Re: openbabel-3.1* in Rawhide
On Sat, Sep 25, 2021 at 5:10 PM Alexander Ploumistos wrote: > I built the latest avogadro2 and avogadro2-libs from the srpm in your > copr for F34 and I hit some graphical glitches again. On Wayland, > Avogadro2 for X11 has a transparent canvas, whereas the other one (I > guess Wayland) doesn't, but as soon as I add a fourth atom to the > drawing, it crashes: > > /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, > _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = > Eigen::Matrix; _Alloc = > std::allocator >; std::vector<_Tp, > _Alloc>::reference = Eigen::Matrix&; std::vector<_Tp, > _Alloc>::size_type = long unsigned int]: Assertion '__n < > this->size()' failed. > Aborted (core dumped) I don't know if this is the same as the inchi-related abort, but that one is caused by this code, on lines 178-180 of molecule_smiles.cpp, in Molecule::ToInChI(): std::string s = ostream.str(); s[s.length() - 1] = '\0'; // Abort happens here return ( QString( s.c_str() ) ); The abort happens because s is the empty string, so s.length() == 0, and assigning to s[-1] just isn't a good idea. I'm pretty sure that line isn't needed anyway. Isn't s.c_str() guaranteed to provide a null-terminated C string? -- Jerry James http://www.jamezone.org/ ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: Linux Plumbers Conference - Open Printing Micro Conference
On Thu, Sep 23, 2021 at 09:01:07PM -0500, Brandon Nielsen wrote: > For anyone looking to play with these right now without a snap, I've started > a copr[0]. I don't have the systemd service working yet, but you can start > the printer app server manually. Can you round out the set with the hplip and gutenprint applications too? https://github.com/OpenPrinting/hplip-printer-app/ https://github.com/OpenPrinting/gutenprint-printer-app/ The latter in particular is of considerable interest to me, and I'd prefer to not have to deal with the snap ecosystem. - Solomon -- Solomon Peachypizza at shaftnet dot org (email&xmpp) @pizza:shaftnet dot org (matrix) High Springs, FL speachy (libra.chat) signature.asc Description: PGP signature ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Re: openbabel-3.1* in Rawhide
On Sat, Sep 25, 2021 at 5:05 PM Alexander Ploumistos wrote: > > I will try with a Fedora 34 VM later and report back. I got pretty much the same results on F34. I think xdrawchem works better with Open Babel 3 than it does with Open Babel 2, at least as far as structure cleanup goes (I installed the current version in F34). With Open Babel 2, SMILES output is also asterisks and trying InChi output crashes the program, so nothing changed there. gnome-chemistry-utils programs can't find the required shared object files in F34 either. I built the latest avogadro2 and avogadro2-libs from the srpm in your copr for F34 and I hit some graphical glitches again. On Wayland, Avogadro2 for X11 has a transparent canvas, whereas the other one (I guess Wayland) doesn't, but as soon as I add a fourth atom to the drawing, it crashes: /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = Eigen::Matrix; _Alloc = std::allocator >; std::vector<_Tp, _Alloc>::reference = Eigen::Matrix&; std::vector<_Tp, _Alloc>::size_type = long unsigned int]: Assertion '__n < this->size()' failed. Aborted (core dumped) However, when given a badly drawn propene or propane molecule, the structure optimization works fine. On X, I did not get the transparent canvas, but I got the crash at the fourth atom. I was able to open some of my existing files though, with up to several thousand atoms and the structure optimization worked fine after I had deformed them. At least any issues are not from Open Babel 3 (I guess). ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Self Introduction: Adam Thiede
