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4dn-dcic / hic2cool

Lightweight converter between hic and cool contact matrices.
MIT License
66 stars 7 forks source link

Installation problem #35

Closed francicco closed 5 years ago

francicco commented 5 years ago

Hi,

I'm having a hard time installing hic2cool. Pip fails:

pip install -e hic2cool/ 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///home/fc464/software/HiCAssembler/hic2cool
    ERROR: Complete output from command python setup.py egg_info:
    ERROR: warning: build_py: byte-compiling is disabled, skipping.

    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:0: warning: "PyUnicode_FromString" redefined
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:194:0: note: this is the location of the previous definition
     # define PyUnicode_FromString PyUnicodeUCS2_FromString
     ^
    ext/_yaml.c: In function ‘__pyx_pf_5_yaml_get_version_string’:
    ext/_yaml.c:1888:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
       __pyx_v_value = yaml_get_version_string();
                     ^
    ext/_yaml.c: In function ‘__pyx_pf_5_yaml_7CParser___init__’:
    ext/_yaml.c:3388:52: warning: passing argument 2 of ‘yaml_parser_set_input’ from incompatible pointer type [-Wincompatible-pointer-types]
         yaml_parser_set_input((&__pyx_v_self->parser), __pyx_f_5_yaml_input_handler, ((void *)__pyx_v_self));
                                                        ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:1367:1: note: expected ‘int (*)(void *, unsigned char *, size_t,  size_t *) {aka int (*)(void *, unsigned char *, long unsigned int,  long unsigned int *)}’ but argument is of type ‘int (*)(void *, char *, size_t,  size_t *) {aka int (*)(void *, char *, long unsigned int,  long unsigned int *)}’
     yaml_parser_set_input(yaml_parser_t *parser,
     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:94:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/stringobject.h:91:32: warning: pointer targets in passing argument 2 of ‘yaml_parser_set_input_string’ differ in signedness [-Wpointer-sign]
     #define PyString_AS_STRING(op) (((PyStringObject *)(op))->ob_sval)
                                    ^
    ext/_yaml.c:3629:59: note: in expansion of macro ‘PyString_AS_STRING’
         yaml_parser_set_input_string((&__pyx_v_self->parser), PyString_AS_STRING(__pyx_v_stream), PyString_GET_SIZE(__pyx_v_stream));
                                                               ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:1341:1: note: expected ‘const unsigned char *’ but argument is of type ‘char *’
     yaml_parser_set_input_string(yaml_parser_t *parser,
     ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c: In function ‘__pyx_f_5_yaml_7CParser__token_to_object’:
    ext/_yaml.c:5463:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag_directive.handle); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 417, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:5463:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag_directive.handle); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 417, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:5475:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag_directive.prefix); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 418, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:5475:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag_directive.prefix); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 418, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:6477:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.alias.value); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 448, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:6477:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.alias.value); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 448, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:6561:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.anchor.value); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 451, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:6561:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.anchor.value); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 451, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:6645:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag.handle); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 454, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:6645:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag.handle); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 454, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:6657:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag.suffix); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 455, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:6657:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_token->data.tag.suffix); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 455, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    ext/_yaml.c:6781:38: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = PyUnicode_DecodeUTF8(__pyx_v_token->data.scalar.value, __pyx_v_token->data.scalar.length, ((char *)"strict")); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 460, __pyx_L1_error)
                                          ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c: In function ‘__pyx_f_5_yaml_7CParser__event_to_object’:
    ext/_yaml.c:8462:42: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
             __pyx_t_4 = PyUnicode_FromString(__pyx_v_tag_directive->handle); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 574, __pyx_L1_error)
                                              ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:8462:21: note: in expansion of macro ‘PyUnicode_FromString’
             __pyx_t_4 = PyUnicode_FromString(__pyx_v_tag_directive->handle); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 574, __pyx_L1_error)
                         ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:8474:42: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
             __pyx_t_4 = PyUnicode_FromString(__pyx_v_tag_directive->prefix); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 575, __pyx_L1_error)
                                              ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:8474:21: note: in expansion of macro ‘PyUnicode_FromString’
             __pyx_t_4 = PyUnicode_FromString(__pyx_v_tag_directive->prefix); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 575, __pyx_L1_error)
                         ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:8717:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.alias.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 586, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:8717:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.alias.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 586, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:8821:40: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.scalar.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 591, __pyx_L1_error)
                                            ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:8821:19: note: in expansion of macro ‘PyUnicode_FromString’
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.scalar.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 591, __pyx_L1_error)
                       ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:8862:40: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.scalar.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 594, __pyx_L1_error)
                                            ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:8862:19: note: in expansion of macro ‘PyUnicode_FromString’
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.scalar.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 594, __pyx_L1_error)
                       ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    ext/_yaml.c:8883:38: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
         __pyx_t_4 = PyUnicode_DecodeUTF8(__pyx_v_event->data.scalar.value, __pyx_v_event->data.scalar.length, ((char *)"strict")); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 595, __pyx_L1_error)
                                          ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:9224:40: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.sequence_start.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 620, __pyx_L1_error)
