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#24 openbabel features on molsketch 0.5.1
Hello developers.
We are compiling molsketch 0.5.1Qt5 on Fedora 27 including shared libraries. This is the build log: https://paste.fedoraproject.org/paste/TWX3HpfkR75IXGtvnSuhyA
molsketch looks not always activate the Openbabel features, altought libobabeliface-qt5.so is compiled
$ ldd /usr/bin/molsketch-qt5
linux-vdso.so.1 (0x00007fff65cf0000)
libmolsketch-qt5.so.0 => /lib64/libmolsketch-qt5.so.0 (0x00007f0418f79000)
libQt5PrintSupport.so.5 => /lib64/libQt5PrintSupport.so.5 (0x00007f0418d0b000)
libQt5Svg.so.5 => /lib64/libQt5Svg.so.5 (0x00007f0418ab5000)
libQt5Widgets.so.5 => /lib64/libQt5Widgets.so.5 (0x00007f0418269000)
libQt5Gui.so.5 => /lib64/libQt5Gui.so.5 (0x00007f0417bab000)
libQt5Network.so.5 => /lib64/libQt5Network.so.5 (0x00007f0417823000)
libQt5Core.so.5 => /lib64/libQt5Core.so.5 (0x00007f0417181000)
libGL.so.1 => /lib64/libGL.so.1 (0x00007f0416ef5000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0416cd6000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f0416950000)
libm.so.6 => /lib64/libm.so.6 (0x00007f04165fb000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f04163e4000)
libc.so.6 => /lib64/libc.so.6 (0x00007f0416001000)
libz.so.1 => /lib64/libz.so.1 (0x00007f0415dea000)
libpng16.so.16 => /lib64/libpng16.so.16 (0x00007f0415bb7000)
libharfbuzz.so.0 => /lib64/libharfbuzz.so.0 (0x00007f041591f000)
libssl.so.1.1 => /lib64/libssl.so.1.1 (0x00007f04156b3000)
libcrypto.so.1.1 => /lib64/libcrypto.so.1.1 (0x00007f041522b000)
libsystemd.so.0 => /lib64/libsystemd.so.0 (0x00007f0414fa1000)
libicui18n.so.57 => /lib64/libicui18n.so.57 (0x00007f0414b2e000)
libicuuc.so.57 => /lib64/libicuuc.so.57 (0x00007f0414789000)
libicudata.so.57 => /lib64/libicudata.so.57 (0x00007f0412d0c000)
libpcre2-16.so.0 => /lib64/libpcre2-16.so.0 (0x00007f0412a94000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f0412890000)
libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f041268e000)
libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f041237a000)
/lib64/ld-linux-x86-64.so.2 (0x00007f0419716000)
libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f0412148000)
libX11.so.6 => /lib64/libX11.so.6 (0x00007f0411e0a000)
libXext.so.6 => /lib64/libXext.so.6 (0x00007f0411bf8000)
libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f0411942000)
libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f041168d000)
libgraphite2.so.3 => /lib64/libgraphite2.so.3 (0x00007f0411461000)
libgcrypt.so.20 => /lib64/libgcrypt.so.20 (0x00007f0411147000)
librt.so.1 => /lib64/librt.so.1 (0x00007f0410f3f000)
liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f0410d19000)
liblz4.so.1 => /lib64/liblz4.so.1 (0x00007f0410b04000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f04108db000)
libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f0410668000)
libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f0410440000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f041022f000)
libgpg-error.so.0 => /lib64/libgpg-error.so.0 (0x00007f041001a000)
libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007f040fd96000)
libXau.so.6 => /lib64/libXau.so.6 (0x00007f040fb92000)
$ ldd /usr/lib64/libmolsketch-qt5.so.0.5.1
linux-vdso.so.1 (0x00007ffc03fea000)
libQt5PrintSupport.so.5 => /lib64/libQt5PrintSupport.so.5 (0x00007f55fe6d4000)
libQt5Svg.so.5 => /lib64/libQt5Svg.so.5 (0x00007f55fe47e000)
libQt5Widgets.so.5 => /lib64/libQt5Widgets.so.5 (0x00007f55fdc32000)
libQt5Gui.so.5 => /lib64/libQt5Gui.so.5 (0x00007f55fd574000)
libQt5Core.so.5 => /lib64/libQt5Core.so.5 (0x00007f55fced2000)
libGL.so.1 => /lib64/libGL.so.1 (0x00007f55fcc46000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f55fca27000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f55fc6a1000)
libm.so.6 => /lib64/libm.so.6 (0x00007f55fc34c000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f55fc135000)
