| Summary: | Ruby does not work with openbabel despites ruby-openbabel is installed | ||
|---|---|---|---|
| Product: | [Fedora] Fedora | Reporter: | Witek Mozga <mozga> |
| Component: | openbabel | Assignee: | Dominik 'Rathann' Mierzejewski <dominik> |
| Status: | CLOSED WONTFIX | QA Contact: | Fedora Extras Quality Assurance <extras-qa> |
| Severity: | unspecified | Docs Contact: | |
| Priority: | unspecified | ||
| Version: | 16 | CC: | dominik, itamar, mmorsi, mtasaka, mtasaka, paul, tagoh, vanmeeuwen+fedora, vondruch |
| Target Milestone: | --- | Keywords: | Reopened |
| Target Release: | --- | ||
| Hardware: | Unspecified | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Fixed In Version: | Doc Type: | Bug Fix | |
| Doc Text: | Story Points: | --- | |
| Clone Of: | Environment: | ||
| Last Closed: | 2013-02-14 01:10:52 UTC | Type: | --- |
| Regression: | --- | Mount Type: | --- |
| Documentation: | --- | CRM: | |
| Verified Versions: | Category: | --- | |
| oVirt Team: | --- | RHEL 7.3 requirements from Atomic Host: | |
| Cloudforms Team: | --- | Target Upstream Version: | |
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Description
Witek Mozga
2012-01-06 07:13:03 UTC
This seems to be issue of openbabel, not ruby. I change the component and let's see what openbabel mainteiner thinks about this issue. Well, swig is easy and also difficult: http://sourceforge.net/tracker/?func=detail&aid=3302142&group_id=1645&atid=101645 One of the workarounds is: - Rename %ruby_sitarch/openbabel.so to %ruby_sitearch/OpenBabel.so - put the following "openbabel.rb" to under %ruby_sitelib openbabel.rb: -------------------------------------------------------- require 'OpenBabel' -------------------------------------------------------- The test case http://openbabel.org/docs/dev/UseTheLibrary/Ruby.html works with this. I`m not sure about Python, either. When I use openbabel from python shel it works. But when I`m trying to run a script it fails. I might do something wrong as I`m a beginner in openbabel scripting but it seems strange. A simple example of Python code that works when I type each line in the python shell (I mean after starting the shell with 'python' command)
import pybel
mol = pybel.readstring("smi", "CC(=O)Br")
print(mol.write("sdf"))
but when the files is saved and invoked like this: python filename
then it says:
Traceback (most recent call last):
File "openbabel.py", line 1, in <module>
import pybel
File "/usr/lib/python2.7/site-packages/pybel.py", line 16, in <module>
import openbabel as ob
File "/winshare/Python/openbabel.py", line 2, in <module>
mol = pybel.readstring("smi", "CC(=O)Br")
AttributeError: 'module' object has no attribute 'readstring'
Actually this was because scripts/CMakeLists.txt is somewhat broken (with containing some typo + issue with character escape rule on cmake and shell). Firstly fixed on F-18. F-17 will see fixed package on testing first. For f16 and f15, I may work later. openbabel-2.3.1-4.fc17 has been submitted as an update for Fedora 17. https://admin.fedoraproject.org/updates/openbabel-2.3.1-4.fc17 openbabel-2.3.1-4.fc17 has been pushed to the Fedora 17 stable repository. If problems still persist, please make note of it in this bug report. This message is a notice that Fedora 15 is now at end of life. Fedora has stopped maintaining and issuing updates for Fedora 15. It is Fedora's policy to close all bug reports from releases that are no longer maintained. At this time, all open bugs with a Fedora 'version' of '15' have been closed as WONTFIX. (Please note: Our normal process is to give advanced warning of this occurring, but we forgot to do that. A thousand apologies.) Package Maintainer: If you wish for this bug to remain open because you plan to fix it in a currently maintained version, feel free to reopen this bug and simply change the 'version' to a later Fedora version. Bug Reporter: Thank you for reporting this issue and we are sorry that we were unable to fix it before Fedora 15 reached end of life. If you would still like to see this bug fixed and are able to reproduce it against a later version of Fedora, you are encouraged to click on "Clone This Bug" (top right of this page) and open it against that version of Fedora. Although we aim to fix as many bugs as possible during every release's lifetime, sometimes those efforts are overtaken by events. Often a more recent Fedora release includes newer upstream software that fixes bugs or makes them obsolete. The process we are following is described here: http://fedoraproject.org/wiki/BugZappers/HouseKeeping Well, this issue was kept open also for F16, where the problem probably still persists => REOPEN This message is a reminder that Fedora 16 is nearing its end of life. Approximately 4 (four) weeks from now Fedora will stop maintaining and issuing updates for Fedora 16. It is Fedora's policy to close all bug reports from releases that are no longer maintained. At that time this bug will be closed as WONTFIX if it remains open with a Fedora 'version' of '16'. Package Maintainer: If you wish for this bug to remain open because you plan to fix it in a currently maintained version, simply change the 'version' to a later Fedora version prior to Fedora 16's end of life. Bug Reporter: Thank you for reporting this issue and we are sorry that we may not be able to fix it before Fedora 16 is end of life. If you would still like to see this bug fixed and are able to reproduce it against a later version of Fedora, you are encouraged to click on "Clone This Bug" and open it against that version of Fedora. Although we aim to fix as many bugs as possible during every release's lifetime, sometimes those efforts are overtaken by events. Often a more recent Fedora release includes newer upstream software that fixes bugs or makes them obsolete. The process we are following is described here: http://fedoraproject.org/wiki/BugZappers/HouseKeeping Fedora 16 changed to end-of-life (EOL) status on 2013-02-12. Fedora 16 is no longer maintained, which means that it will not receive any further security or bug fix updates. As a result we are closing this bug. If you can reproduce this bug against a currently maintained version of Fedora please feel free to reopen this bug against that version. Thank you for reporting this bug and we are sorry it could not be fixed. |