                                            ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:9224:19: note: in expansion of macro ‘PyUnicode_FromString’
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.sequence_start.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 620, __pyx_L1_error)
                       ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:9265:40: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.sequence_start.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 623, __pyx_L1_error)
                                            ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:9265:19: note: in expansion of macro ‘PyUnicode_FromString’
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.sequence_start.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 623, __pyx_L1_error)
                       ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:9497:40: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.mapping_start.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 637, __pyx_L1_error)
                                            ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:9497:19: note: in expansion of macro ‘PyUnicode_FromString’
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.mapping_start.anchor); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 637, __pyx_L1_error)
                       ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:9538:40: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.mapping_start.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 640, __pyx_L1_error)
                                            ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:9538:19: note: in expansion of macro ‘PyUnicode_FromString’
           __pyx_t_4 = PyUnicode_FromString(__pyx_v_event->data.mapping_start.tag); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 640, __pyx_L1_error)
                       ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c: In function ‘__pyx_f_5_yaml_7CParser__compose_node’:
    ext/_yaml.c:11211:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.alias.anchor); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 734, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:11211:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.alias.anchor); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 734, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:11531:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.scalar.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 750, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:11531:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.scalar.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 750, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:11587:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.sequence_start.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 753, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:11587:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.sequence_start.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 753, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:11643:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.mapping_start.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 756, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:11643:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_6 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.mapping_start.anchor); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 756, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    ext/_yaml.c: In function ‘__pyx_f_5_yaml_7CParser__compose_scalar_node’:
    ext/_yaml.c:12301:36: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
       __pyx_t_2 = PyUnicode_DecodeUTF8(__pyx_v_self->parsed_event.data.scalar.value, __pyx_v_self->parsed_event.data.scalar.length, ((char *)"strict")); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 791, __pyx_L1_error)
                                        ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c:12524:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.scalar.tag); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 804, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:12524:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_2 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.scalar.tag); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 804, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c: In function ‘__pyx_f_5_yaml_7CParser__compose_sequence_node’:
    ext/_yaml.c:13062:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.sequence_start.tag); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 837, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:13062:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.sequence_start.tag); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 837, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.c: In function ‘__pyx_f_5_yaml_7CParser__compose_mapping_node’:
    ext/_yaml.c:13687:38: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness [-Wpointer-sign]
         __pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.mapping_start.tag); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 876, __pyx_L1_error)
                                          ^
    ext/_yaml.h:6:66: note: in definition of macro ‘PyUnicode_FromString’
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                                      ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:38:0,
                     from ext/_yaml.c:4:
    /usr/include/string.h:395:15: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     extern size_t strlen (const char *__s)
                   ^
    In file included from ext/_yaml.c:596:0:
    ext/_yaml.h:6:54: warning: pointer targets in passing argument 1 of ‘PyUnicodeUCS2_DecodeUTF8’ differ in signedness [-Wpointer-sign]
     #define PyUnicode_FromString(s) PyUnicode_DecodeUTF8((s), strlen(s), "strict")
                                                          ^
    ext/_yaml.c:13687:17: note: in expansion of macro ‘PyUnicode_FromString’
         __pyx_t_3 = PyUnicode_FromString(__pyx_v_self->parsed_event.data.mapping_start.tag); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 876, __pyx_L1_error)
                     ^
    In file included from /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/Python.h:85:0,
                     from ext/_yaml.c:4:
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:174:31: note: expected ‘const char *’ but argument is of type ‘yaml_char_t * {aka unsigned char *}’
     # define PyUnicode_DecodeUTF8 PyUnicodeUCS2_DecodeUTF8
                                   ^
    /usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/include/python2.7/unicodeobject.h:750:23: note: in expansion of macro ‘PyUnicode_DecodeUTF8’
     PyAPI_FUNC(PyObject*) PyUnicode_DecodeUTF8(
                           ^
    ext/_yaml.c: In function ‘__pyx_pf_5_yaml_8CEmitter___init__’:
    ext/_yaml.c:15018:53: warning: passing argument 2 of ‘yaml_emitter_set_output’ from incompatible pointer type [-Wincompatible-pointer-types]
       yaml_emitter_set_output((&__pyx_v_self->emitter), __pyx_f_5_yaml_output_handler, ((void *)__pyx_v_self));
                                                         ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:1829:1: note: expected ‘int (*)(void *, unsigned char *, size_t) {aka int (*)(void *, unsigned char *, long unsigned int)}’ but argument is of type ‘int (*)(void *, char *, size_t) {aka int (*)(void *, char *, long unsigned int)}’
     yaml_emitter_set_output(yaml_emitter_t *emitter,
     ^
    ext/_yaml.c: In function ‘__pyx_f_5_yaml_8CEmitter__object_to_event’:
    ext/_yaml.c:16370:44: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
             __pyx_v_tag_directives_end->handle = PyString_AS_STRING(__pyx_v_handle);
                                                ^
    ext/_yaml.c:16485:44: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
             __pyx_v_tag_directives_end->prefix = PyString_AS_STRING(__pyx_v_prefix);
                                                ^
    ext/_yaml.c:16822:62: warning: pointer targets in passing argument 2 of ‘yaml_alias_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = ((yaml_alias_event_initialize(__pyx_v_event, __pyx_v_anchor) == 0) != 0);
