Bug 701690

Summary: LibSBML with python binding compile on F14, not on F15
Product: [Fedora] Fedora Reporter: Pierre Blavy <pierreblavy>
Component: swigAssignee: Adam Tkac <atkac>
Status: CLOSED WONTFIX QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: unspecified Docs Contact:
Priority: unspecified    
Version: 15CC: atkac, ovasik
Target Milestone: ---   
Target Release: ---   
Hardware: x86_64   
OS: Linux   
Whiteboard:
Fixed In Version: Doc Type: Bug Fix
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2011-05-04 15:14:04 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:

Description Pierre Blavy 2011-05-03 15:09:51 UTC 
Description of problem:
LibSBML compilation with python support crashes on F15. Used to work on F14 with the same script.


How reproducible:
Always




Steps to Reproduce:
1. Use the following script (don't need to be root, local install only)


#!/bin/sh
p=`pwd`
mkdir extern-lib/libsbml
wget http://downloads.sourceforge.net/project/sbml/libsbml/4.2.0/libsbml-4.2.0-src.tar.gz
tar -xf libsbml-*-src.tar.gz
rm libsbml-*-src.tar.gz

mkdir -p $p/extern-lib/libsbml

cd libsbml-*
  ./configure --prefix="$p/extern-lib/libsbml" --with-python
 make
 make install
cd ..


  
Actual results:
F14 : compilation OK
F15 : compilation fails, error log in additionnal info.



Expected results:
Compile libsbml with python support



Additional info:

---F15 error log (pwd = /data/bioasp-0.04/bioasp-0.05/) ---

UnitFormulaFormatter.cpp: In member function ‘UnitDefinition* UnitFormulaFormatter::getSpeciesExtentUnitDefinition(const Species*)’:
UnitFormulaFormatter.cpp:2054:23: attention : deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
libsbml_wrap.cpp:3125:13: erreur: ‘ptrdiff_t’ does not name a type
libsbml_wrap.cpp:3162:21: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3162:39: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3177:34: erreur: declaration of ‘operator+=’ as non-function
libsbml_wrap.cpp:3177:30: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3177:44: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3182:34: erreur: declaration of ‘operator-=’ as non-function
libsbml_wrap.cpp:3182:30: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3182:44: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3187:33: erreur: declaration of ‘operator+’ as non-function
libsbml_wrap.cpp:3187:30: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3187:43: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3192:33: erreur: declaration of ‘operator-’ as non-function
libsbml_wrap.cpp:3192:30: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3192:43: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3197:5: erreur: ‘ptrdiff_t’ does not name a type
libsbml_wrap.cpp:3226:23: erreur: ‘SWIG_From_ptrdiff_t’ declared as an ‘inline’ variable
libsbml_wrap.cpp:3226:23: erreur: ‘ptrdiff_t’ was not declared in this scope
libsbml_wrap.cpp:3226:23: note: suggested alternatives:
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
libsbml_wrap.cpp:3227:1: erreur: expected ‘,’ or ‘;’ before ‘{’ token
libsbml_wrap.cpp:3279:39: erreur: ‘ptrdiff_t’ has not been declared
libsbml_wrap.cpp: In function ‘int SWIG_AsVal_ptrdiff_t(PyObject*, int*)’:
libsbml_wrap.cpp:3283:50: erreur: expected type-specifier before ‘ptrdiff_t’
libsbml_wrap.cpp:3283:50: erreur: expected ‘>’ before ‘ptrdiff_t’
libsbml_wrap.cpp:3283:50: erreur: expected ‘(’ before ‘ptrdiff_t’
libsbml_wrap.cpp:3283:50: erreur: ‘ptrdiff_t’ was not declared in this scope
libsbml_wrap.cpp:3283:50: note: suggested alternatives:
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
libsbml_wrap.cpp:3283:64: erreur: expected ‘)’ before ‘;’ token
libsbml_wrap.cpp: At global scope:
libsbml_wrap.cpp:3874:15: erreur: ‘swig::check_index’ declared as an ‘inline’ variable
libsbml_wrap.cpp:3874:15: erreur: ‘ptrdiff_t’ was not declared in this scope
libsbml_wrap.cpp:3874:15: note: suggested alternatives:
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
libsbml_wrap.cpp:3874:35: erreur: expected primary-expression before ‘size’
libsbml_wrap.cpp:3874:41: erreur: expected primary-expression before ‘bool’
libsbml_wrap.cpp:3874:60: erreur: expression list treated as compound expression in initializer [-fpermissive]
libsbml_wrap.cpp:3874:62: erreur: expected ‘,’ or ‘;’ before ‘{’ token
libsbml_wrap.cpp:101341:1: erreur: expected ‘}’ at end of input
make[3]: *** [libsbml_wrap.lo] Erreur 1
make[2]: *** [python-recurse] Erreur 2
make[1]: *** [bindings-recurse] Erreur 2
make: *** [src-recurse] Erreur 2
libsbml_wrap.cpp:3125:13: erreur: ‘ptrdiff_t’ does not name a type
libsbml_wrap.cpp:3162:21: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3162:39: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3177:34: erreur: declaration of ‘operator+=’ as non-function
libsbml_wrap.cpp:3177:30: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3177:44: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3182:34: erreur: declaration of ‘operator-=’ as non-function
libsbml_wrap.cpp:3182:30: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3182:44: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3187:33: erreur: declaration of ‘operator+’ as non-function
libsbml_wrap.cpp:3187:30: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3187:43: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3192:33: erreur: declaration of ‘operator-’ as non-function
libsbml_wrap.cpp:3192:30: erreur: expected ‘;’ at end of member declaration
libsbml_wrap.cpp:3192:43: erreur: expected ‘)’ before ‘n’
libsbml_wrap.cpp:3197:5: erreur: ‘ptrdiff_t’ does not name a type
libsbml_wrap.cpp:3226:23: erreur: ‘SWIG_From_ptrdiff_t’ declared as an ‘inline’ variable
libsbml_wrap.cpp:3226:23: erreur: ‘ptrdiff_t’ was not declared in this scope
libsbml_wrap.cpp:3226:23: note: suggested alternatives:
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
libsbml_wrap.cpp:3227:1: erreur: expected ‘,’ or ‘;’ before ‘{’ token
libsbml_wrap.cpp:3279:39: erreur: ‘ptrdiff_t’ has not been declared
libsbml_wrap.cpp: In function ‘int SWIG_AsVal_ptrdiff_t(PyObject*, int*)’:
libsbml_wrap.cpp:3283:50: erreur: expected type-specifier before ‘ptrdiff_t’
libsbml_wrap.cpp:3283:50: erreur: expected ‘>’ before ‘ptrdiff_t’
libsbml_wrap.cpp:3283:50: erreur: expected ‘(’ before ‘ptrdiff_t’
libsbml_wrap.cpp:3283:50: erreur: ‘ptrdiff_t’ was not declared in this scope
libsbml_wrap.cpp:3283:50: note: suggested alternatives:
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
libsbml_wrap.cpp:3283:64: erreur: expected ‘)’ before ‘;’ token
libsbml_wrap.cpp: At global scope:
libsbml_wrap.cpp:3874:15: erreur: ‘swig::check_index’ declared as an ‘inline’ variable
libsbml_wrap.cpp:3874:15: erreur: ‘ptrdiff_t’ was not declared in this scope
libsbml_wrap.cpp:3874:15: note: suggested alternatives:
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
/usr/lib/gcc/x86_64-redhat-linux/4.6.0/../../../../include/c++/4.6.0/x86_64-redhat-linux/bits/c++config.h:1737:28: note:   ‘std::ptrdiff_t’
libsbml_wrap.cpp:3874:35: erreur: expected primary-expression before ‘size’
libsbml_wrap.cpp:3874:41: erreur: expected primary-expression before ‘bool’
libsbml_wrap.cpp:3874:60: erreur: expression list treated as compound expression in initializer [-fpermissive]
libsbml_wrap.cpp:3874:62: erreur: expected ‘,’ or ‘;’ before ‘{’ token
libsbml_wrap.cpp:101341:1: erreur: expected ‘}’ at end of input
make[3]: *** [libsbml_wrap.lo] Erreur 1
make[2]: *** [python-recurse] Erreur 2
make[1]: *** [bindings-recurse] Erreur 2
make: *** [src-recurse] Erreur 2
Comment 1 Pierre Blavy 2011-05-04 15:14:04 UTC 
It's a LibSBML bug.

Can be fixed by removing libsbml_wrap.cpp
and calling ./configure with the --swig flag

see : http://sourceforge.net/tracker/?func=detail&aid=3296800&group_id=71971&atid=942737