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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
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