Qt 5.11.1 Release, see also http://blog.qt.io/blog/2018/05/22/qt-5-11-released/ and http://blog.qt.io/blog/2018/06/19/qt-5-11-1-released/
The new version of ugene introduces a lot of major features for NGS data analysis:
Quality control: a new tool Trimmomatic was integrated for quality control of NGS reads. It allows one to cut Illumina adapters, trim reads ends by quality, trim reads by length, etc.
De novo assembly: SPAdes was updated to version 3.12.0. Graphical interface for the tool in UGENE was updated. It is now possible to input hybrid data, for example, assemble Illumina and Oxford Nanopore reads.
Metagenomics: a new infrastructure for taxonomy classification of whole-genome shotgun sequencing data was developed. This includes tools Kraken, CLARK, DIAMOND, WEVOTE and other. Reference data for the tools are also provided: NCBI taxonomy information; RefSeq data for viruses, bacteria, human; etc.
Transcriptomics: a new tool StringTie was integrated.
Updates may require up to 24 hours to propagate to mirrors. If the following command doesn't work, please retry later:
sudo dnf upgrade --refresh --advisory=FEDORA-2018-bea1e0b465
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This update has been submitted for testing by rdieter.
This update has obsoleted ugene-1.31.0-2.fc28, and has inherited its bugs and notes.
rdieter edited this update.
This update has been pushed to testing.
rdieter edited this update.
works for me
Works for me..
Works great! LGTM! =)
works for me
rdieter edited this update.
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This update has been submitted for testing by rdieter.
This update breaks QtWebEngine on a large set of machines on a primary architecture (all ARM machines without NEON) because the skia-neon patch is missing. It additionally also breaks QtWebEngine on a large set of machines on a secondary architecture (all i686 machines without SSE2) because the no-sse2 patch is missing. The no-sse2 patch is definitely hard to port, the skia-neon patch probably not that much. I never approved this version for anything other than Rawhide.
In addition, the QtWebEngine security fixes are not documented in the update's description and the update is not marked as a security update.
This prevents cura-lulzbot from starting.
karma: -1
This update has been pushed to testing.
works
rdieter edited this update.
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Plasma, Dolphin, Konsole, Ksysguard and others are running fine with Qt 5.11.1. Ksysguard's process table columns and sorting are retained when restarting it which wasn't happening with Qt 5.10.1.
Works for me.
jgrulich edited this update.
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The dnf error I got when trying to update to pipewire-0.2.3-1 due to xdg-desktop-portal-kde-5.13.4-2's missing requirement of libspa-lib.so.1 was resolved after I updated to xdg-desktop-portal-kde-5.13.4-3 from Koji. FEDORA-2018-973e14809c
This update has been pushed to testing.
Updating Qt to new major version in stable Fedora release is not good because it breaks all applications using Qt Private API (for example Telegram Desktop).
To my knowledge, this is very much discouraged in https://fedoraproject.org/wiki/Updates_Policy
This breaks ABI and apparently also breaks other packages. Setting the unstable threshold to -8 is also a bit optimistic.
Not suitable for a stable release. Breaks third party apps that use changed symbols.
rdieter edited this update.
kde-sig understands and accepts that private api is an issue, and that all fedora software that uses private api has been rebuilt and included in this update (save one, that's still FTBFS).
Qt's private api is not something we can support, so if third party software uses those, it's (mostly) on them and not (primarily) our responsibility.
Not work paste from buffer by click on mouse scroll between applications.
package hedgewars-0.9.24.1-1.fc28.x86_64 requires libQt5Core.so.5(Qt_5.10.1_PRIVATE_API)(64bit), but none of the providers can be installed
@vascom the opposite is true here! the first time since 3 years after KDE5 was thrown to us i can select and paste without replace the real clipboard with the selected text which made it terrible to work as software developer when the text you want to replace with CTRL+V replaces the clipboard instead
jgrulich edited this update.
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jgrulich edited this update.
New build(s):
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unstable threshold: -16 It is serious?
@xvitaly stop giving negative karma because something outside the Fedora repos is using private API's without understanding the word private - Fedora does QT updates virtually forever
@hreindl No. I will not. Maintainers are cheating. After receiving lots of negative carma they reset it by rebuilding one of packages and even set unstable treshold to -16. This is not fair. I will report this issue to FESCo.
