Package Details: ugene-git 38.1.r485.g113d9908d0-1

Git Clone URL: https://aur.archlinux.org/ugene-git.git (read-only, click to copy)
Package Base: ugene-git
Description: A free cross-platform genome analysis suite.
Upstream URL: http://ugene.unipro.ru/
Licenses: GPL
Conflicts: ugene, ugene-bin
Provides: ugene, ugene-bin
Submitter: WFCody
Maintainer: WFCody
Last Packager: WFCody
Votes: 2
Popularity: 0.000000
First Submitted: 2018-11-09 08:24 (UTC)
Last Updated: 2021-12-14 04:30 (UTC)

Latest Comments

WFCody commented on 2021-12-14 04:30 (UTC)

Installation works again

WFCody commented on 2021-11-23 11:07 (UTC)

The thing that makes me prefer the ugene (source) distribution over the binary one is that when you build it from source, it follows Qt theming while the binary one at least last time I used it was using the generic light colour scheme that did not fit the rest of my environment.

gaballench commented on 2021-11-23 10:43 (UTC)

Hello @WFCody! Thanks for your reply. I agree, before the commits in this year it would build without issues. I tried yesterday with the last three commits (back to September 2021 I think) and it won't build.

@hottea, thanks for the suggestion. I ended up installing that package ugene-bin which just runs, although I haven't tried it yet.

Anyway please let me known if the build logs are helpful for you in any way and I can make them available for you in case you still want to maintain the package.

Cheers!

WFCody commented on 2021-11-23 05:34 (UTC)

Thanks for the report. Very weird. Last time I rebuild to check this issue it worked fine. I am quite displeased with that they changed how binaries got installed. The old way was working fine.

I am actually considering abandoning this package and start using the versioned package that hottea linked below myself. The features I wanted from -git were already long integrated in released versions.

hottea commented on 2021-11-23 01:13 (UTC)

@gaballench You could try this one if you don't need -git pkg. You could also install it from here without building it from the source.

gaballench commented on 2021-11-22 18:47 (UTC) (edited on 2021-11-22 19:26 (UTC) by gaballench)

Hello! I'm building the latest version in the git repo and it finishes without errors, however, there's no binary at the end of the process:

[EDIT: I found the log from makepkg but could not find any error during building]

user@machine:ugene-git$ makepkg -sicCfL
#####[lots of compilation output for >3h]#####
==> Tidying install...
  -> Removing libtool files...
  -> Purging unwanted files...
  -> Removing static library files...
  -> Stripping unneeded symbols from binaries and libraries...
  -> Compressing man and info pages...
==> Checking for packaging issues...
==> Creating package "ugene-git"...
  -> Generating .PKGINFO file...
  -> Generating .BUILDINFO file...
  -> Generating .MTREE file...
  -> Compressing package...
==> Leaving fakeroot environment.
==> Finished making: ugene-git 38.1.r450.gceaed19c3e-1 (Mon 22 Nov 2021 06:26:53 PM GMT)
==> Installing package ugene-git with pacman -U...
[sudo] password for user: 
loading packages...
warning: ugene-git-38.1.r450.gceaed19c3e-1 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...

Packages (1) ugene-git-38.1.r450.gceaed19c3e-1


:: Proceed with installation? [Y/n] y
(1/1) checking keys in keyring                                                   [##############################################] 100%
(1/1) checking package integrity                                                 [##############################################] 100%
(1/1) loading package files                                                      [##############################################] 100%
(1/1) checking for file conflicts                                                [##############################################] 100%
(1/1) checking available disk space                                              [##############################################] 100%
:: Processing package changes...
(1/1) reinstalling ugene-git                                                     [##############################################] 100%
:: Running post-transaction hooks...
(1/2) Arming ConditionNeedsUpdate...
(2/2) Updating the desktop file MIME type cache...
==> Cleaning up...
user@@machine:ugene-git$ ugene
bash: ugene: command not found
user@machine:ugene-git$ ugene -ui
bash: ugene: command not found
user@machine:ugene-git$ ls
PKGBUILD
user@machine:~$ whereis ugene
ugene: /usr/bin/ugene
user@machine:~$ ls -la /usr/bin | grep " ug"
lrwxrwxrwx 1 root root       16 Nov 22 16:19 ugene -> /opt/ugene/ugene
user@machine:~$ ls /opt | grep ugene
user@machine:~$

I have also tried with just -sic as I usually installed/updated it without success.

