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Hi All,
I'm trying to install HTseq-0.4.7p1 on a Mac OS 10.6, with Python 2.6.5, gcc 4.2.1. Below is the full output from "python setup.py install".
Any ideas on how to overcome this would be highly appreciated.
Boel
I'm trying to install HTseq-0.4.7p1 on a Mac OS 10.6, with Python 2.6.5, gcc 4.2.1. Below is the full output from "python setup.py install".
Code:
$ python setup.py install running install running bdist_egg running egg_info writing HTSeq.egg-info/PKG-INFO writing top-level names to HTSeq.egg-info/top_level.txt writing dependency_links to HTSeq.egg-info/dependency_links.txt reading manifest file 'HTSeq.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'HTSeq.egg-info/SOURCES.txt' installing library code to build/bdist.macosx-10.3-fat/egg running install_lib running build_py running build_ext building 'HTSeq._StepVector' extension c++ -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g -bundle -undefined dynamic_lookup build/temp.macosx-10.3-fat-2.6/src/StepVector_wrap.o src/step_vector.h -o build/lib.macosx-10.3-fat-2.6/HTSeq/_StepVector.so src/step_vector.h:4:15: error: map: No such file or directory src/step_vector.h:5:21: error: stdexcept: No such file or directory src/step_vector.h:6:18: error: limits: No such file or directory src/step_vector.h:7:36: error: iostream: No such file or directory src/step_vector.h:12: error: ISO C++ forbids declaration of 'map' with no type src/step_vector.h:12: error: invalid use of '::' src/step_vector.h:12: error: expected ';' before '<' token src/step_vector.h:16: error: 'map' in namespace 'std' does not name a type src/step_vector.h:16: error: expected unqualified-id before '<' token src/step_vector.h:22: error: 'const_iterator' does not name a type src/step_vector.h:23: error: 'const_iterator' does not name a type src/step_vector.h:24: error: 'const_iterator' does not name a type src/step_vector.h: In constructor 'step_vector<T>::step_vector(long int, long int)': src/step_vector.h:32: error: 'm' was not declared in this scope src/step_vector.h: In member function 'const T step_vector<T>::operator[](long int) const': src/step_vector.h:39: error: 'out_of_range' is not a member of 'std' src/step_vector.h:41: error: 'out_of_range' is not a member of 'std' src/step_vector.h:42: error: 'const_iterator' was not declared in this scope src/step_vector.h:42: error: expected `;' before 'it' src/step_vector.h:43: error: 'it' was not declared in this scope src/step_vector.h: In member function 'void step_vector<T>::set_value(long int, long int, T)': src/step_vector.h:51: error: 'out_of_range' is not a member of 'std' src/step_vector.h:53: error: 'out_of_range' is not a member of 'std' src/step_vector.h:55: error: 'out_of_range' is not a member of 'std' src/step_vector.h:62: error: 'm' was not declared in this scope src/step_vector.h:67: error: 'map' in namespace 'std' does not name a type src/step_vector.h:67: error: expected unqualified-id before '<' token src/step_vector.h:68: error: 'left' was not declared in this scope src/step_vector.h:69: error: there are no arguments to 'assert' that depend on a template parameter, so a declaration of 'assert' must be available src/step_vector.h:69: error: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) src/step_vector.h:72: error: 'map' in namespace 'std' does not name a type src/step_vector.h:72: error: expected unqualified-id before '<' token src/step_vector.h:73: error: 'it' was not declared in this scope src/step_vector.h:75: error: 'it' was not declared in this scope src/step_vector.h:75: error: there are no arguments to 'assert' that depend on a template parameter, so a declaration of 'assert' must be available src/step_vector.h:77: error: 'm' was not declared in this scope src/step_vector.h:83: error: 'm' was not declared in this scope src/step_vector.h:88: error: 'm' was not declared in this scope src/step_vector.h:92: error: 'map' in namespace 'std' does not name a type src/step_vector.h:92: error: expected unqualified-id before '<' token src/step_vector.h:93: error: 'leftleft' was not declared in this scope src/step_vector.h: In member function 'void step_vector<T>::add_value(long int, long int, T)': src/step_vector.h:109: error: 'out_of_range' is not a member of 'std' src/step_vector.h:111: error: 'out_of_range' is not a member of 'std' src/step_vector.h:113: error: 'out_of_range' is not a member of 'std' src/step_vector.h:117: error: 'm' was not declared in this scope src/step_vector.h:120: error: 'map' in namespace 'std' does not name a type src/step_vector.h:120: error: expected unqualified-id before '<' token src/step_vector.h:121: error: 'it' was not declared in this scope src/step_vector.h:130: error: 'm' was not declared in this scope src/step_vector.h:134: error: 'm' was not declared in this scope src/step_vector.h: In member function 'void step_vector<T>::apply_to_values(long int, long int, void (*)(T&))': src/step_vector.h:142: error: 'out_of_range' is not a member of 'std' src/step_vector.h:144: error: 'out_of_range' is not a member of 'std' src/step_vector.h:146: error: 'out_of_range' is not a member of 'std' src/step_vector.h:150: error: 'm' was not declared in this scope src/step_vector.h:153: error: 'map' in namespace 'std' does not name a type src/step_vector.h:153: error: expected unqualified-id before '<' token src/step_vector.h:154: error: 'it' was not declared in this scope src/step_vector.h:163: error: 'm' was not declared in this scope src/step_vector.h:168: error: 'm' was not declared in this scope src/step_vector.h: At global scope: src/step_vector.h:174: error: no 'typename step_vector<T>::const_iterator step_vector<T>::get_values(long int) const' member function declared in class 'step_vector<T>' src/step_vector.h:174: error: template definition of non-template 'typename step_vector<T>::const_iterator step_vector<T>::get_values(long int) const' src/step_vector.h: In member function 'typename step_vector<T>::const_iterator step_vector<T>::get_values(long int) const': src/step_vector.h:176: error: 'm' was not declared in this scope src/step_vector.h: At global scope: src/step_vector.h:180: error: no 'typename step_vector<T>::const_iterator step_vector<T>::begin() const' member function declared in class 'step_vector<T>' src/step_vector.h:180: error: template definition of non-template 'typename step_vector<T>::const_iterator step_vector<T>::begin() const' src/step_vector.h: In member function 'typename step_vector<T>::const_iterator step_vector<T>::begin() const': src/step_vector.h:182: error: 'm' was not declared in this scope src/step_vector.h: At global scope: src/step_vector.h:186: error: no 'typename step_vector<T>::const_iterator step_vector<T>::end() const' member function declared in class 'step_vector<T>' src/step_vector.h:186: error: template definition of non-template 'typename step_vector<T>::const_iterator step_vector<T>::end() const' src/step_vector.h: In member function 'typename step_vector<T>::const_iterator step_vector<T>::end() const': src/step_vector.h:188: error: 'm' was not declared in this scope src/step_vector.h:4:15: error: map: No such file or directory src/step_vector.h:5:21: error: stdexcept: No such file or directory src/step_vector.h:6:18: error: limits: No such file or directory src/step_vector.h:7:36: error: iostream: No such file or directory src/step_vector.h:12: error: ISO C++ forbids declaration of 'map' with no type src/step_vector.h:12: error: invalid use of '::' src/step_vector.h:12: error: expected ';' before '<' token src/step_vector.h:16: error: 'map' in namespace 'std' does not name a type src/step_vector.h:16: error: expected unqualified-id before '<' token src/step_vector.h:22: error: 'const_iterator' does not name a type src/step_vector.h:23: error: 'const_iterator' does not name a type src/step_vector.h:24: error: 'const_iterator' does not name a type src/step_vector.h: In constructor 'step_vector<T>::step_vector(long int, long int)': src/step_vector.h:32: error: 'm' was not declared in this scope src/step_vector.h: In member function 'const T step_vector<T>::operator[](long int) const': src/step_vector.h:39: error: 'out_of_range' is not a member of 'std' src/step_vector.h:41: error: 'out_of_range' is not a member of 'std' src/step_vector.h:42: error: 'const_iterator' was not declared in this scope src/step_vector.h:42: error: expected `;' before 'it' src/step_vector.h:43: error: 'it' was not declared in this scope src/step_vector.h: In member function 'void step_vector<T>::set_value(long int, long int, T)': src/step_vector.h:51: error: 'out_of_range' is not a member of 'std' src/step_vector.h:53: error: 'out_of_range' is not a member of 'std' src/step_vector.h:55: error: 'out_of_range' is not a member of 'std' src/step_vector.h:62: error: 'm' was not declared in this scope src/step_vector.h:67: error: 'map' in