Happy Saturday, devel, good to meet you. I've used Fedora and its downstreams (RHEL & rebuilds) for a long time and would like to contribute back in any way I can. I'm introducing myself per guidelines here: https://docs.fedoraproject.org/en-US/package-maintainers/Joining_the_Package_Maintainers/#join_the_important_mailing_lists There is some more obscure software I'd like to package, but I'd also like to help where it's most needed. I have a full time sysadmin job and a family so can't promise a lot of time, but will do what I can. Thank you for your time. -Adam Thiede ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Fedora-Rawhide-20210925.n.0 compose check report
Missing expected images: Xfce raw-xz armhfp Compose FAILS proposed Rawhide gating check! 1 of 43 required test results missing Unsatisfied gating requirements that could not be mapped to openQA tests: MISSING: fedora.Cloud_Base-qcow2-qcow2.x86_64.64bit - compose.cloud_autocloud Failed openQA tests: 7/206 (x86_64), 12/141 (aarch64) New failures (same test not failed in Fedora-Rawhide-20210924.n.0): ID: 1001625 Test: x86_64 Workstation-live-iso desktop_login URL: https://openqa.fedoraproject.org/tests/1001625 ID: 1001641 Test: x86_64 KDE-live-iso desktop_login URL: https://openqa.fedoraproject.org/tests/1001641 ID: 1001673 Test: x86_64 Cloud_Base-qcow2-qcow2 base_package_install_remove@uefi URL: https://openqa.fedoraproject.org/tests/1001673 ID: 1001691 Test: aarch64 Server-dvd-iso install_repository_hd_variation@uefi URL: https://openqa.fedoraproject.org/tests/1001691 ID: 1001700 Test: aarch64 Server-dvd-iso install_blivet_standard_partition_ext4@uefi URL: https://openqa.fedoraproject.org/tests/1001700 ID: 1001729 Test: aarch64 Server-dvd-iso server_cockpit_basic@uefi URL: https://openqa.fedoraproject.org/tests/1001729 ID: 1001745 Test: aarch64 Workstation-raw_xz-raw.xz desktop_browser@uefi URL: https://openqa.fedoraproject.org/tests/1001745 ID: 1001823 Test: x86_64 universal upgrade_2_minimal_uefi@uefi URL: https://openqa.fedoraproject.org/tests/1001823 ID: 1001864 Test: aarch64 universal install_package_set_minimal@uefi URL: https://openqa.fedoraproject.org/tests/1001864 ID: 1001869 Test: aarch64 universal install_mirrorlist_graphical@uefi URL: https://openqa.fedoraproject.org/tests/1001869 Old failures (same test failed in Fedora-Rawhide-20210924.n.0): ID: 1001638 Test: x86_64 KDE-live-iso apps_startstop URL: https://openqa.fedoraproject.org/tests/1001638 ID: 1001752 Test: aarch64 Workstation-raw_xz-raw.xz gedit@uefi URL: https://openqa.fedoraproject.org/tests/1001752 ID: 1001785 Test: x86_64 universal install_european_language URL: https://openqa.fedoraproject.org/tests/1001785 ID: 1001847 Test: aarch64 universal install_cyrillic_language@uefi URL: https://openqa.fedoraproject.org/tests/1001847 ID: 1001852 Test: aarch64 universal upgrade_minimal_64bit@uefi URL: https://openqa.fedoraproject.org/tests/1001852 ID: 1001857 Test: aarch64 universal upgrade_server_domain_controller@uefi URL: https://openqa.fedoraproject.org/tests/1001857 ID: 1001883 Test: aarch64 universal install_european_language@uefi URL: https://openqa.fedoraproject.org/tests/1001883 ID: 1001894 Test: x86_64 universal install_asian_language URL: https://openqa.fedoraproject.org/tests/1001894 ID: 1001896 Test: aarch64 universal install_asian_language@uefi URL: https://openqa.fedoraproject.org/tests/1001896 Soft failed openQA tests: 4/206 (x86_64), 5/141 (aarch64) (Tests completed, but using a workaround for a known bug) Old soft failures (same test soft failed in Fedora-Rawhide-20210924.n.0): ID: 1001612 Test: x86_64 Workstation-live-iso gedit URL: https://openqa.fedoraproject.org/tests/1001612 ID: 1001654 Test: x86_64 Silverblue-dvd_ostree-iso evince URL: https://openqa.fedoraproject.org/tests/1001654 ID: 1001655 Test: x86_64 Silverblue-dvd_ostree-iso gedit URL: https://openqa.fedoraproject.org/tests/1001655 