                                                                  ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:553:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_alias_event_initialize(yaml_event_t *event, yaml_char_t *anchor);
     ^
    ext/_yaml.c:17537:63: warning: pointer targets in passing argument 2 of ‘yaml_scalar_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = ((yaml_scalar_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
                                                                   ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:578:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_scalar_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:17537:79: warning: pointer targets in passing argument 3 of ‘yaml_scalar_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = ((yaml_scalar_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
                                                                                   ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:578:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_scalar_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:17537:92: warning: pointer targets in passing argument 4 of ‘yaml_scalar_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = ((yaml_scalar_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
                                                                                                ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:578:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_scalar_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:17971:71: warning: pointer targets in passing argument 2 of ‘yaml_sequence_start_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_3 = ((yaml_sequence_start_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_sequence_style) == 0) != 0);
                                                                           ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:601:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_sequence_start_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:17971:87: warning: pointer targets in passing argument 3 of ‘yaml_sequence_start_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_3 = ((yaml_sequence_start_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_sequence_style) == 0) != 0);
                                                                                           ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:601:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_sequence_start_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:18405:70: warning: pointer targets in passing argument 2 of ‘yaml_mapping_start_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = ((yaml_mapping_start_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_mapping_style) == 0) != 0);
                                                                          ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:633:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_mapping_start_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:18405:86: warning: pointer targets in passing argument 3 of ‘yaml_mapping_start_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = ((yaml_mapping_start_event_initialize(__pyx_v_event, __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_mapping_style) == 0) != 0);
                                                                                          ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:633:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_mapping_start_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c: In function ‘__pyx_pf_5_yaml_8CEmitter_12serialize’:
    ext/_yaml.c:19975:42: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
           __pyx_v_tag_directives_end->handle = PyString_AS_STRING(__pyx_v_handle);
                                              ^
    ext/_yaml.c:20090:42: warning: pointer targets in assignment differ in signedness [-Wpointer-sign]
           __pyx_v_tag_directives_end->prefix = PyString_AS_STRING(__pyx_v_prefix);
                                              ^
    ext/_yaml.c: In function ‘__pyx_f_5_yaml_8CEmitter__serialize_node’:
    ext/_yaml.c:20947:65: warning: pointer targets in passing argument 2 of ‘yaml_alias_event_initialize’ differ in signedness [-Wpointer-sign]
         __pyx_t_2 = ((yaml_alias_event_initialize((&__pyx_v_event), __pyx_v_anchor) == 0) != 0);
                                                                     ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:553:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_alias_event_initialize(yaml_event_t *event, yaml_char_t *anchor);
     ^
    ext/_yaml.c:21758:68: warning: pointer targets in passing argument 2 of ‘yaml_scalar_event_initialize’ differ in signedness [-Wpointer-sign]
           __pyx_t_2 = ((yaml_scalar_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
                                                                        ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:578:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_scalar_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:21758:84: warning: pointer targets in passing argument 3 of ‘yaml_scalar_event_initialize’ differ in signedness [-Wpointer-sign]
           __pyx_t_2 = ((yaml_scalar_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
                                                                                        ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:578:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_scalar_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:21758:97: warning: pointer targets in passing argument 4 of ‘yaml_scalar_event_initialize’ differ in signedness [-Wpointer-sign]
           __pyx_t_2 = ((yaml_scalar_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_value, __pyx_v_length, __pyx_v_plain_implicit, __pyx_v_quoted_implicit, __pyx_v_scalar_style) == 0) != 0);
                                                                                                     ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:578:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_scalar_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:22145:76: warning: pointer targets in passing argument 2 of ‘yaml_sequence_start_event_initialize’ differ in signedness [-Wpointer-sign]
           __pyx_t_2 = ((yaml_sequence_start_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_sequence_style) == 0) != 0);
                                                                                ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:601:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_sequence_start_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:22145:92: warning: pointer targets in passing argument 3 of ‘yaml_sequence_start_event_initialize’ differ in signedness [-Wpointer-sign]
           __pyx_t_2 = ((yaml_sequence_start_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_sequence_style) == 0) != 0);
                                                                                                ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:601:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_sequence_start_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:22675:75: warning: pointer targets in passing argument 2 of ‘yaml_mapping_start_event_initialize’ differ in signedness [-Wpointer-sign]
           __pyx_t_2 = ((yaml_mapping_start_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_mapping_style) == 0) != 0);
                                                                               ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:633:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_mapping_start_event_initialize(yaml_event_t *event,
     ^
    ext/_yaml.c:22675:91: warning: pointer targets in passing argument 3 of ‘yaml_mapping_start_event_initialize’ differ in signedness [-Wpointer-sign]
           __pyx_t_2 = ((yaml_mapping_start_event_initialize((&__pyx_v_event), __pyx_v_anchor, __pyx_v_tag, __pyx_v_implicit, __pyx_v_mapping_style) == 0) != 0);
                                                                                               ^
    In file included from ext/_yaml.h:2:0,
                     from ext/_yaml.c:596:
    /usr/include/yaml.h:633:1: note: expected ‘yaml_char_t * {aka unsigned char *}’ but argument is of type ‘char *’
     yaml_mapping_start_event_initialize(yaml_event_t *event,
     ^
    warning: install_lib: byte-compiling is disabled, skipping.