namespace 'std' does not name a type src/step_vector.h:67: error: expected unqualified-id before '<' token src/step_vector.h:68: error: 'left' was not declared in this scope src/step_vector.h:69: error: there are no arguments to 'assert' that depend on a template parameter, so a declaration of 'assert' must be available src/step_vector.h:69: error: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) src/step_vector.h:72: error: 'map' in namespace 'std' does not name a type src/step_vector.h:72: error: expected unqualified-id before '<' token src/step_vector.h:73: error: 'it' was not declared in this scope src/step_vector.h:75: error: 'it' was not declared in this scope src/step_vector.h:75: error: there are no arguments to 'assert' that depend on a template parameter, so a declaration of 'assert' must be available src/step_vector.h:77: error: 'm' was not declared in this scope src/step_vector.h:83: error: 'm' was not declared in this scope src/step_vector.h:88: error: 'm' was not declared in this scope src/step_vector.h:92: error: 'map' in namespace 'std' does not name a type src/step_vector.h:92: error: expected unqualified-id before '<' token src/step_vector.h:93: error: 'leftleft' was not declared in this scope src/step_vector.h: In member function 'void step_vector<T>::add_value(long int, long int, T)': src/step_vector.h:109: error: 'out_of_range' is not a member of 'std' src/step_vector.h:111: error: 'out_of_range' is not a member of 'std' src/step_vector.h:113: error: 'out_of_range' is not a member of 'std' src/step_vector.h:117: error: 'm' was not declared in this scope src/step_vector.h:120: error: 'map' in namespace 'std' does not name a type src/step_vector.h:120: error: expected unqualified-id before '<' token src/step_vector.h:121: error: 'it' was not declared in this scope src/step_vector.h:130: error: 'm' was not declared in this scope src/step_vector.h:134: error: 'm' was not declared in this scope src/step_vector.h: In member function 'void step_vector<T>::apply_to_values(long int, long int, void (*)(T&))': src/step_vector.h:142: error: 'out_of_range' is not a member of 'std' src/step_vector.h:144: error: 'out_of_range' is not a member of 'std' src/step_vector.h:146: error: 'out_of_range' is not a member of 'std' src/step_vector.h:150: error: 'm' was not declared in this scope src/step_vector.h:153: error: 'map' in namespace 'std' does not name a type src/step_vector.h:153: error: expected unqualified-id before '<' token src/step_vector.h:154: error: 'it' was not declared in this scope src/step_vector.h:163: error: 'm' was not declared in this scope src/step_vector.h:168: error: 'm' was not declared in this scope src/step_vector.h: At global scope: src/step_vector.h:174: error: no 'typename step_vector<T>::const_iterator step_vector<T>::get_values(long int) const' member function declared in class 'step_vector<T>' src/step_vector.h:174: error: template definition of non-template 'typename step_vector<T>::const_iterator step_vector<T>::get_values(long int) const' src/step_vector.h: In member function 'typename step_vector<T>::const_iterator step_vector<T>::get_values(long int) const': src/step_vector.h:176: error: 'm' was not declared in this scope src/step_vector.h: At global scope: src/step_vector.h:180: error: no 'typename step_vector<T>::const_iterator step_vector<T>::begin() const' member function declared in class 'step_vector<T>' src/step_vector.h:180: error: template definition of non-template 'typename step_vector<T>::const_iterator step_vector<T>::begin() const' src/step_vector.h: In member function 'typename step_vector<T>::const_iterator step_vector<T>::begin() const': src/step_vector.h:182: error: 'm' was not declared in this scope src/step_vector.h: At global scope: src/step_vector.h:186: error: no 'typename step_vector<T>::const_iterator step_vector<T>::end() const' member function declared in class 'step_vector<T>' src/step_vector.h:186: error: template definition of non-template 'typename step_vector<T>::const_iterator step_vector<T>::end() const' src/step_vector.h: In member function 'typename step_vector<T>::const_iterator step_vector<T>::end() const': src/step_vector.h:188: error: 'm' was not declared in this scope lipo: can't open input file: /var/folders/we/wetvVYAgH5eCkHQa0bDhKk+++TI/-Tmp-//ccgShYJi.out (No such file or directory) error: command 'c++' failed with exit status 1
Boel
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