ID: 1001666 Test: x86_64 Cloud_Base-qcow2-qcow2 cloud_autocloud@uefi URL: https://openqa.fedoraproject.org/tests/1001666 ID: 1001675 Test: aarch64 Minimal-raw_xz-raw.xz install_arm_image_deployment_upload@uefi URL: https://openqa.fedoraproject.org/tests/1001675 ID: 1001732 Test: aarch64 Server-raw_xz-raw.xz install_arm_image_deployment_upload@uefi URL: https://openqa.fedoraproject.org/tests/1001732 ID: 1001751 Test: aarch64 Workstation-raw_xz-raw.xz evince@uefi URL: https://openqa.fedoraproject.org/tests/1001751 ID: 1001753 Test: aarch64 Workstation-raw_xz-raw.xz desktop_update_graphical@uefi URL: https://openqa.fedoraproject.org/tests/1001753 ID: 1001759 Test: aarch64 Cloud_Base-qcow2-qcow2 cloud_autocloud@uefi URL: https://openqa.fedoraproject.org/tests/1001759 Passed openQA tests: 195/206 (x86_64), 123/141 (aarch64) New passes (same test not passed in Fedora-Rawhide-20210924.n.0): ID: 1001547 Test: x86_64 Server-boot-iso install_default@uefi URL: https://openqa.fedoraproject.org/tests/1001547 ID: 1001685 Test: aarch64 Server-dvd-iso install_blivet_lvm_ext4@uefi URL: https://openqa.fedoraproject.org/tests/1001685 ID: 1001694 Test: aarch64 Server-dvd-iso install_vncconnect_client@uefi URL: https://openqa.fedoraproject.org/tests/1001694 ID: 1001695 Test: aarch64 Server-dvd-iso install_vncconnect_server@uefi URL: https://openqa.fedoraproject.org/tests/1001695 ID: 1001698 Test: aarch64 Server-dvd-iso install_default_upload@uefi URL: https://openqa.fedoraproject.org/tests/1001698 ID: 1001699 Test: aarch64 Server-dvd-iso base_selinux@uefi URL: https://openqa.fedoraproject.org/tests/10016
Re: openbabel-3.1* in Rawhide
Hello Antonio,
On Fri, Sep 24, 2021 at 7:50 PM Antonio T. sagitter
wrote:
>
> Even the porting to openbabel3 of 'xdrawchem' is done.
> Please, can anyone that uses these software test them?
I spun up a Fedora 35 VM and installed everything from your copr,
didn't mess with any system settings. Here's what I've got.
* xdrawchem:
I hadn't used it since Molsketch was revived a few years ago and I'm
not sure if everything was working as expected. My guess was that
structure refinement ("clean up molecule") and the SMILES/InChi output
had to do with Open Babel, so I tried those. For SMILES, regardless of
the atom type, I always get an asterisk, e.g. for butane. Double
bonds and such are correctly placed in the star-filled strings though.
InChi crashed the program:
==
*** Open Babel Warning in InChI code
#1 :Unsupported in this mode element '*'
==
*** Open Babel Error in InChI code
InChI generation failed
/usr/include/c++/11/bits/basic_string.h:1058:
std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference
std::__cxx11::basic_string<_CharT, _Traits,
_Alloc>::operator[](std::__cxx11::basic_string<_CharT, _Traits,
_Alloc>::size_type) [with _CharT = char; _Traits =
std::char_traits; _Alloc = std::allocator;
std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::reference =
char&; std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type
= long unsigned int]: Assertion '__pos <= size()' failed.
Aborted (core dumped)
Structure cleanup sort of works, but as 2D projections of the actual
3D structures, which is not that great-looking for a 2D drawing
program.
* gnome-chemistry-utils:
While the (right) gnome-chemistry-utils-libs package is installed, I
could not get the individual programs to start, e.g.
$ gcrystal
gcrystal: error while loading shared libraries: libgcu-0.14.so.0:
cannot open shared object file: No such file or directory
$ gchemcalc
gchemcalc: error while loading shared libraries: libgcugtk-0.14.so.0:
cannot open shared object file: No such file or directory
* Avogadro2:
Avogadro appears to be working, but I can't see anything on the
canvas, it displays whatever window is behind it on the screen, or the
wallpaper if there's nothing else there. Maybe a Wayland bug?