    warning: install_lib: byte-compiling is disabled, skipping.

    zip_safe flag not set; analyzing archive contents...

    Installed /home/fc464/software/HiCAssembler/hic2cool/.eggs/PyYAML-5.1.1-py2.7-linux-x86_64.egg
    Searching for pysam>0.8
    Reading https://pypi.org/simple/pysam/
    Downloading https://files.pythonhosted.org/packages/1b/7d/68b6555c7bb414b655495305d2add784c251fc83d4e698878e6d1d35fc9a/pysam-0.15.2-cp27-cp27m-manylinux1_x86_64.whl#sha256=34dd4cf08cbdea1329a140f5446c319992460d400b9851c0cb5607f3c58ad256
    Best match: pysam 0.15.2
    Processing pysam-0.15.2-cp27-cp27m-manylinux1_x86_64.whl
    Installing pysam-0.15.2-cp27-cp27m-manylinux1_x86_64.whl to /home/fc464/software/HiCAssembler/hic2cool/.eggs

    Installed /home/fc464/software/HiCAssembler/hic2cool/.eggs/pysam-0.15.2-py2.7-linux-x86_64.egg
    Searching for pypairix
    Reading https://pypi.org/simple/pypairix/
    Downloading https://files.pythonhosted.org/packages/5a/52/6e44173759dcdaee003cf668fe8764b468c5b698e58f09540953961e6d36/pypairix-0.3.7.tar.gz#sha256=c1b47c05f92b5be628923c60a27344503ddeba5d8f35a3752d646271d38e0525
    Best match: pypairix 0.3.7
    Processing pypairix-0.3.7.tar.gz
    Writing /tmp/easy_install-U1i2uV/pypairix-0.3.7/setup.cfg
    Running pypairix-0.3.7/setup.py -q bdist_egg --dist-dir /tmp/easy_install-U1i2uV/pypairix-0.3.7/egg-dist-tmp-F2N6i7
    src/bgzf.c:102:14: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     static BGZF *bgzf_read_init()
                  ^
    src/bgzf.c: In function ‘bgzf_block_length’:
    src/bgzf.c:331:27: warning: unused variable ‘remaining’ [-Wunused-variable]
      int count, block_length, remaining;
                               ^
    src/bgzf.c:330:40: warning: unused variable ‘compressed_block’ [-Wunused-variable]
      uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block;
                                            ^
    src/bgzf.c: In function ‘bgzf_close’:
    src/bgzf.c:456:11: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
      int ret, count, block_length;
               ^
    src/bgzip.c:36:12: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     static int bgzip_main_usage()
                ^
    In file included from src/index.c:7:0:
    src/bam_endian.h:6:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     static inline int bam_is_big_endian()
                       ^
    In file included from src/index.c:4:0:
    src/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
      static inline kh_##name##_t *kh_init_##name() {      \
                                   ^
    src/khash.h:453:2: note: in expansion of macro ‘KHASH_INIT’
      KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
      ^
    src/index.c:51:1: note: in expansion of macro ‘KHASH_MAP_INIT_INT’
     KHASH_MAP_INIT_INT(i, ti_binlist_t)
     ^
    src/khash.h:129:31: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
      static inline kh_##name##_t *kh_init_##name() {      \
                                   ^
    src/khash.h:484:2: note: in expansion of macro ‘KHASH_INIT’
      KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
      ^
    src/index.c:52:1: note: in expansion of macro ‘KHASH_MAP_INIT_STR’
     KHASH_MAP_INIT_STR(s, int)
     ^
    src/index.c: In function ‘ti_parse_region2d’:
    src/index.c:864:69: warning: passing argument 1 of ‘ti_get_region_split_character’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             char region_split_character = ti_get_region_split_character(idx);
                                                                         ^
    In file included from src/index.c:11:0:
    src/pairix.h:218:14: note: expected ‘ti_index_t * {aka struct __ti_index_t *}’ but argument is of type ‘const ti_index_t * {aka const struct __ti_index_t *}’
             char ti_get_region_split_character(ti_index_t *idx);
                  ^
    src/index.c:878:30: warning: passing argument 1 of ‘ti_get_sc2’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             int dim = ti_get_sc2(idx)+1==0?1:2;
                                  ^
    In file included from src/index.c:11:0:
    src/pairix.h:209:13: note: expected ‘ti_index_t * {aka struct __ti_index_t *}’ but argument is of type ‘const ti_index_t * {aka const struct __ti_index_t *}’
             int ti_get_sc2(ti_index_t *idx);
                 ^
    src/index.c: In function ‘ti_querys_2d_general’:
    src/index.c:1219:31: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
              char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list);
                                   ^
    src/index.c:1236:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types]
              sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list);
                                                               ^
    In file included from src/index.c:11:0:
    src/pairix.h:131:28: note: expected ‘const char **’ but argument is of type ‘char **’
             sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs);
                                ^
    src/index.c:1242:30: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
              *sp=0; char *chr1 = reg;
                                  ^
    src/index.c:1246:31: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
              char **chrpairlist = ti_seqname(t->idx, &n_seqpair_list);
                                   ^
