[Bug 423648] Re: Package heavily out of date
Hi all, I couldn't help to notice that this package was not yet integrated in Lucid Lynx... http://packages.ubuntu.com/search?suite=lucidsearchon=nameskeywords=clustalx Anything else we should do? Thank you. -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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 Sorry, Fabrice -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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. -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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! -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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 -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
Great news indeed! -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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? -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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/143). 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 -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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. -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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 -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
** Branch linked: lp:debian/sid/clustalx -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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 ** Changed in: clustalx (Ubuntu) Status: Incomplete = New -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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 ** Changed in: clustalx (Ubuntu) Importance: Undecided = Wishlist ** Changed in: clustalx (Ubuntu) Status: New = Incomplete -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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. -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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! -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
[Bug 423648] Re: Package heavily out of date
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. -- Package heavily out of date https://bugs.launchpad.net/bugs/423648 You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
