[Bug 997190] New: openbabel cannot find plugins
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 Bug ID: 997190 Summary: openbabel cannot find plugins Classification: openSUSE Product: openSUSE Tumbleweed Version: Current Hardware: Other OS: Other Status: NEW Severity: Normal Priority: P5 - None Component: Other Assignee: bnc-team-screening@forge.provo.novell.com Reporter: blind_commisioner@hotmail.com QA Contact: qa-bugs@suse.de Found By: --- Blocker: --- User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:48.0) Gecko/20100101 Firefox/48.0 Build Identifier: Openbabel cannot find any of the .so files that it uses as plugins and so almost all of its features fail to work. As a workround, it can be pointed at the plugins by setting "export BABEL_LIBDIR=/usr/lib64/openbabel/2.3.2/" (on bash) in which case it works again. Reproducible: Always Steps to Reproduce: 1. Type "babel -L format" Actual Results: formats is not a recognized plugin type. Those with instances of sub-types loaded are: ops Expected Results: A long list starting with "abinit -- ABINIT Output Format [Read-only]" -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 Wolfgang Brehm <wolfgang.brehm@googlemail.com> changed: What |Removed |Added ---------------------------------------------------------------------------- Priority|P5 - None |P4 - Low CC| |wolfgang.brehm@googlemail.c | |om -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 jochen gaedcke <gaedckej@yahoo.de> changed: What |Removed |Added ---------------------------------------------------------------------------- Priority|P4 - Low |P3 - Medium CC| |gaedckej@yahoo.de Hardware|Other |x86-64 OS|Other |SUSE Other Severity|Normal |Major -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 Tomáš Chvátal <tchvatal@suse.com> changed: What |Removed |Added ---------------------------------------------------------------------------- Assignee|kde-maintainers@suse.de |opensuse-kde-bugs@opensuse. | |org -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c1 Wolfgang Bauer <wbauer@tmo.at> changed: What |Removed |Added ---------------------------------------------------------------------------- Priority|P3 - Medium |P5 - None CC| |wbauer@tmo.at Assignee|opensuse-kde-bugs@opensuse. |bnc-team-screening@forge.pr |org |ovo.novell.com --- Comment #1 from Wolfgang Bauer <wbauer@tmo.at> --- openbabel is not maintained by the KDE team. Back to screening... Although, I suppose a question is whether this is still an issue in current packages. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c2 --- Comment #2 from Wolfgang Bauer <wbauer@tmo.at> --- PS, it seems to work as expected in Leap 42.3 here. But that still comes with openbabel 2.3.1. Haven't tested Tumbleweed (or Leap 15.0) though, which habe openbabel 2.4.1. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c3 --- Comment #3 from David Woods <blind_commisioner@hotmail.com> --- The openbabel package currently in Tumbleweed (2.4.1 built 21st Feb) does not include any executables which would seem to be a new and more limiting bug.
From the changelog it seems that the "babel" command that I reported the bug on is being deprecated in favour of the "obabel" command, however neither command is present in the Tumbleweed version.
-- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c4 Wolfgang Bauer <wbauer@tmo.at> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |IN_PROGRESS Summary|openbabel cannot find |openbabel does not contain |plugins |command line tools --- Comment #4 from Wolfgang Bauer <wbauer@tmo.at> --- (In reply to David Woods from comment #3)
The openbabel package currently in Tumbleweed (2.4.1 built 21st Feb) does not include any executables which would seem to be a new and more limiting bug.
Indeed. That also breaks kalzium's "Convert chemical files" function in TW and Leap 15.0 which uses "babel". I had a look, the tools get deleted intentionally after the build. There is no mention why in the current package changelog, but I found https://api.opensuse.org/package/rdiff/science/openbabel?linkrev=base&rev=3 that contained this line: Tue Mar 6 03:27:19 UTC 2012 - stecue@gmail.com - Only lib files packed to coexist with openbabel >= 2.3 (removed from the changelog in later package updates) So this apparently was done to allow to coinstall 2.4 with the stable 2.3.x, but that should no longer be relevant. I'll submit a fix and hope the maintainers accept it... As to the originally reported problem, I suppose this was caused by a version mismatch between openbabel and libopenbabel. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c5 Wolfgang Bauer <wbauer@tmo.at> changed: What |Removed |Added ---------------------------------------------------------------------------- Summary|openbabel does not contain |openbabel cannot find |command line tools |plugins --- Comment #5 from Wolfgang Bauer <wbauer@tmo.at> --- (In reply to Wolfgang Bauer from comment #4)
As to the originally reported problem, I suppose this was caused by a version mismatch between openbabel and libopenbabel.
Hm, that seems to not have been the case. Unfortunately that bug is back now in my modified package with the tools added back. According to strace, it tries to find the libs in /usr/usr/lib64/openbabel/2.4.1 ... Need to investigate. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c6 --- Comment #6 from Wolfgang Bauer <wbauer@tmo.at> --- Ok, the problem is that $LIB_INSTALL_DIR is set to %{_libdir} (which is the absolute libdir path, /usr/lib64) by the %cmake rpm macro, but the CMakeLists.txt prepends $CMAKE_INSTALL_PREFIX because it would set it relative only itself. Fixed it by explicitly unsetting $LIB_INSTALL_DIR when calling %cmake. https://api.opensuse.org/request/show/606845 Btw: (In reply to David Woods from comment #0)
Steps to Reproduce: 1. Type "babel -L format"
With 2.4.1, it apparently needs to be "babel -L formats". With "format" I still get a similar error message here: ormat is not a recognized plugin type. Those with instances of sub-types loaded are: charges descriptors fingerprints forcefields formats loaders ops "formats" results in the expected list now though. -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c7 --- Comment #7 from Wolfgang Bauer <wbauer@tmo.at> --- (In reply to Wolfgang Bauer from comment #6)
With 2.4.1, it apparently needs to be "babel -L formats". With "format" I still get a similar error message here: ormat is not a recognized plugin type. Those with instances of sub-types loaded are: charges descriptors fingerprints forcefields formats loaders ops
"formats" results in the expected list now though.
Although, that's actually the same with openbabel 2.3.1 (in Leap 42.3) as well. ;-) -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c8 Wolfgang Bauer <wbauer@tmo.at> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |asharff@globalphasing.com --- Comment #8 from Wolfgang Bauer <wbauer@tmo.at> --- *** Bug 1093344 has been marked as a duplicate of this bug. *** -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 Wolfgang Bauer <wbauer@tmo.at> changed: What |Removed |Added ---------------------------------------------------------------------------- Summary|openbabel cannot find |openbabel cannot find |plugins |plugins, and the command | |line tools are missing -- You are receiving this mail because: You are on the CC list for the bug.
http://bugzilla.opensuse.org/show_bug.cgi?id=997190 http://bugzilla.opensuse.org/show_bug.cgi?id=997190#c10 Wolfgang Bauer <wbauer@tmo.at> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|IN_PROGRESS |RESOLVED Resolution|--- |FIXED --- Comment #10 from Wolfgang Bauer <wbauer@tmo.at> --- The updated package has been accepted to openSUSE:Factory and openSUSE:Leap:15.0 meanwile, so this should be fixed in one of the next snapshots... -- You are receiving this mail because: You are on the CC list for the bug.
participants (1)
-
bugzilla_noreply＠novell.com