    src/index.c:1263:59: warning: passing argument 2 of ‘ti_querys_2d_multi’ from incompatible pointer type [-Wincompatible-pointer-types]
              sequential_iter_t *siter = ti_querys_2d_multi(t, regions, n_sub_list);
                                                               ^
    In file included from src/index.c:11:0:
    src/pairix.h:131:28: note: expected ‘const char **’ but argument is of type ‘char **’
             sequential_iter_t *ti_querys_2d_multi(pairix_t *t, const char **regs, int nRegs);
                                ^
    src/index.c: In function ‘ti_query_2d_tid’:
    src/index.c:1417:24: warning: return makes integer from pointer without a cast [-Wint-conversion]
      if (name == 0) return ti_iter_first();
                            ^
    src/index.c: In function ‘create_merged_iter’:
    src/index.c:1469:6: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
          if( miter->iu = calloc(n,sizeof(iter_unit*))) {
          ^
    src/index.c: In function ‘merged_ti_read’:
    src/index.c:1537:19: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             miu[i]->s = ti_iter_read(miu[i]->t->fp, miu[i]->iter, miu[i]->len, seqonly);
                       ^
    src/index.c:1543:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
           miu[0]->s = ti_iter_read(miu[0]->t->fp, miu[0]->iter, miu[0]->len, seqonly); // get next entry for the flushed iter
                     ^
    src/index.c: In function ‘sequential_ti_read’:
    src/index.c:1573:15: warning: initialization discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
         char *s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
                   ^
    src/index.c:1576:9: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
           s = ti_iter_read(siter->t->fp,siter->iter[siter->curr], len, 0);
             ^
    src/index.c: In function ‘get_unique_merged_seqname’:
    src/index.c:1643:22: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
                 seqnames = ti_seqname(tbs[i]->idx,&len);
                          ^
    src/index.c: In function ‘flip_region’:
    src/index.c:1744:19: warning: variable ‘split_pos’ set but not used [-Wunused-but-set-variable]
         int l, i, l2, split_pos;
                       ^
    src/index.c: In function ‘querys_2D_wrapper’:
    src/index.c:1911:34: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             char *reg2 = flip_region(reg, get_region_split_character(tb));
                                      ^
    src/index.c:1743:7: note: expected ‘char *’ but argument is of type ‘const char *’
     char *flip_region ( char* s, char region_split_character) {
           ^
    src/index.c: In function ‘check_triangle’:
    src/index.c:1971:23: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
         char **seqnames = ti_seqname(idx,&len);
                           ^
    src/index.c:1977:64: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
               if(ti_get_tid(idx, reg2)!=-1) { free(seqnames); free(reg2); return(0); }  // not a triangle
                                                                    ^
    In file included from src/khash.h:94:0,
                     from src/index.c:4:
    /usr/include/stdlib.h:482:13: note: expected ‘void *’ but argument is of type ‘const char *’
     extern void free (void *__ptr) __THROW;
                 ^
    src/index.c:1978:14: warning: passing argument 1 of ‘free’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             free(reg2);
                  ^
    In file included from src/khash.h:94:0,
                     from src/index.c:4:
    /usr/include/stdlib.h:482:13: note: expected ‘void *’ but argument is of type ‘const char *’
     extern void free (void *__ptr) __THROW;
                 ^
    src/pairixmodule.c: In function ‘pairix_new’:
    src/pairixmodule.c:367:9: warning: unused variable ‘i’ [-Wunused-variable]
         int i;
             ^
    src/pairixmodule.c: In function ‘pairix_querys_2D’:
    src/pairixmodule.c:559:28: warning: passing argument 1 of ‘flip_region’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
             reg2 = flip_region(reg, get_region_split_character(self->tb));
                                ^
    In file included from src/pairixmodule.c:34:0:
    src/pairix.h:223:15: note: expected ‘char *’ but argument is of type ‘const char *’
             char* flip_region(char *s, char region_split_character);
                   ^
    src/pairixmodule.c: In function ‘pairix_get_blocknames’:
    src/pairixmodule.c:603:23: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
       char **blocknames = ti_seqname(self->tb->idx, &n);
                           ^
    src/pairixmodule.c: In function ‘pairix_get_header’:
    src/pairixmodule.c:693:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
         while ((s = sequential_ti_read(siter, &len)) != 0) {
                   ^
    src/pairixmodule.c:704:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
         while ((s = sequential_ti_read(siter, &len)) != 0) {
                   ^
    src/pairixmodule.c: In function ‘pairix_get_chromsize’:
    src/pairixmodule.c:726:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
         while ((s = sequential_ti_read(siter, &len)) != 0) {
                   ^
    src/pairixmodule.c:738:15: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
         while ((s = sequential_ti_read(siter, &len)) != 0) {
                   ^
    warning: install_lib: byte-compiling is disabled, skipping.

