Our automated repository checks [1] have detected that the 'science' repository contains ebuilds that trigger fatal errors during the cache regeneration. This usually means that the ebuilds call 'die' in global scope indicating serious issues or have other serious QA violations. Global-scope failures prevent the ebuild not only from being installed but also from being properly processed by the Package Manager. Since metadata can not be obtained for those ebuilds, no cache entries are created for them and the Package Manager needs to retry running them every time it stumbles upon them. This involves both a serious slowdown and repeating error output while performing dependency resolution. The most common cause of global-scope failures is use of removed or banned APIs in old ebuilds. In particular, this includes eclasses being removed or removing support for old EAPIs. Nonetheless there are also other issues such as performing illegal operations in global scope (external program calls), malformed bash in ebuilds or malformed metadata.xml. The error log for the repository can be found at: https://qa-reports.gentoo.org/output/repos/science.html In particular, please look for highlighted '!!! ERROR' and '!!! caught exception' lines. The former usually mean failures coming from eclasses and the ebuild itself, while exceptions usually mean malformed ebuilds or metadata.xml. Please note that due to technical limitations of pkgcore, the processing stops on the first error found. Once solved, please wait ~30 minutes for the report to refresh in case new errors may appear. Please fix the issue ASAP, possibly via removing unmaintained, old ebuilds. We reserve the right to remove the repository from our list if we do not receive any reply within 4 weeks. [1]:https://wiki.gentoo.org/wiki/Project:Repository_mirror_and_CI
Ping.
ACK, will do on Sunday.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/proj/sci.git/commit/?id=955116fde829ade97ea11c5a48db3433f4f5e3bb commit 955116fde829ade97ea11c5a48db3433f4f5e3bb Author: Benda Xu <heroxbd@gentoo.org> AuthorDate: 2018-09-10 01:30:49 +0000 Commit: Benda Xu <heroxbd@gentoo.org> CommitDate: 2018-09-10 01:34:53 +0000 sci-biology/ugene: drop old versions. Bug: https://bugs.gentoo.org/663110 Package-Manager: Portage-2.3.48, Repoman-2.3.10 sci-biology/ugene/Manifest | 2 -- sci-biology/ugene/ugene-1.13.3.ebuild | 34 ---------------------------------- sci-biology/ugene/ugene-1.16.1.ebuild | 34 ---------------------------------- 3 files changed, 70 deletions(-)
Hi Martin, we are looking into the packages in science overlay that causing repository check failures. Some sci-biology packages are still using qt4 which has been completely removed from Gentoo. Would you please fix them? @Michal, sci-biology/kmergenie seems strange, I can't reproduce the error shown in the repository check page at https://qa-reports.gentoo.org/output/repos/science.html
Look at the first error only, it doesn't recover properly afterwards. Then wait for it to update.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/proj/sci.git/commit/?id=b521d9270e23a0666d0805885a969f6a8a1ab9bc commit b521d9270e23a0666d0805885a969f6a8a1ab9bc Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> AuthorDate: 2018-09-10 17:20:19 +0000 Commit: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> CommitDate: 2018-09-10 17:20:19 +0000 sci-biology/ngsview: drop an outdated package requiring qt3 The was masked out and was written for qt3. It is unclear if it would compile using newer qmake. Also, sys-libs/db-4.3:*[cxx] dependency would have to be improved and inlcude and libdir paths would need to be inserted into the Makefiles. Removing. Bug: https://bugs.gentoo.org/663110 sci-biology/ngsview/Manifest | 1 - sci-biology/ngsview/metadata.xml | 15 --------------- sci-biology/ngsview/ngsview-0.91.ebuild | 34 --------------------------------- 3 files changed, 50 deletions(-)
Thanks Martin! And thanks Michal for your hints.
Hi Christophe, Could you please have a look into sci-misc/elmer-gui to evaluate if qt4 can be safely dropped? Thanks, Benda
I assume sci-biology/amos will popup later too. It was written for qt3, it was possoble to compile the hawkeye binary using qt4 too. Please test yourself if it can compile with qt5.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/proj/sci.git/commit/?id=5e6e183d8bca94b14d155524d8feeaaf4286e7dd commit 5e6e183d8bca94b14d155524d8feeaaf4286e7dd Author: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> AuthorDate: 2018-09-11 14:09:28 +0000 Commit: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> CommitDate: 2018-09-11 14:09:28 +0000 sci-biology/amos: adjust to SLOTed jellyfish and drop qt4 Jellyfish resides in ${EPREFIX}/usr/include/jellyfish1/ now. The package needed qt4 with qt3support enabled to compile hawkeye utility. Let's try with qt5 core only. Also enabling compilation of all utilities if they pass configure checks. Currently, jellyfish linking fails with some cxx linking error, maybe my -lm or -lpthreads needs to be recompiled with gcc-8.2.0 too? Also, boot is somehow not picked up. Bug: https://bugs.gentoo.org/show_bug.cgi?id=663110 Package-Manager: Portage-2.3.48, Repoman-2.3.10 sci-biology/amos/amos-3.1.0-r2.ebuild | 20 +++++++--- sci-biology/amos/amos-9999.ebuild | 21 +++++++---- .../files/amos-3.1.0-rename_to_jellyfish1.patch | 43 ++++++++++++++++++++++ 3 files changed, 71 insertions(+), 13 deletions(-)
@Benda: Sorry, I have not been using the elemer packages in quite a while, nor doo I have a gentoo machine available currently. But from what I see the elmer related ebuild would need to be updated since the sources moved to github: https://github.com/ElmerCSC/elmerfem/tree/devel/ElmerGUI However it still seems to require some >=dev-qt/qt*-4.8:4 packages.
(In reply to Christophe Paccolat from comment #11) > @Benda: Sorry, I have not been using the elemer packages in quite a while, > nor doo I have a gentoo machine available currently. But from what I see the > elmer related ebuild would need to be updated since the sources moved to > github: > https://github.com/ElmerCSC/elmerfem/tree/devel/ElmerGUI > > However it still seems to require some >=dev-qt/qt*-4.8:4 packages. Looking at CMakeList.txt it looks like QT5 is supported in the main branch and in the latest release. I don't know how much work it would be to update the package.
(In reply to Michał Górny from comment #13) > Ping. Ack will act on Sep. 26. https://archives.gentoo.org/gentoo-science/message/39ac88dfe6652e29926131f023f566dd
This is fixed, apparently.
