Package Details: ugene 1.22.0-1

Git Clone URL: https://aur.archlinux.org/ugene.git (read-only)
Package Base: ugene
Description: A free cross-platform genome analysis suite.
Upstream URL: http://ugene.net/
Licenses: GPL
Submitter: bmpvieira
Maintainer: WFCody
Last Packager: WFCody
Votes: 16
Popularity: 0.847366
First Submitted: 2010-02-25 18:22
Last Updated: 2016-04-14 11:45

Latest Comments

WFCody commented on 2016-04-14 11:48

Thanks to Ugene developer dkandrov, the issue has been patched. Most likely a bug introduced by the newest gcc.

WFCody commented on 2016-04-14 07:23

I opened an issue on Github
https://github.com/ugeneunipro/ugene/issues/12

I really don't know what is wrong at this moment. I will fix the package as soon as I do.

boina commented on 2016-04-13 21:02

So we can't use the PKGBUILD to install ugene? or is there a workaround that I don't see.

My Best,
thanks, jose.

WFCody commented on 2016-04-11 16:36

I do indeed get the same issue.

isnan and isinf should be defined by <cmath> which is not explicitly included in that file.

https://github.com/ugeneunipro/ugene/blob/master/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.cpp

math.h should be included by this file

https://github.com/ugeneunipro/ugene/blob/master/src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.h

so in fact isinf et al should be defined!

boina commented on 2016-04-11 12:01

Hello!! so I made some progress but I'm stuck again.
The problem was not with locales. Packages qt5-script and qt5-svg were missing. They should be included as dependencies.
Now it starts compiling and goes well for a long time before crashing with the following errors:

src/hmmer3/hmmer3_funcs.cpp:36:22: error: ‘isnan’ no se declaró en este ámbito
return !isnan( x ) && !isinf( x );

AND

src/hmmer3/hmmer3_funcs.cpp:36:37: error: ‘isinf’ no se declaró en este ámbito
return !isnan( x ) && !isinf( x );

I don't know if this could be for something related to my system or maybe another non-satisfied dependency??

Any ideas?
Thanks, Jose.

boina commented on 2016-04-08 07:49

Thank you very much. I'm sure it's that because my system has Spanish locales.
Unfortunately trying to override locales did not work. Still giving the same error.

Best, jose.

WFCody commented on 2016-04-08 04:08

Most likely because it tried to compile it in spanish/italian/other latin language (sorry, don't know which).

src/ugeneui/transl lists english.ts and russian.ts

In the updated version, I have tried to override local locales by setting LC_ALL=C and build in english by default by setting a value to two variables that get defined in ugene.pro.
My test build generated both russian and english translations again so I don't know if setting those variables will do anything outside of ugene.pro

boina commented on 2016-04-07 23:29

Hello!!
I can't uptade to version 1.21 because it is giving me the following error:
Any idea what could be missing??

Thanks in advanced, Jose.


==> Iniciando build()…
Project MESSAGE: Cannot generate translations: no lrelease binary found
Project MESSAGE: Cannot generate translations: no lrelease binary found
Project MESSAGE: Cannot generate translations: no lrelease binary found
Project MESSAGE: Cannot generate translations: no lrelease binary found
Reading /tmp/yaourt-tmp-netlak/aur-ugene/src/ugene-1.21.0/src/libs_3rdparty/breakpad/breakpad.pro
Reading /tmp/yaourt-tmp-netlak/aur-ugene/src/ugene-1.21.0/src/libs_3rdparty/qscore/qscore.pro
Project ERROR: Unknown module(s) in QT: script
==> ERROR: Se produjo un fallo en build().
Cancelando…

talavis commented on 2015-10-26 18:18

I will keep it at qt4 until the developer says otherwise. Also, I wouldn't mind if someone else want to handle the pkg, as I don't use it very often.

WFCody commented on 2015-10-26 17:26

I can report that the latest (1.18.0) version builds (and runs) perfectly fine with Qt5. I have done a few multiple sequence alignments and opened some old projects with it.

Out of curiosity, I just changed qmake-qt4 to qmake-qt5 in this PKGBUILD (and updated sources). The resulting package was 5.87 MiB smaller (installed) than the previous (1.17.0) version linked against Qt4.

I also confirmed that the package indeed is linked against Qt5 by
ldd /usr/lib/ugene/ugeneui

below is a trimmed diff of the outputs
12,81c12,97
< libQtWebKit.so.4 => /usr/lib/libQtWebKit.so.4 (0x00007f561f196000)
< libQtXml.so.4 => /usr/lib/libQtXml.so.4 (0x00007f561ef4f000)
< libQtGui.so.4 => /usr/lib/libQtGui.so.4 (0x00007f561e216000)
< libQtNetwork.so.4 => /usr/lib/libQtNetwork.so.4 (0x00007f561dec2000)
< libQtCore.so.4 => /usr/lib/libQtCore.so.4 (0x00007f561d9ba000)
---
> libQt5WebKitWidgets.so.5 => /usr/lib/libQt5WebKitWidgets.so.5 (0x00007fd276df3000)
> libQt5WebKit.so.5 => /usr/lib/libQt5WebKit.so.5 (0x00007fd274753000)
> libQt5Widgets.so.5 => /usr/lib/libQt5Widgets.so.5 (0x00007fd273e9e000)
> libQt5Gui.so.5 => /usr/lib/libQt5Gui.so.5 (0x00007fd273735000)
> libQt5Xml.so.5 => /usr/lib/libQt5Xml.so.5 (0x00007fd2734f8000)
> libQt5Network.so.5 => /usr/lib/libQt5Network.so.5 (0x00007fd27319f000)
> libQt5Core.so.5 => /usr/lib/libQt5Core.so.5 (0x00007fd272ab1000)
> libQt5Sensors.so.5 => /usr/lib/libQt5Sensors.so.5 (0x00007fd271f38000)
> libQt5PrintSupport.so.5 => /usr/lib/libQt5PrintSupport.so.5 (0x00007fd271cc5000)
> libQt5OpenGL.so.5 => /usr/lib/libQt5OpenGL.so.5 (0x00007fd271a6a000)


All other libraries found by ldd were also reported in the diff since they had different adresses.

I have no idea what the new dependencies should be if the package switches to Qt5 though.

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