    warning: install_lib: byte-compiling is disabled, skipping.

    zip_safe flag not set; analyzing archive contents...
    Moving pypairix-0.3.7-py2.7-linux-x86_64.egg to /home/fc464/software/HiCAssembler/hic2cool/.eggs

    Installed /home/fc464/software/HiCAssembler/hic2cool/.eggs/pypairix-0.3.7-py2.7-linux-x86_64.egg
    Searching for pyfaidx
    Reading https://pypi.org/simple/pyfaidx/
    Downloading https://files.pythonhosted.org/packages/75/a5/7e2569527b3849ea28d79b4f70d7cf46a47d36459bc59e0efa4e10e8c8b2/pyfaidx-0.5.5.2.tar.gz#sha256=9ac22bdc7b9c5d995d32eb9dc278af9ba970481636ec75c0d687d38c26446caa
    Best match: pyfaidx 0.5.5.2
    Processing pyfaidx-0.5.5.2.tar.gz
    Writing /tmp/easy_install-VBtocw/pyfaidx-0.5.5.2/setup.cfg
    Running pyfaidx-0.5.5.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-VBtocw/pyfaidx-0.5.5.2/egg-dist-tmp-p7kNWb
    warning: no files found matching 'docs/build/html/*'
    warning: build_py: byte-compiling is disabled, skipping.

    warning: install_lib: byte-compiling is disabled, skipping.

    zip_safe flag not set; analyzing archive contents...
    Moving pyfaidx-0.5.5.2-py2.7.egg to /home/fc464/software/HiCAssembler/hic2cool/.eggs

