1594498 – libsbml FTFBS with python 3.7

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Bug 1594498 - libsbml FTFBS with python 3.7

Summary: libsbml FTFBS with python 3.7

Keywords:
Status:	CLOSED RAWHIDE
Alias:	None
Product:	Fedora
Classification:	Fedora
Component:	libsbml
Sub Component:
Version:	rawhide
Hardware:	Unspecified
OS:	Unspecified
Priority:	unspecified
Severity:	unspecified
Target Milestone:	---
Assignee:	Zbigniew Jędrzejewski-Szmek
QA Contact:	Fedora Extras Quality Assurance
Docs Contact:
URL:
Whiteboard:
Depends On:
Blocks:	PYTHON37
TreeView+	depends on / blocked

Reported:	2018-06-23 19:00 UTC by Antonio T. (sagitter)
Modified:	2018-06-27 20:54 UTC (History)
CC List:	2 users (show)
Fixed In Version:
Doc Type:	If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed:	2018-06-27 20:54:07 UTC
Type:	Bug
Embargoed:
Dependent Products:

Attachments	(Terms of Use)

Description Antonio T. (sagitter) 2018-06-23 19:00:01 UTC

Description of problem:
Python3 binding of libsbml does not compile with Python 3.7.0.

Version-Release number of selected component (if applicable):
libsbml-5.17.0

Actual results:

[  0%] Swig Python source
make[2]: Leaving directory '/builddir/build/BUILD/libSBML-5.17.0-Source/build'
make -f src/bindings/ruby/CMakeFiles/binding_ruby_swig.dir/build.make src/bindings/ruby/CMakeFiles/binding_ruby_swig.dir/build
cd /builddir/build/BUILD/libSBML-5.17.0-Source/build/src/bindings/python && /usr/bin/python3 /builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/swigdoc.py --language python --top /builddir/build/BUILD/libSBML-5.17.0-Source --master /builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/libsbml.i --output /builddir/build/BUILD/libSBML-5.17.0-Source/build/src/bindings/python/pydoc-doxygen.i --define USE_COMP --define USE_FBC --define USE_GROUPS --define USE_LAYOUT --define USE_MULTI --define USE_QUAL --define USE_RENDER --define USE_COMP --define USE_FBC --define USE_GROUPS --define USE_MULTI --define USE_QUAL --define USE_RENDER
Swig: Java Bindings
make[2]: Entering directory '/builddir/build/BUILD/libSBML-5.17.0-Source/build'
[  0%] Swig Ruby source
cd /builddir/build/BUILD/libSBML-5.17.0-Source/build/src/bindings/ruby && /usr/bin/swig -I/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/ruby/../swig/ -I/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/ruby -I/builddir/build/BUILD/libSBML-5.17.0-Source/build/src -I/builddir/build/BUILD/libSBML-5.17.0-Source/src -I/builddir/build/BUILD/libSBML-5.17.0-Source/include -c++ -ruby -DLIBSBML_COMPILED_IN_SRC -DUSE_LIBXML -DUSE_BZ2 -DUSE_ZLIB -DUSE_COMP -DUSE_FBC -DUSE_GROUPS -DUSE_LAYOUT -DUSE_MULTI -DUSE_QUAL -DUSE_RENDER -DUSE_COMP -DUSE_FBC -DUSE_GROUPS -DUSE_MULTI -DUSE_QUAL -DUSE_RENDER -o /builddir/build/BUILD/libSBML-5.17.0-Source/build/src/bindings/ruby/libsbml_wrap.cpp /builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/ruby/libsbml.i
Traceback (most recent call last):
  File "/usr/lib64/python3.7/sre_parse.py", line 1021, in parse_template
    this = chr(ESCAPES[this][1])
KeyError: '\\s'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/swigdoc.py", line 1924, in <module>
    main(sys.argv)
  File "/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/swigdoc.py", line 1881, in main
    processFile(file, stream, language, preprocessor_defines)
  File "/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/swigdoc.py", line 1697, in processFile
    processFunctions(ostream, header.functions)
  File "/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/swigdoc.py", line 1673, in processFunctions
    ostream.write(generateFunctionDocString(f.name, f.docstring, f.args, f.isInternal,f))
  File "/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/swigdoc.py", line 1617, in generateFunctionDocString
    doc = rewriteDocstringForPython(docstring)
  File "/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/swigdoc.py", line 1397, in rewriteDocstringForPython
    docstring = translateAllowingBreaks(breakable_translations, docstring)
  File "/builddir/build/BUILD/libSBML-5.17.0-Source/src/bindings/python/../swig/swigdoc.py", line 816, in translateAllowingBreaks
    new_pattern = re.sub(' ', r'\s+\*?\s*', pair[0])
  File "/usr/lib64/python3.7/re.py", line 192, in sub
    return _compile(pattern, flags).sub(repl, string, count)
  File "/usr/lib64/python3.7/re.py", line 309, in _subx
    template = _compile_repl(template, pattern)
  File "/usr/lib64/python3.7/re.py", line 300, in _compile_repl
    return sre_parse.parse_template(repl, pattern)
  File "/usr/lib64/python3.7/sre_parse.py", line 1024, in parse_template
    raise s.error('bad escape %s' % this, len(this))
re.error: bad escape \s at position 0
make[2]: *** [src/bindings/python/CMakeFiles/binding_python_swig.dir/build.make:622: src/bindings/python/libsbml_wrap.cpp] Error 1
make[2]: Leaving directory '/builddir/build/BUILD/libSBML-5.17.0-Source/build'
make[1]: *** [CMakeFiles/Makefile2:3127: src/bindings/python/CMakeFiles/binding_python_swig.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Scanning dependencies of target sbml-static
make[2]: Leaving directory '/builddir/build/BUILD/libSBML-5.17.0-Source/build'
make -f src/CMakeFiles/sbml-static.dir/build.make src/CMakeFiles/sbml-static.dir/build
Scanning dependencies of target sbml
make[2]: Leaving directory '/builddir/build/BUILD/libSBML-5.17.0-Source/build'


Additional info:
Bug reported to upstream: https://sourceforge.net/p/sbml/libsbml/461/

Comment 1 Antonio T. (sagitter) 2018-06-23 19:01:02 UTC

Full build log: https://kojipkgs.fedoraproject.org//work/tasks/2066/27752066/build.log

Comment 2 Antonio T. (sagitter) 2018-06-27 20:54:07 UTC

Fixed on libsbml-5.17.0-3

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