libc.so.6 => /lib64/libc.so.6 (0x00007f55fbd52000)
libz.so.1 => /lib64/libz.so.1 (0x00007f55fbb3b000)
libpng16.so.16 => /lib64/libpng16.so.16 (0x00007f55fb908000)
libharfbuzz.so.0 => /lib64/libharfbuzz.so.0 (0x00007f55fb670000)
libsystemd.so.0 => /lib64/libsystemd.so.0 (0x00007f55fb3e6000)
libicui18n.so.57 => /lib64/libicui18n.so.57 (0x00007f55faf73000)
libicuuc.so.57 => /lib64/libicuuc.so.57 (0x00007f55fabce000)
libicudata.so.57 => /lib64/libicudata.so.57 (0x00007f55f9151000)
libpcre2-16.so.0 => /lib64/libpcre2-16.so.0 (0x00007f55f8ed9000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f55f8cd5000)
libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f55f8ad3000)
libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f55f87bf000)
/lib64/ld-linux-x86-64.so.2 (0x00007f55fec95000)
libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f55f858d000)
libX11.so.6 => /lib64/libX11.so.6 (0x00007f55f824f000)
libXext.so.6 => /lib64/libXext.so.6 (0x00007f55f803d000)
libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f55f7d87000)
libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f55f7ad2000)
libgraphite2.so.3 => /lib64/libgraphite2.so.3 (0x00007f55f78a6000)
libgcrypt.so.20 => /lib64/libgcrypt.so.20 (0x00007f55f758c000)
librt.so.1 => /lib64/librt.so.1 (0x00007f55f7384000)
liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f55f715e000)
liblz4.so.1 => /lib64/liblz4.so.1 (0x00007f55f6f49000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f55f6d20000)
libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f55f6aad000)
libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f55f6885000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f55f6674000)
libgpg-error.so.0 => /lib64/libgpg-error.so.0 (0x00007f55f645f000)
libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007f55f61db000)
libXau.so.6 => /lib64/libXau.so.6 (0x00007f55f5fd7000)
$ ldd -r /usr/lib64/libobabeliface-qt5.so.0.5.1
linux-vdso.so.1 (0x00007fff54ffe000)
libmolsketch-qt5.so.0 => /lib64/libmolsketch-qt5.so.0 (0x00007f7c270fc000)
libopenbabel.so.5 => /lib64/libopenbabel.so.5 (0x00007f7c26cb2000)
libQt5PrintSupport.so.5 => /lib64/libQt5PrintSupport.so.5 (0x00007f7c26a44000)
libQt5Svg.so.5 => /lib64/libQt5Svg.so.5 (0x00007f7c267ee000)
libQt5Widgets.so.5 => /lib64/libQt5Widgets.so.5 (0x00007f7c25fa2000)
libQt5Gui.so.5 => /lib64/libQt5Gui.so.5 (0x00007f7c258e4000)
libQt5Core.so.5 => /lib64/libQt5Core.so.5 (0x00007f7c25242000)
libGL.so.1 => /lib64/libGL.so.1 (0x00007f7c24fb6000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f7c24d97000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f7c24a11000)
libm.so.6 => /lib64/libm.so.6 (0x00007f7c246bc000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f7c244a5000)
libc.so.6 => /lib64/libc.so.6 (0x00007f7c240c2000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f7c23ebe000)
libz.so.1 => /lib64/libz.so.1 (0x00007f7c23ca7000)
libpng16.so.16 => /lib64/libpng16.so.16 (0x00007f7c23a74000)
libharfbuzz.so.0 => /lib64/libharfbuzz.so.0 (0x00007f7c237dc000)
libsystemd.so.0 => /lib64/libsystemd.so.0 (0x00007f7c23552000)
libicui18n.so.57 => /lib64/libicui18n.so.57 (0x00007f7c230df000)
libicuuc.so.57 => /lib64/libicuuc.so.57 (0x00007f7c22d3a000)
libicudata.so.57 => /lib64/libicudata.so.57 (0x00007f7c212bd000)
libpcre2-16.so.0 => /lib64/libpcre2-16.so.0 (0x00007f7c21045000)
libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f7c20e43000)
libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f7c20b2f000)
/lib64/ld-linux-x86-64.so.2 (0x00007f7c2765d000)
libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f7c208fd000)
libX11.so.6 => /lib64/libX11.so.6 (0x00007f7c205bf000)
libXext.so.6 => /lib64/libXext.so.6 (0x00007f7c203ad000)
libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f7c200f7000)
libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f7c1fe42000)