Any suggestions are appreciated, I will try to re-build a couple commits below HEAD which was my working version to see if that helps temporarily.

WFCody commented on 2021-11-09 12:17 (UTC)

I just tried a rebuild and there were no issues

WFCody commented on 2021-10-17 16:32 (UTC)

Thanks @hottea I will look into it. There was such an issue recently because they changed how things got installed. Perhaps have they changed it again.

hottea commented on 2021-10-17 03:42 (UTC)

You might wanna update the package(), the finnal zst only contains the desktop file, see also https://aur.archlinux.org/packages/ugene/.

Rhinoceros commented on 2021-08-14 00:35 (UTC)

Sounds good. Sorry, to clarify, I meant the option might be a bit lost because users wouldn't know that an alternative were available unless there were another package.

WFCody commented on 2021-08-13 16:55 (UTC) (edited on 2021-08-13 16:56 (UTC) by WFCody)

The modification is very simple (I think). Just opencl-headers to depends() and OPENCL_INC_PATH=/usr/include/CL UGENE_OPENCL_DETECTED=1 as extra qmake arguments.

I am test-compiling with those modifications right now and I see that it picked up on those arguments during the build, so I think it worked.

Rhinoceros commented on 2021-08-13 16:10 (UTC)

Yeah, that might be a good option. It might get a bit lost though. An alternative could be to make a second package, e.g. ugene-opencl-git or similar.

WFCody commented on 2021-08-13 15:32 (UTC)

I am considering whether I should make an optional setting in the PKGBUILD to build UGene with OpenCL enabled...

Rhinoceros commented on 2021-08-13 15:19 (UTC)

Hmmm, I had a closer look, and I think upstream have created branches for 39.0 and 39.1. I think master contains all the code from those branches, but that's why git describe isn't picking up those tags. A bit annoying, but I'm not sure what you can do about it in an automated way.

WFCody commented on 2021-08-13 10:09 (UTC)

Yes I have also noticed that the git package names do not correspond to release versions. This one is however following master git so it should be the latest possible.

Rhinoceros commented on 2021-07-19 13:51 (UTC)

I just made this package. For some reason pkgver is 38.1.r271.gff2fb9afe8-1, even though the latest tagged version is 39.0.

WFCody commented on 2021-05-14 04:29 (UTC)

I just got a package deletion request for ugene-git arguing that it is the same as ugene-bin which is of course not true. This is built from source.

Right now very busy but will update this package to include all the individual (from source) packages in ugene-external-tools as optdepends since the metapackage has been removed.

nmruser commented on 2020-01-21 14:53 (UTC)

Cannot compile: Got the following error message:

src/client/linux/handler/exception_handler.cc:109:12: error: ‘int tgkill(pid_t, pid_t, int)’ was declared ‘extern’ and later ‘static’ [-fpermissive] 109 | static int tgkill(pid_t tgid, pid_t tid, int sig) { | ^~~~~~ In file included from /usr/include/signal.h:374, from src/client/linux/handler/exception_handler.h:33, from src/client/linux/handler/exception_handler.cc:66: /usr/include/bits/signal_ext.h:29:12: note: previous declaration of ‘int tgkill(__pid_t, __pid_t, int)’ 29 | extern int tgkill (__pid_t __tgid, __pid_t __tid, int __signal); | ^~~~~~

snowball commented on 2019-08-09 06:33 (UTC)

Also depends on qt5-websockets