Bug 2112710
| Summary: | OpenBabel doesn't work; needs libdir specification | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Susi Lehtola <susi.lehtola> |
| Component: | openbabel | Assignee: | Antonio T. sagitter <trpost> |
| Status: | CLOSED ERRATA | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | 36 | CC: | alex.ploumistos, dominik, niklas.kappel, scitech-bugs, susi.lehtola, trpost |
| Target Milestone: | --- | Keywords: | Reopened |
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Unspecified | ||
| Whiteboard: | |||
| Fixed In Version: | openbabel-3.1.1-12.fc37 openbabel-3.1.1-15.fc36 openbabel-3.1.1-15.fc37 | Doc Type: | If docs needed, set a value |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2022-11-10 22:08:49 UTC | Type: | Bug |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
| Embargoed: | |||
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Description
Susi Lehtola
2022-07-31 20:33:25 UTC
> You need to set BABEL_LIBDIR in e.g. a profile file.
Could rpaths in binary files be enough?
(In reply to Antonio T. sagitter from comment #1) > > You need to set BABEL_LIBDIR in e.g. a profile file. > > Could rpaths in binary files be enough? RPaths are generally not allowed in Fedora https://docs.fedoraproject.org/en-US/packaging-guidelines/#_beware_of_rpath but it appears that there's a special policy for internal libraries. > You need to set BABEL_LIBDIR in e.g. a profile file.
Can you show me an example about how to include a profile file in the rpms please?
xtb package uses profile files to set paths https://src.fedoraproject.org/rpms/xtb/blob/3ccdb86c183530b7268d1851627b08de61ec3529/f/xtb.spec FEDORA-2022-e415638af6 has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2022-e415638af6 FEDORA-2022-e415638af6 has been pushed to the Fedora 37 stable repository. If problem still persists, please make note of it in this bug report. Still doesn't work *** Bug 2087071 has been marked as a duplicate of this bug. *** (In reply to Susi Lehtola from comment #7) > Still doesn't work Have you tried sourcing the profile in /etc/profile.d/? I had to reboot because of a kernel update and I don't have any issue. FEDORA-2022-68f29e4459 has been submitted as an update to Fedora 36. https://bodhi.fedoraproject.org/updates/FEDORA-2022-68f29e4459 (In reply to Alexander Ploumistos from comment #9) > (In reply to Susi Lehtola from comment #7) > > Still doesn't work > > Have you tried sourcing the profile in /etc/profile.d/? > I had to reboot because of a kernel update and I don't have any issue. the update was never filed to Fedora 36 which is what this bug is about Oops, my bad, from your answer I got that the update was not working for you. FEDORA-2022-68f29e4459 has been pushed to the Fedora 36 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2022-68f29e4459` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-68f29e4459 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates. FEDORA-2022-f457b7a068 has been pushed to the Fedora 37 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2022-f457b7a068` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-f457b7a068 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates. FEDORA-2022-608aa85d22 has been submitted as an update to Fedora 37. https://bodhi.fedoraproject.org/updates/FEDORA-2022-608aa85d22 FEDORA-2022-30f18333d1 has been submitted as an update to Fedora 36. https://bodhi.fedoraproject.org/updates/FEDORA-2022-30f18333d1 FEDORA-2022-608aa85d22 has been pushed to the Fedora 37 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2022-608aa85d22` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-608aa85d22 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates. FEDORA-2022-30f18333d1 has been pushed to the Fedora 36 testing repository. Soon you'll be able to install the update with the following command: `sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2022-30f18333d1` You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2022-30f18333d1 See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates. Version 3.1.1-15 changed the BABEL_LIBDIR from /usr/lib64/openbabel/ (on 64-bit) to /usr/lib64/openbabel3/. As a result, running `obabel -L formats` is broken again as is every other program that requires Open Babel at runtime. Was this done by accident?
The upstream CMakeLists.txt has this section for the plugin directory (on linux):
set(LIB_SUFFIX "" CACHE STRING "Suffix of the directory name, e.g. 64 for lib64")
if(UNIX)
set(LIB_INSTALL_DIR "lib${LIB_SUFFIX}"
CACHE PATH "Install dir for libraries")
if(ENABLE_VERSIONED_FORMATS)
set(OB_PLUGIN_INSTALL_DIR "${LIB_INSTALL_DIR}/openbabel/${BABEL_VERSION}"
CACHE PATH "Install dir for plugins")
else()
set(OB_PLUGIN_INSTALL_DIR "${LIB_INSTALL_DIR}/openbabel"
CACHE PATH "Install dir for plugins")
endif()
Is there any point in enabling versioned formats? If that is the case, then we should patch all of Open Babel's dependencies.
If not, can we just drop the "3" from the path, or is it going to cause problems?
By the way, @susi.lehtola the script you mentioned in bug 2130870, where is it from? Upstream Open Babel does not append the version number to the folder name.
(In reply to Alexander Ploumistos from comment #19) > By the way, @susi.lehtola the script you mentioned in bug 2130870, > where is it from? Upstream Open Babel does not append the version number to > the folder name. All this information is available in bug 2130870. FEDORA-2022-30f18333d1 has been pushed to the Fedora 36 stable repository. If problem still persists, please make note of it in this bug report. As I wrote in comment 19, the https://src.fedoraproject.org/rpms/openbabel/c/f58d73c656a50c6787797426a8b97c8b250063ad?branch=f36 commit broke the program again. Executables are looking for plugins in /usr/lib64/openbabel/, but the path has changed to /usr/lib64/openbabel3/: $ obabel -v -L formats ============================== *** Open Babel Error in LoadAllPlugins Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable. ============================== *** Open Babel Error in LoadAllPlugins Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable. ============================== *** Open Babel Error in LoadAllPlugins Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable. ============================== *** Open Babel Error in LoadAllPlugins Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable. ============================== *** Open Babel Error in LoadAllPlugins Unable to find OpenBabel plugins. Try setting the BABEL_LIBDIR environment variable. formats is not a recognized plugin type. Those with instances of sub-types loaded are: ops Reopening. FEDORA-2022-608aa85d22 has been pushed to the Fedora 37 stable repository. If problem still persists, please make note of it in this bug report. |