    Installed /home/fc464/software/HiCAssembler/hic2cool/.eggs/pyfaidx-0.5.5.2-py2.7.egg
    Searching for pandas>=0.19
    Reading https://pypi.org/simple/pandas/
    Downloading https://files.pythonhosted.org/packages/3e/a7/bfbaa1b8b2abc129793c329b37e69c54f5fd9a06f21a283ff91b17eaca73/pandas-0.25.0rc0.tar.gz#sha256=7fa6e3264009127c3b2c2dbd7257ec1301940c0bea0daae983d9d3ac0d7bb8a1
    Best match: pandas 0.25.0rc0
    Processing pandas-0.25.0rc0.tar.gz
    Writing /tmp/easy_install-hMeZV8/pandas-0.25.0rc0/setup.cfg
    Running pandas-0.25.0rc0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-hMeZV8/pandas-0.25.0rc0/egg-dist-tmp-ZJ62cY
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/home/fc464/software/HiCAssembler/hic2cool/setup.py", line 58, in <module>
        "Topic :: Scientific/Engineering :: Bio-Informatics"
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/__init__.py", line 144, in setup
        _install_setup_requires(attrs)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/__init__.py", line 139, in _install_setup_requires
        dist.fetch_build_eggs(dist.setup_requires)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/dist.py", line 717, in fetch_build_eggs
        replace_conflicting=True,
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
        replace_conflicting=replace_conflicting
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
        return self.obtain(req, installer)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
        return installer(requirement)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/dist.py", line 784, in fetch_build_egg
        return cmd.easy_install(req)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 679, in easy_install
        return self.install_item(spec, dist.location, tmpdir, deps)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 705, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 890, in install_eggs
        return self.build_and_install(setup_script, setup_base)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1158, in build_and_install
        self.run_setup(setup_script, setup_base, args)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1144, in run_setup
        run_setup(setup_script, args)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
        raise
      File "/usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/lib/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
        yield
      File "/usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/python-2.7.13-yubmrmnjlffovbkco3hpujao4asp6pyl/lib/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
        saved_exc.resume()
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
        six.reraise(type, exc, self._tb)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
        yield saved
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
        yield
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
        _execfile(setup_script, ns)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 45, in _execfile
        exec(code, globals, locals)
      File "/tmp/easy_install-hMeZV8/pandas-0.25.0rc0/setup.py", line 21, in <module>
        'scipy<=1.2.1',
      File "/tmp/easy_install-hMeZV8/pandas-0.25.0rc0/versioneer.py", line 1629
        print("Adding sample versioneer config to setup.cfg", file=sys.stderr)
                                                                  ^
    SyntaxError: invalid syntax
    ----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /home/fc464/software/HiCAssembler/hic2cool/

I need it for HiCAssembler which ueses python 2.7. Any conflict here?

Thanks F

carlvitzthum commented 5 years ago

Hi @francicco

Thanks for raising the issue! The problem was caused by a new release of pandas 4 days ago (0.25.0rc0) that deprecates Python 2. I have pinned the previous pandas version to fix the problem. Please use hic2cool==0.7.3 to get this change -- it's in the master branch, if you are using an editable install.

One more note: hic2cool will be ending support for Python 2.7 upon its official end of life. See here for more info.

Best, Carl

francicco commented 5 years ago

Hi @carlvitzthum,

Thanks for the reply. I have to use Python2 because HiCAssembler needs it. So, this is what I'm doing:

virtualenv HiCAssembler
source HiCAssembler/bin/activate
pip install git+https://github.com/4dn-dcic/hic2cool.git

But I get the error anyway

Collecting git+https://github.com/4dn-dcic/hic2cool.git
  Cloning https://github.com/4dn-dcic/hic2cool.git to /tmp/pip-cy808A-build
    Complete output from command python setup.py egg_info:
    /usr/lib64/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'long_description_content_type'
      warnings.warn(msg)
    warning: no files found matching 'CHANGES.md'
    no previously-included directories found matching 'docs/_build'
    no previously-included directories found matching 'docs/_static'
    no previously-included directories found matching 'docs/_templates'
    warning: no previously-included files matching '__pycache__/*' found anywhere in distribution
    warning: no previously-included files matching '*.so' found anywhere in distribution
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '.git*' found anywhere in distribution
    warning: no previously-included files matching '.deps/*' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    warning: build_py: byte-compiling is disabled, skipping.

    warning: install_lib: byte-compiling is disabled, skipping.

    warning: easy_install: byte-compiling is disabled, skipping.

    Installed /tmp/pip-cy808A-build/.eggs/cooler-0.8.5-py2.7.egg
    Searching for pandas<=0.24.2
    Reading https://pypi.python.org/simple/pandas/
    Downloading https://files.pythonhosted.org/packages/b2/4c/b6f966ac91c5670ba4ef0b0b5613b5379e3c7abdfad4e7b89a87d73bae13/pandas-0.24.2.tar.gz#sha256=4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2
    Best match: pandas 0.24.2
    Processing pandas-0.24.2.tar.gz
    Writing /tmp/easy_install-YFBOOD/pandas-0.24.2/setup.cfg
    Running pandas-0.24.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-YFBOOD/pandas-0.24.2/egg-dist-tmp-mO0Txh
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-cy808A-build/setup.py", line 60, in <module>
        "Topic :: Scientific/Engineering :: Bio-Informatics"
      File "/usr/lib64/python2.7/distutils/core.py", line 112, in setup
        _setup_distribution = dist = klass(attrs)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/dist.py", line 315, in __init__
        self.fetch_build_eggs(attrs['setup_requires'])
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/dist.py", line 361, in fetch_build_eggs
        replace_conflicting=True,
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 850, in resolve
        dist = best[req.key] = env.best_match(req, ws, installer)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1122, in best_match
        return self.obtain(req, installer)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1134, in obtain
        return installer(requirement)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/dist.py", line 429, in fetch_build_egg
        return cmd.easy_install(req)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 665, in easy_install
        return self.install_item(spec, dist.location, tmpdir, deps)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 695, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 876, in install_eggs
        return self.build_and_install(setup_script, setup_base)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1115, in build_and_install
        self.run_setup(setup_script, setup_base, args)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1101, in run_setup
        run_setup(setup_script, args)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 251, in run_setup
        raise
      File "/usr/lib64/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 198, in setup_context
        yield
      File "/usr/lib64/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 169, in save_modules
        saved_exc.resume()
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 144, in resume
        six.reraise(type, exc, self._tb)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 157, in save_modules
        yield saved
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 198, in setup_context
        yield
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 248, in run_setup
        DirectorySandbox(setup_dir).run(runner)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 278, in run
        return func()
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 246, in runner
        _execfile(setup_script, ns)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 47, in _execfile
        exec(code, globals, locals)
      File "/tmp/easy_install-YFBOOD/pandas-0.24.2/setup.py", line 746, in <module>