libgraphite2.so.3 => /lib64/libgraphite2.so.3 (0x00007f7c1fc16000)
libgcrypt.so.20 => /lib64/libgcrypt.so.20 (0x00007f7c1f8fc000)
librt.so.1 => /lib64/librt.so.1 (0x00007f7c1f6f4000)
liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f7c1f4ce000)
liblz4.so.1 => /lib64/liblz4.so.1 (0x00007f7c1f2b9000)
libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f7c1f090000)
libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f7c1ee1d000)
libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f7c1ebf5000)
libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f7c1e9e4000)
libgpg-error.so.0 => /lib64/libgpg-error.so.0 (0x00007f7c1e7cf000)
libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007f7c1e54b000)
libXau.so.6 => /lib64/libXau.so.6 (0x00007f7c1e347000)
My first question is: are binary files and libraries correctly linked? (I don't see molsketch-qt5 linked to libobabeliface-qt5.so)
Do you know any known regression with Qt-5.9.1?
Which tools/libraries molsketch needs to properly work?
Output from command-line:
$ molsketch-qt5 Info: ((null):0, (null)) Clearing list of molecules. Count: 0 Warning: ((null):0, (null)) :icons/document-new.svg:602:58: Could not resolve property: linearGradient5167 Warning: ((null):0, (null)) :icons/document-new.svg:602:58: Could not resolve property: linearGradient5167 Warning: ((null):0, (null)) :icons/document-open.svg:4290: Could not resolve property: pattern5614 Warning: ((null):0, (null)) :icons/document-open.svg:4290: Could not resolve property: pattern5626 Warning: ((null):0, (null)) :icons/document-open.svg:4290: Could not resolve property: pattern5614 Warning: ((null):0, (null)) :icons/document-open.svg:4290: Could not resolve property: pattern5626 Warning: ((null):0, (null)) QObject::connect: No such slot Molsketch::MolScene::convertImage() Warning: ((null):0, (null)) :icons/preferences-system.svg:1713: Could not resolve property: linearGradient4636 Warning: ((null):0, (null)) :icons/preferences-system.svg:1713: Could not resolve property: linearGradient4592 Warning: ((null):0, (null)) :icons/preferences-system.svg:1713: Could not resolve property: linearGradient4247 Warning: ((null):0, (null)) :icons/preferences-system.svg:1713: Could not resolve property: linearGradient4636 Warning: ((null):0, (null)) :icons/preferences-system.svg:1713: Could not resolve property: linearGradient4592 Warning: ((null):0, (null)) :icons/preferences-system.svg:1713: Could not resolve property: linearGradient4247 Warning: ((null):0, (null)) :icons/help-contents.svg:7092: Could not resolve property: linearGradient3592 Warning: ((null):0, (null)) :icons/help-contents.svg:7092: Could not resolve property: linearGradient7999 Warning: ((null):0, (null)) :icons/help-contents.svg:7092: Could not resolve property: radialGradient2943 Warning: ((null):0, (null)) :icons/help-contents.svg:7092: Could not resolve property: linearGradient3592 Warning: ((null):0, (null)) :icons/help-contents.svg:7092: Could not resolve property: linearGradient7999 Warning: ((null):0, (null)) :icons/help-contents.svg:7092: Could not resolve property: radialGradient2943 Warning: ((null):0, (null)) QGraphicsScene::removeItem: item 0x5645a4d211b0's scene (0x0) is different from this scene (0x5645a46feb60) Warning: ((null):0, (null)) QIODevice::write (QProcess): device not open Warning: ((null):0, (null)) QGraphicsScene::removeItem: item 0x5645a4d211b0's scene (0x0) is different from this scene (0x5645a46feb60) Info: ((null):0, (null)) Clearing list of molecules. Count: 0
Regards.
It seems that you are packaging from the archive's content rather than the install target's result. The result seems to make sense, though. I didn't think obabeliface should be a legitimate include as it's only used by the main app anyhow.
Let's see what Antonio thinks. Then I'll upload my changes and you can start a new RPM build. Sounds alright?
