Installation error: command 'gcc' failed with exit status 1

[11033...@qq.com]

HI

I got an error when I install trust using python setup.py install (my python is python3.5 installed by anaconda):

trust/getOverlapInfo.cpp: In function ‘int* compare_Lgreaterthan64(uint64_t*, int, int, uint64_t*, int, int, int, int*)’:
trust/getOverlapInfo.cpp:88:45: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
             printf("pre = %llu\n", prefix[i]);
                                             ^
trust/getOverlapInfo.cpp:93:45: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
             printf("suf = %llu\n", suffix[i]);
                                             ^
trust/getOverlapInfo.cpp: In function ‘PyObject* _compare_Lgreaterthan64(PyObject*, PyObject*)’:
trust/getOverlapInfo.cpp:214:49: error: ‘PyInt_AsUnsignedLongLongMask’ was not declared in this scope
         _x[i] = PyInt_AsUnsignedLongLongMask(obj);
                                                 ^
trust/getOverlapInfo.cpp:219:49: error: ‘PyInt_AsUnsignedLongLongMask’ was not declared in this scope
         _y[i] = PyInt_AsUnsignedLongLongMask(obj);
                                                 ^
trust/getOverlapInfo.cpp: In function ‘void initgetOverlapInfo_C()’:
trust/getOverlapInfo.cpp:254:65: error: ‘Py_InitModule’ was not declared in this scope
     (void) Py_InitModule("getOverlapInfo_C", GreateModuleMethods);
                                                                 ^
error: command 'gcc' failed with exit status 1

Could you be kind to give me some advice on how to solve this problem? Thanks!

Yang

[Bo Li]

TRUST is written in python 2. Please change your python version and try again.

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[11033...@qq.com]

Thank you! The problem is solved!

在 2018年8月20日星期一 UTC+8下午8:45:16，Bo Li写道：

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[sull...@gmail.com]

Hello,

I think I am getting a similar problem during installation. I'm running python 2.7. I am able to change directory but running python setup.py install gives me the following error:

running install

running bdist_egg

running egg_info

writing requirements to trust.egg-info/requires.txt

writing trust.egg-info/PKG-INFO

writing top-level names to trust.egg-info/top_level.txt

writing dependency_links to trust.egg-info/dependency_links.txt

reading manifest file 'trust.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

writing manifest file 'trust.egg-info/SOURCES.txt'

installing library code to build/bdist.macosx-10.6-intel/egg

running install_lib

running build_py

running build_ext

building 'trust/getOverlapInfo_C' extension

/usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c trust/getOverlapInfo.cpp -o build/temp.macosx-10.6-intel-2.7/trust/getOverlapInfo.o

warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the

      libc++ standard library instead [-Wstdlibcxx-not-found]

trust/getOverlapInfo.cpp:12:10: fatal error: 'iostream' file not found

#include <iostream>

         ^~~~~~~~~~

1 warning and 1 error generated.

error: command '/usr/bin/clang' failed with exit status 1

Do you know what might be going on here?

Thank you!

Kevin

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[Bo Li]

Hi Jian,

Could you please help with this?

Thanks,

Bo

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[Jian Zhang]

Hi Kevin,

Sorry for the delay response. I have some connection issues with my gmail account recently.

Could you please try "g++ -fPIC -shared getOverlapInfo.cpp -o getOverlaoInfo_C.so -I /usr/include/python2.7/ -Ipython2.7" ?

If the above command doesn't work, I think you probably need to re install g++.

reference: https://stackoverflow.com/questions/30543286/fatal-error-iostream-no-such-file-or-directory-in-compiling-c-program-using-gc

Thanks,

Jian

Bo Li <li...@umich.edu> 于2019年5月29日周三 下午11:58写道：