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Old 02-22-2011, 12:14 PM   #1
Boel
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Location: Stockholm, Sweden

Join Date: Oct 2009
Posts: 62
Default HTSeq installation: error: command 'c++' failed with exit status 1

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".

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
Any ideas on how to overcome this would be highly appreciated.

Boel
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Old 02-22-2011, 11:21 PM   #2
Bruins
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Posts: 78
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just a hunch: you are a regular user. Try being root (su -).
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