If it matters, kde-sig does not generally use autokarma for larger updates. We greatly prefer to closely review all feeeback to allow us to decide what is best. I set a generally unreasonable value for unstable karma to avoid the possibility of this update being set to obsolete without our diligent input and review first.
Seems good.
karma: +1
Works okay for me.
Wrt hedgewars issue mentioned, I filed a bug, https://bugzilla.redhat.com/show_bug.cgi?id=1625239 and pull request to address it, https://src.fedoraproject.org/rpms/hedgewars/pull-request/2
Parts of kalzium's interface haven't been showing up after I updated to Qt 5.11.1 which all appeared correctly when I was using 5.10.1. I filed the following bugzilla entry about the kalzium issues to inform its maintainers in more detail. https://bugzilla.redhat.com/show_bug.cgi?id=1625282
rdieter edited this update.
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no regressions noted
The issue with kalzium's interface I referred to was still present after I downgraded to Qt 5.10.1, and so the problem is most likely not in Qt 5.11.1 but maybe in some other package such as in kf5*5.48.
This fixes adding or removing columns in Kmail.
Issue with Telegram now resolved.
The issue I mentioned with kalzium was caused by unintentionally abnormal configuration settings in ~/.config/kalziumrc and is now resolved; that problem was unrelated to the Qt 5.11.1 or kf5 5.48 updates. A user has reported the same dnf error I saw after pipewire-0.2.3 was pushed to stable, so a way to get xdg-desktop-portal-kde-5.13.4-4 into stable more quickly than the rest of this update might be advisable.
xdg-desktop-portal-kde-5.13.4-4 depends on libQt5Core.so.5(Qt_5.11) so moving xdg-desktop-portal-kde-5.13.4-4 to stable without the rest of this update would just lead to other dnf errors. I don't know how to get around that other than a rebuild of xdg-desktop-portal-kde-5.13.4 with Qt 5.10.1.
Anyone able to confirm that and open a bug? I don't have a Fedora 28 workstation at hand.
Of course those using just the updates repo could skip the pipewire-0.2.3 update or just enable updates testing to upgrade to it and xdg-desktop-portal-kde-5.13.4-4. I'm sorry about the mixup.
I installed cura-lulzbot on F28. cura-lulzbot started without problems after about 3 minutes, and its interface functioned fine. I don't have a 3d printer to test cura-lulzbot with.
This update has been pushed to testing.
This update has been pushed to testing.
breaking telegram desktop
@mattf Thank you!
Good.
@robbinespu
Report that to telegram-desktop maintainer(s) (it's not part of fedora), they'll need to rebuild it.
Latest version of this update seems to fix cura-lulzbot.
karma: +1
Working for me.
The Fedora Updates Policy mentions that KDE SIG was given an exception for stable releases https://fedoraproject.org/wiki/Updates_Policy Standard support for the Qt 5.10 branch ends on October 30, 2018, while the 5.11 branch is supported for a year after its release on May 22 according to https://en.wikipedia.org/wiki/Qt_version_history
The dnf error I mentioned with pipewire-0.2.3 and xdg-desktop-portal-kde-5.13.4-2 has been reported by a few others https://bugzilla.redhat.com/show_bug.cgi?id=1626133 https://bugzilla.redhat.com/show_bug.cgi?id=1626823 FEDORA-2018-973e14809c
rdieter edited this update.
This update has been submitted for batched by rdieter.
This update has been submitted for stable by bodhi.
This update has been pushed to stable.
@xvitaly Is there any solution for Telegram Desktop in sight? (As you're aware of the problem, I didn't open a rpmfusion bug.)
@samoht0 I've just rebuilt telegram-desktop package and it works. Yes, please open an rpmfusion bug if it is not opened.
@samoht0 Fixed version already in RPM Fusion Koji. Tomorrow it will be pushed to stable repositories.
@xvitaly Thanks for your efforts.
@nerijus Ah, good news. As xvitaly maintains the package I considered it unnecessary to set an extra reminder in bugzilla (if not explicitly requested)...