalx fails to build currently in Lucid (https://launchpad.net/~plessy/+archive/plessy/+build/1432222).

About the patch (there is only one, http://patch-tracker.debian.org/patch/series/view/clustalx/2.0.12-1/hardcode-accessory-file-locations.patch). Its purpose it to let Clustal X find accessory files like the help when it is invoked from /usr/bin.

Have a nice day

[Stunts (f-pinamartins)]

Just out of curiosity, does the current version (1.83-4) build on Lucid?
Or does the latest version, built on karmic work on lucid?
I will also attempt to contact the author about this issue and see what can be done.

[Stunts (f-pinamartins)]

I have a reply from the author:

>Hi Francisco,
>
>The quoted compiler error is:
>
>moc_AlignmentFormatOptions.cpp:14:2: error: #error "This file was
>generated using the moc from 4.5.0. It"
>moc_AlignmentFormatOptions.cpp:15:2: error: #error "cannot be used with
>the include files from this version of Qt."
>moc_AlignmentFormatOptions.cpp:16:2: error: #error "(The moc has changed
>too much.)"
>
>So, it looks like the moc*files were created with Qt 4.5 (by us) but you
>are using 4.6 to compile them.
>
>If I'm correct, then you can just delete the moc*cpp files and run Qt's
>qmake again (4.6), which will recreate them. That should hopefully fix
>the problem.
>
>Please let me know, if this worked (or not).
>
>Cheers,
>Andreas

I do not have Lucid Lynx here, but Charles, can you try and build it using these instructions?
Thank you!

[Charles Plessy (plessy)]

Excellent! I added $(RM) moc_* to the clean target in debian/rules and the package builds fine on Lucid:

https://launchpad.net/~plessy/+archive/plessy/+build/1472225

I will update the Debian package soon.

Have a nice day,

--
Charles

[Stunts (f-pinamartins)]

Great news indeed!

[Stunts (f-pinamartins)]

Hi all,
I couldn't help to notice that this package was not yet integrated in Lucid Lynx...

http://packages.ubuntu.com/search?suite=lucid&searchon=names&keywords=clustalx

Anything else we should do?

Thank you.

[Fabrice Coutadeur (fabricesp)]

Hi,

Sorry for the late answer (my motherboard died more than one moth ago, and I'm still trying to get a fully working env).

As far as I can tell, Charles uploaded a new version 2.1.12-2 that should fix the FTBFS, so you should change the title and the description of the bug report to reflect that (requestsync can help you with the content of the sync request).
The bad news is that as we are past Feature Freeze, you should follow the FFe process described at https://wiki.ubuntu.com/FreezeExceptionProcess.

Sorry,
Fabrice

[Stunts (f-pinamartins)]

I have done what you recommended.
I hope I followed all the necessary guidelines.

[Charles Plessy (plessy)]

Hi all,

For the record, the reason why Debian's clustalx has not migrated in testing is only the lack of autobuilders for non-free packages. There is no release-critical problem in clustalx 2.0.12-2.

Cheers,

--
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan

[StefanPotyra (sistpoty)]

Ack, FFe granted, please go ahead.

[Fabrice Coutadeur (fabricesp)]

package builds and installs, sync request ACK'd

[Jamie Strandboge (jdstrand)]

2010-03-26 17:28:17 INFO - <clustalx_2.0.12-2.dsc: downloading from http://ftp.debian.org/debian/>
[Updating] clustalx (1.83-4 [Ubuntu] < 2.0.12-2 [Debian])
 * Trying to add clustalx...
2010-03-26 17:28:17 INFO - <clustalx_2.0.12-2.diff.gz: downloading from http://ftp.debian.org/debian/>
2010-03-26 17:28:17 INFO - <clustalx_2.0.12.orig.tar.gz: downloading from http://ftp.debian.org/debian/>
I: clustalx [multiverse] -> clustalx_1.83-4 [multiverse].