I will try with a Fedora 34 VM later and report back.
P.S.: I have never used ghemical, so I didn't try it.
___
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Fedora rawhide compose report: 20210925.n.0 changes
OLD: Fedora-Rawhide-20210924.n.0 NEW: Fedora-Rawhide-20210925.n.0 = SUMMARY = Added images:0 Dropped images: 0 Added packages: 36 Dropped packages:2 Upgraded packages: 67 Downgraded packages: 0 Size of added packages: 105.52 MiB Size of dropped packages:44.04 MiB Size of upgraded packages: 475.19 MiB Size of downgraded packages: 0 B Size change of upgraded packages: -79.99 MiB Size change of downgraded packages: 0 B = ADDED IMAGES = = DROPPED IMAGES = = ADDED PACKAGES = Package: golang-github-antchfx-htmlquery-1.2.3-1.fc36 Summary: Htmlquery is golang XPath package for HTML query RPMs:golang-github-antchfx-htmlquery-devel Size:14.90 KiB Package: golang-github-antchfx-xmlquery-1.3.6-1.fc36 Summary: Xmlquery is Golang XPath package for XML query RPMs:golang-github-antchfx-xmlquery-devel Size:26.23 KiB Package: golang-github-aquasecurity-dep-parser-0-0.1.20210920gitb95c2c0.fc36 Summary: Dependency Parser for Multiple Programming Languages RPMs:golang-github-aquasecurity-dep-parser-devel Size:65.95 KiB Package: golang-github-aquasecurity-pep440-version-0-0.2.20210920git22b2f89.fc36 Summary: A golang library for parsing PEP 440 compliant Python versions RPMs:golang-github-aquasecurity-pep440-version-devel Size:23.00 KiB Package: golang-github-aquasecurity-version-0-0.1.20210920git637058c.fc36 Summary: A Go library for parsing and verifying versions and version constraints RPMs:golang-github-aquasecurity-version-devel Size:32.40 KiB Package: golang-github-bmatcuk-doublestar-3-3.0.0-1.fc36 Summary: Implements support for double star (**) matches RPMs:golang-github-bmatcuk-doublestar-3-devel Size:19.69 KiB Package: golang-github-c4milo-unpackit-0.1.0-2.fc36 Summary: Go package to natively decompress and unarchive tar.gz, tar.bzip2, tar.xz, zip and tar files RPMs:golang-github-c4milo-unpackit-devel Size:20.32 KiB Package: golang-github-docker-slim-1.36.4-4.fc36 Summary: Minify your Docker container image by up to 30x RPMs:golang-github-docker-slim golang-github-docker-slim-devel Size:20.45 MiB Package: golang-github-docker-slim-uilive-0.0.2-2.20210920gitc7c9d1c.fc36 Summary: Uilive is a go library for updating terminal output in realtime RPMs:golang-github-docker-slim-uilive-devel Size:153.24 KiB Package: golang-github-docker-slim-uiprogress-0.0.1-2.20210920git9d4396e.fc36 Summary: A go library to render progress bars in terminal applications RPMs:golang-github-docker-slim-uiprogress-devel Size:1.41 MiB Package: golang-github-docker-slim-update-0-0.2.20210920gited40247.fc36 Summary: Build self-updating Golang programs RPMs:golang-github-docker-slim-update-devel Size:29.92 KiB Package: golang-github-doug-martin-goqu-8-8.6.0-1.fc36 Summary: SQL builder and query library for golang RPMs:golang-github-doug-martin-goqu-8-devel Size:133.69 KiB Package: golang-github-genuinetools-pkg-0-0.1.20210920git2fcf164.fc36 Summary: A home for various Go packages to be imported by other projects RPMs:golang-github-genuinetools-pkg-devel Size:17.73 KiB Package: golang-github-gocolly-colly-2-2.1.0-2.20210920git2f09941.fc36 Summary: Elegant Scraper and Crawler Framework for Golang RPMs:golang-github-gocolly-colly-2 golang-github-gocolly-colly-2-devel Size:3.18 MiB Package: