Description of problem: Avogadro2 binary software is not in distribution. Version-Release number of selected component (if applicable): 1.90 How reproducible: urpmi avogadrolibs try finding avogadro binary... There's none. Steps to Reproduce: 1. 2. 3.
Why does this report have status "NEW - FIXED"? That shouldn't be possible, CC'ing LpSolit and stormi. In the summary of avogadrolibs I read: > The code in this repository is a rewrite of Avogadro with source > code split across a libraries repository and an application repository. Maybe packaging avogadroapp was forgotten or impossible https://github.com/OpenChemistry/avogadroapp/archive/1.90.0.tar.gz Assigning to the avogadrolibs maintainer.
Assignee: bugsquad => geiger.david68210Summary: Avogadro2 binairy is not provided => Avogadro2 binary is not providedCC: (none) => LpSolit, marja11, shlomif
CC: LpSolit, shlomif => (none)
>> The code in this repository is a rewrite of Avogadro with source >> code split across a libraries repository and an application repository. >Maybe packaging avogadroapp was forgotten or impossible >https://github.com/OpenChemistry/avogadroapp/archive/1.90.0.tar.gz I've just compiled it under mageia 6 without any issues. So seems to be forgotten. JB
Thanks for your report jb butet! Now package avogadro2 imported on Cauldron and also on mga6/Core/Backports_testing repo. Please test it, thanks in advance.
It seems I can't find avogadro2 in mga6/Core/Backports_testing repo.
CC: (none) => dimdob1
Hmmmm strange! So re-submitted avogadro2 in mga6/Core/Backports_testing repo.
(In reply to David GEIGER from comment #5) > Hmmmm strange! > > So re-submitted avogadro2 in mga6/Core/Backports_testing repo. Thanks! Now I have found it in Backports_testing repo. Based on my tests, it seems it works with no issues so far.
Assigning to QA, Advisory: ======================== avogadro2 package is missing on a mga6 system while we have avogadrolibs who might needs/uses it. So this update fixes this missing package backporting it. ======================== Packages in 6/core/backports_testing: ======================== avogadro2-1.90.0-1.mga6.i586.rpm avogadro2-1.90.0-1.mga6.x86_64.rpm Source RPM: ======================== avogadro2-1.90.0-1.mga6.src.rpm
Version: Cauldron => 6Assignee: geiger.david68210 => qa-bugsComponent: RPM Packages => Backports
mga6, x86_64 Confirmed that there is no avogadro2 package. Enabled backports testing and found it available. (medium "Core Release") avogadrolibs 1.90.0 2.mga6 x86_64 lib64inchi1 1.0.4 7.mga6 x86_64 lib64openbabel4 2.3.2 19.mga6 x86_64 lib64pgm5.2_0 5.2.122 3.mga6 x86_64 lib64symspg0 1.9.9 1.mga6 x86_64 molequeue 0.8.0 2.mga6 x86_64 openbabel 2.3.2 19.mga6 x86_64 (medium "Core Updates") lib64zmq5 4.2.2 1.1.mga6 x86_64 (medium "Core Backports Testing") avogadro2 1.90.0 1.mga6 x86_64 Installation OK. $ ls /bin/avogadro* /bin/avogadro2* Running avogadro2 launches a gui for displaying molecules with their bonds. Clicking on the display area shows what looks like a methane molecule. One for the experts. Looks good for 64-bits.
CC: (none) => tarazed25Whiteboard: (none) => MGA6-64-OK
MGA6-32 MATE on IBM Thinkpad R50e Installed avogadro2-1.90.0-1.mga6 and avogadrolibs-1.90.0-2.mga6, plus dependencies they draw in. I'll consider myself as the expert in the house, as I hold a degree in chemical engineering (abandonned that professionaly in 1971 to go programming), but at CLI: $ avogadro2 Extension plugins dynamically found... 20 OBProcess::executeObabel: Running "obabel" "-L formats read" OBProcess::executeObabel: Running "obabel" "-L formats write" OBProcess::executeObabel: Running "obabel" "-L forcefields" OBProcess::executeObabel: Running "obabel" "-V" QProcess: Destroyed while process ("obabel") is still running. "obabel not found! Disabling Open Babel plugin actions." Checking for generator scripts in "/usr/bin/../lib/avogadro2/scripts/inputGenerators" Checking for file format scripts in "/usr/bin/../lib/avogadro2/scripts/formatScripts" Could not register format User Script: ZYX Example Format due to name conflict. Could not register format User Script: ZYX Example Format due to name conflict. "Navigator" added "Editor" added "Selection" added "Manipulator" added "BondCentric" added "MeasureTool" added "PlayerTool" added Gtk-Message: GtkDialog mapped without a transient parent. This is discouraged. The GUI launches allright, but I the working area still shows the terminal window underneath it, and I cannot create any molecule, just no reaction at all when clicking with the "Draw" tool selected.