      File "/usr/lib64/python2.7/distutils/core.py", line 112, in setup
        _setup_distribution = dist = klass(attrs)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/dist.py", line 315, in __init__
        self.fetch_build_eggs(attrs['setup_requires'])
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/dist.py", line 361, in fetch_build_eggs
        replace_conflicting=True,
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 850, in resolve
        dist = best[req.key] = env.best_match(req, ws, installer)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1122, in best_match
        return self.obtain(req, installer)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1134, in obtain
        return installer(requirement)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/dist.py", line 429, in fetch_build_egg
        return cmd.easy_install(req)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 665, in easy_install
        return self.install_item(spec, dist.location, tmpdir, deps)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 695, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 876, in install_eggs
        return self.build_and_install(setup_script, setup_base)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1115, in build_and_install
        self.run_setup(setup_script, setup_base, args)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1101, in run_setup
        run_setup(setup_script, args)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 251, in run_setup
        raise
      File "/usr/lib64/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 198, in setup_context
        yield
      File "/usr/lib64/python2.7/contextlib.py", line 35, in __exit__
        self.gen.throw(type, value, traceback)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 169, in save_modules
        saved_exc.resume()
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 144, in resume
        six.reraise(type, exc, self._tb)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 157, in save_modules
        yield saved
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 198, in setup_context
        yield
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 248, in run_setup
        DirectorySandbox(setup_dir).run(runner)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 278, in run
        return func()
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 246, in runner
        _execfile(setup_script, ns)
      File "/home/fc464/software/HiCAssembler/lib/python2.7/site-packages/setuptools/sandbox.py", line 47, in _execfile
        exec(code, globals, locals)
      File "/tmp/easy_install-YFBOOD/pandas-0.24.2/temp/easy_install-WGCjoH/numpy-1.17.0rc1/setup.py", line 31, in <module>
        version = this_version,
    RuntimeError: Python version >= 3.5 required.

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-cy808A-build/
You are using pip version 9.0.1, however version 19.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
francicco commented 5 years ago

If I install it with Python3 I get these errors when I install HiCAssembler

ERROR: hicmatrix 7 has requirement cooler==0.8.2, but you'll have cooler 0.8.5 which is incompatible.
ERROR: hicexplorer 2.2.1.1 has requirement cooler==0.8.2, but you'll have cooler 0.8.5 which is incompatible.

If I remove cooler==0.8.5 and install cooler==0.8.2 then hic2cool complains:

ERROR: hic2cool 0.7.3 has requirement cooler>=0.8.5, but you'll have cooler 0.8.2 which is incompatible.

What to do? F

carlvitzthum commented 5 years ago

Hi @francicco

Both of the following work for me in clean Python 2.7 virtual environments:

pip install hic2cool==0.7.3
pip install git+https://github.com/4dn-dcic/hic2cool.git

As such, it installs correctly in an isolated and the problem is not from the hic2cool side. I took a quick look at the HiCAssembler requirements file and the way they have set up their package, it will automatically attempt to use the newest versions of packages when installing. This may be the cause of the original issue; it was what I fixed in hic2cool version 0.7.3 (my comment above).

I quickly looked into your problem and here's some feedback that may be helpful:

I will not downgrade the cooler version for hic2cool, since it requires features in 0.8.5. I hope this is helpful.

Best, Carl

francicco commented 5 years ago

It's a mess. I manually installed (via pip install -e .) all dependencies using python 2.7 with the exception of matplotlib. HiCExplorer now complains because it wants matplotlib==3.0.*, but matplotlib now wants Python3.

F