Also, I should probably really set up a Jenkins or something...
I'm always daunted by devel and debug subpackages, I'm only fairly certain about the contents of the main package.
Sure thing.
Following the install target, there is a incongruity between the headers automatically installed by Make and those ones preserved in the
debugsourcerpms; this situation turns on some warnings ofrpmlintcheck tool.If you think that not all headers are useful for developing/debugging, please let us know which are really needed. Potential false-positive warnings can be ignored.
I'm totally open to any suggestions from your side. My reasoning was that if somebody wanted to use anything at all, it would be the libmolsketch part, not the app or the openbabel adapter. Is this assumption wrong? (or, more directly: what do you usually provide a -devel package for? An executable or a library?)
It's not wrong. We can leave everything as it is at present.
Ok, in that case: I just uploaded the fix with the header installation and the FSF addresses in the license texts (as well as the GPL 2 license text) as "snapshots/latest" and you should now be good to go for the package build.
I retrieved the newest snapshot, I reverted Antonio's patch and now I have in my spec file:
and these are the contents of the devel subpackage:
usr/ └── include └── libmolsketch ├── abstractxmlobject.h ├── actions │ ├── abstractitemaction.h │ ├── abstractrecursiveitemaction.h │ ├── alignmentaction.h │ ├── arrowtypeaction.h │ ├── arrowtypewidget.h │ ├── bondtypeaction.h │ ├── bondtypewidget.h │ ├── coloraction.h │ ├── connectaction.h │ ├── deleteaction.h │ ├── drawaction.h │ ├── flipbondaction.h │ ├── flipstereobondsaction.h │ ├── frameaction.h │ ├── frametypeaction.h │ ├── frametypewidget.h │ ├── genericaction.h │ ├── incdecaction.h │ ├── itemgrouptypeaction.h │ ├── itemtypeaction.h │ ├── itemtypeselectionaction.h │ ├── itemtypewidget.h │ ├── linewidthaction.h │ ├── mechanismarrowaction.h │ ├── multiaction.h │ ├── periodictablewidget.h │ ├── reactionarrowaction.h │ ├── ringaction.h │ ├── rotateaction.h │ ├── textaction.h │ └── transformcommand.h ├── arrow.h ├── arrowpopup.h ├── atom.h ├── atompopup.h ├── bond.h ├── boundingboxlinker.h ├── commands.h ├── constants.h ├── coordinatedelegate.h ├── coordinatemodel.h ├── coordinatetableview.h ├── electronsystem.h ├── element.h ├── fileio.h ├── frame.h ├── generics.h ├── graphicsitem.h ├── grid.h ├── helptextemptydock.h ├── helptextonemptylabel.h ├── librarymodel.h ├── libraryview.h ├── lineupaction.h ├── lonepair.h ├── math2d.h ├── mimemolecule.h ├── molecule.h ├── moleculemodelitem.h ├── moleculepopup.h ├── molscene.h ├── molview.h ├── propertieswidget.h ├── qtversionmacros.h ├── radicalelectron.h ├── scenepropertiesdialog.h ├── scenesettings.h ├── stringify.h ├── TextInputItem.h ├── textitem.h └── xmlobjectinterface.hThe OpenBabel adapter source is no longer packaged (I understood that's what was agreed upon, if not I can repackage everything).
Local builds were successful, I will do a couple more in koji to check if everything is OK in every arch and update the review request accordingly.
I still see that
molsketch-debuginfo.x86_64: E: useless-provides debuginfo(build-id), which I suspect that it can be ignored.OpenBabel integration works fine.
It looks different than http://www.gnu.org/licenses/old-licenses/gpl-2.0.txt.
Ah, alright. The link is http://www.gnu.org/licenses/old-licenses/gpl-2.0.html
How urgently do I need to update? (obviously, LGPL is now also "lesser" instead of "library" GPL...)
Last edit: Hendrik Vennekate 2018-02-08
It's not urgent.
Alright, I'd prefer waiting until the next release then.
Ok, by now I've fixed that as well (at least on github) ;)
Hello Hendrik,
Molsketch packages have been built for f26, f27 and rawhide and they are queued for testing. I think you can close this bug now.
Thank you both for all your help and efforts.
Best regards
Alex
Hi Alex,
thanks for the heads-up; that's great news!
And thank you and Antonio for sticking with me here and packaging for Fedora!
Best wishes,
Hendrik