CC: (none) => herman.viaene
Cross-checking against the terminal output in comment 9... $ avogadro2 Extension plugins dynamically found... 20 OBProcess::executeObabel: Running "obabel" "-L formats read" OBProcess::executeObabel: Running "obabel" "-L formats write" OBProcess::executeObabel: Running "obabel" "-L forcefields" OBProcess::executeObabel: Running "obabel" "-V" "obabel" found: "obabel: Open Babel 2.3.2 -- Jun 3 2017 -- 13:45:14" Checking for generator scripts in "/usr/bin/../lib64/avogadro2/scripts/inputGenerators" Checking for file format scripts in "/usr/bin/../lib64/avogadro2/scripts/formatScripts" Could not register format User Script: ZYX Example Format due to name conflict. Could not register format User Script: ZYX Example Format due to name conflict. "Navigator" added "Editor" added "Selection" added "Manipulator" added "BondCentric" added "MeasureTool" added "PlayerTool" added Gtk-Message: GtkDialog mapped without a transient parent. This is discouraged. The draw area is opaque and can be used freely. Created some odd molecules with O, N, C and H atoms. Right click deleted an atom. Van der Waals changed to the appearance of overlapping force-fields. $ locate avogadro2/scripts/ /usr/lib64/avogadro2/scripts/formatScripts /usr/lib64/avogadro2/scripts/inputGenerators /usr/lib64/avogadro2/scripts/formatScripts/zyx.py /usr/lib64/avogadro2/scripts/formatScripts/zyx.pyc /usr/lib64/avogadro2/scripts/formatScripts/zyx.pyo /usr/lib64/avogadro2/scripts/inputGenerators/apbs.py /usr/lib64/avogadro2/scripts/inputGenerators/apbs.pyc /usr/lib64/avogadro2/scripts/inputGenerators/apbs.pyo [...] $ locate openbabel /usr/lib64/libopenbabel.so.4 /usr/lib64/libopenbabel.so.4.0.2 /usr/lib64/openbabel /usr/lib64/openbabel/APIInterface.so [...] /usr/share/openbabel/2.3.2 /usr/share/openbabel/2.3.2/MACCS.txt /usr/share/openbabel/2.3.2/SMARTS_InteLigand.txt /usr/share/openbabel/2.3.2/UFF.prm /usr/share/openbabel/2.3.2/aromatic.txt /usr/share/openbabel/2.3.2/atomtyp.txt /usr/share/openbabel/2.3.2/babel_povray3.inc /usr/share/openbabel/2.3.2/bondtyp.txt /usr/share/openbabel/2.3.2/element.txt [...] No clues there to explain the failure for 32-bits. Maybe you can do a check Herman, just in case something is missing?
Referring to comment 10. Ran this up in a 32-bit mga6 vbox and it worked properly, just as in the 64-bit version.
(In reply to Herman Viaene from comment #9) AFAIK avogadro2 uses new version of OpenGL to render the molecules (and for that matter newer Qt5). Please check your video card whether it supports the new OpenGL (I assume its integrated video card) at certain resolutions and refresh rate (maybe on Lenovo web site). Lower the resolution and the refresh rate of your monitor and try again avogadro.
OK, that's the reason: this old thing does not support newer OpenGL. That has come up in the past with other updates. So, I cannot object this update going through.
OK Herman. I'll give the 32-bit OK and the validated flag if it is applicable.
Whiteboard: MGA6-64-OK => MGA6-32-OK MGA6-64-OKKeywords: (none) => validated_backport
avogadro2-1.90.0-1.mga6.src.rpm moved
CC: (none) => tmbStatus: NEW => RESOLVEDResolution: (none) => FIXED