golang-github-gosidekick-goconfig-1.3.0-2.fc36 Summary: Populates the fields of a struct with parameters from command line RPMs:compat-golang-github-crgimenes-goconfig-devel golang-github-gosidekick-goconfig-devel Size:41.65 KiB Package: golang-github-guregu-null-3.5.0-1.fc36 Summary: Reasonable handling of nullable values RPMs:golang-github-guregu-null-devel Size:21.94 KiB Package: golang-github-hooklift-assert-0.1.0-1.fc36 Summary: Minimalist assertion library for Go RPMs:golang-github-hooklift-assert-devel Size:14.34 KiB Package: golang-github-kennygrant-sanitize-1.2.4-1.fc36 Summary: Functions for sanitizing text in golang strings RPMs:golang-github-kennygrant-sanitize-devel Size:16.81 KiB Package: golang-github-knqyf263-apk-version-0-0.1.20210920git041fdbb.fc36 Summary: A golang library for parsing apk package versions RPMs:golang-github-knqyf263-apk-version-devel Size:19.97 KiB Package: golang-github-knqyf263-deb-version-0-0.1.20210920git09fca49.fc36 Summary: A golang library for parsing deb package versions RPMs:golang-github-knqyf263-deb-version-devel Size:13.55 KiB Package: golang-github-knqyf263-rpm-version-0-0.1.20210920git74609b8.fc36 Summary: A golang library for parsing rpm package versions RPMs:golang-github-knqyf263-rpm-version-devel Size:23.53 KiB Package: golang-github-ldelossa-responserecorder-1.0.1-1.fc36 Summary: A ResponseRecorder for production RPMs:golang-github-ldelossa-responserecorder-devel Size:11.02 KiB Package: golang-github-nuveo-log-0-0.1.20210920git44d02db.fc36
Fedora-Cloud-34-20210925.0 compose check report
No missing expected images. Soft failed openQA tests: 1/8 (x86_64), 1/8 (aarch64) (Tests completed, but using a workaround for a known bug) Old soft failures (same test soft failed in Fedora-Cloud-34-20210924.0): ID: 1001414 Test: x86_64 Cloud_Base-qcow2-qcow2 cloud_autocloud URL: https://openqa.fedoraproject.org/tests/1001414 ID: 1001422 Test: aarch64 Cloud_Base-qcow2-qcow2 cloud_autocloud@uefi URL: https://openqa.fedoraproject.org/tests/1001422 Passed openQA tests: 7/8 (x86_64), 7/8 (aarch64) -- Mail generated by check-compose: https://pagure.io/fedora-qa/check-compose ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Orphaning two python packages
I'm going to orphan python-graphene-sqlalchemy and python-graphql-server as I've lost interest in maintaining them. Graphql-server is updated and already uses latest python packaging guidelines. Graphene-sqlalchemy could be updated to 3.0.0b1, but that would require an update to latest beta for python-graphene and aiodataloader as a new package in Fedora. Mattia ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
Fedora-Cloud-33-20210925.0 compose check report
No missing expected images. Soft failed openQA tests: 1/8 (x86_64), 1/8 (aarch64) (Tests completed, but using a workaround for a known bug) Old soft failures (same test soft failed in Fedora-Cloud-33-20210924.0): ID: 1001281 Test: x86_64 Cloud_Base-qcow2-qcow2 cloud_autocloud URL: https://openqa.fedoraproject.org/tests/1001281 ID: 1001289 Test: aarch64 Cloud_Base-qcow2-qcow2 cloud_autocloud@uefi URL: https://openqa.fedoraproject.org/tests/1001289 Passed openQA tests: 7/8 (x86_64), 7/8 (aarch64) -- Mail generated by check-compose: https://pagure.io/fedora-qa/check-compose ___ devel mailing list -- devel@lists.fedoraproject.org To unsubscribe send an email to devel-le...@lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure
