python setup install error

[jshousephd]

john@john-linux:~/raslpipe-1.2-alpha$ python setup.py install ---> pavement.install ---> pavement.prepare ---> pavement.install_dependencies ---> pavement.install_python_dependencies pip install -r requirements-dev.txt --download-cache raslpipe/download/.pip_cache Downloading/unpacking pytest==2.5.1 (from -r requirements-dev.txt (line 5)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F2c%2Fe8%2F28d5668bb1d81cab9aa28b715a2c3a6bfdae5b56789f3d5ebc49b8b9fdbd%2Fpytest-2.5.1.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/pytest/setup.py) egg_info for package pytest

Downloading/unpacking py==1.4.19 (from -r requirements-dev.txt (line 6)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2Fe1%2F57%2Fd85d0f91d0d429b2397887179478e43562904967931109fd62d3f0bd0897%2Fpy-1.4.19.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/py/setup.py) egg_info for package py

warning: no files found matching 'distribute_setup.py'

Downloading/unpacking mock==1.0.1 (from -r requirements-dev.txt (line 7)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F15%2F45%2F30273ee91feb60dabb8fbb2da7868520525f02cf910279b3047182feed80%2Fmock-1.0.1.zip Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/mock/setup.py) egg_info for package mock

warning: no files found matching '*.png' under directory 'docs'
warning: no files found matching '*.css' under directory 'docs'
warning: no files found matching '*.html' under directory 'docs'
warning: no files found matching '*.js' under directory 'docs'

Downloading/unpacking flake8==2.1.0 (from -r requirements-dev.txt (line 10)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F8c%2Fa7%2Fbce19129cb750a4f0720440801de328eafb18dd6bb94638d7bd350a8eead%2Fflake8-2.1.0.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/flake8/setup.py) egg_info for package flake8

Downloading/unpacking mccabe==0.2.1 (from -r requirements-dev.txt (line 11)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2Fec%2Fb1%2F79c08edbb2a652f2f697c2b71dc08ede14e615bf6aa325237a32e0ed36f0%2Fmccabe-0.2.1.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/mccabe/setup.py) egg_info for package mccabe

Downloading/unpacking pep8==1.4.6 (from -r requirements-dev.txt (line 12)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2Ffa%2F46%2F3e82153575bd163bdf2e599652cb331b67cdecc3dbc69bb23d354c02354b%2Fpep8-1.4.6.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/pep8/setup.py) egg_info for package pep8

warning: no previously-included files matching '*.pyc' found under directory 'docs'
warning: no previously-included files matching '*.pyo' found under directory 'docs'
warning: no previously-included files matching '*.pyc' found under directory 'testsuite'
warning: no previously-included files matching '*.pyo' found under directory 'testsuite'
no previously-included directories found matching 'docs/_build'

Downloading/unpacking pyflakes==0.7.3 (from -r requirements-dev.txt (line 13)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2Ffb%2Fe0%2F7f25ff400803340626499d5fa8555f49f014768c7221664578b85ba3b229%2Fpyflakes-0.7.3.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/pyflakes/setup.py) egg_info for package pyflakes

Downloading/unpacking Sphinx==1.2 (from -r requirements-dev.txt (line 16)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F1d%2F1c%2Fd71b589c9f77165d5d3a776df746f9102f323f045c00b8746693fa321717%2FSphinx-1.2-py27-none-any.whl Downloading/unpacking docutils==0.11 (from -r requirements-dev.txt (line 17)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F7f%2F49%2F3ff69dcb212900199462a291886e2f30f57ab3a69dc88e31eda6404a17c0%2Fdocutils-0.11.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/docutils/setup.py) egg_info for package docutils

warning: no files found matching 'MANIFEST'
warning: no files found matching '*' under directory 'extras'
warning: no previously-included files matching '.cvsignore' found under directory '*'
warning: no previously-included files matching '*.pyc' found under directory '*'
warning: no previously-included files matching '*~' found under directory '*'
warning: no previously-included files matching '.DS_Store' found under directory '*'

Downloading/unpacking Jinja2==2.7.1 (from -r requirements-dev.txt (line 18)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F47%2F83%2F679b5592feb54e948d6599edf5dac61d2991778c3ecbef6b8041663f4740%2FJinja2-2.7.1.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/Jinja2/setup.py) egg_info for package Jinja2

warning: no files found matching '*' under directory 'custom_fixers'
warning: no previously-included files matching '*' found under directory 'docs/_build'
warning: no previously-included files matching '*.pyc' found under directory 'jinja2'
warning: no previously-included files matching '*.pyc' found under directory 'docs'
warning: no previously-included files matching '*.pyo' found under directory 'jinja2'
warning: no previously-included files matching '*.pyo' found under directory 'docs'

Downloading/unpacking MarkupSafe==0.18 (from -r requirements-dev.txt (line 19)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F98%2Fcf%2F197c3b0f73224b84eb419a967f87565bcc0b0c1147012397e6bd2d45e253%2FMarkupSafe-0.18.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/MarkupSafe/setup.py) egg_info for package MarkupSafe

Downloading/unpacking Pygments==1.6 (from -r requirements-dev.txt (line 20)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2Fe8%2F90%2F992eb125901873d81440480a7cf40a40aa5f8b2e41a67fbc568db6c21595%2FPygments-1.6.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/Pygments/setup.py) egg_info for package Pygments

Downloading/unpacking Paver==1.2.1 (from -r requirements-dev.txt (line 23)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F97%2F40%2F691207ce05f302025314b8e3ab31e13c5bcb7bdb9d61182e1c340f1530ec%2FPaver-1.2.1.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/Paver/setup.py) egg_info for package Paver Downloading/unpacking colorama==0.2.7 (from -r requirements-dev.txt (line 24)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F33%2Fcc%2F3fb8058c58ea5b2d578b7f2a2e5845ae03efe0921fb316c1d570130ddd3e%2Fcolorama-0.2.7.zip Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/colorama/setup.py) egg_info for package colorama

Downloading/unpacking ruffus (from -r requirements-dev.txt (line 25)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F97%2Ffe%2F12445c6793350ab5dbf76cb87a122b9e9aab9a9040a2801004806d985216%2Fruffus-2.6.3.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/ruffus/setup.py) egg_info for package ruffus

Downloading/unpacking pyyaml (from -r requirements-dev.txt (line 26)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F04%2F60%2Fabfb3a665ee0569b60c89148b7187ddd8a36cb65e254fba945ae1315645d%2FPyYAML-3.11.zip Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/pyyaml/setup.py) egg_info for package pyyaml

Requirement already satisfied (use --upgrade to upgrade): setuptools in ./raslpipe/lib/python2.7/site-packages (from -r requirements-dev.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): six>=1.3 in ./raslpipe/lib/python2.7/site-packages (from -r requirements-dev.txt (line 28)) Downloading/unpacking termcolor (from -r requirements-dev.txt (line 29)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F8a%2F48%2Fa76be51647d0eb9f10e2a4511bf3ffb8cc1e6b14e9e4fab46173aa79f981%2Ftermcolor-1.1.0.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/termcolor/setup.py) egg_info for package termcolor

Downloading/unpacking bunch==1.0.1 (from -r requirements-dev.txt (line 30)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2Fcc%2F56%2Fceef9c8c12600a1ceb3dcefdd9e5094c72fbdba0c3af785b4a69205022c1%2Fbunch-1.0.1.zip Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/bunch/setup.py) egg_info for package bunch

Downloading/unpacking python-dateutil (from -r requirements-dev.txt (line 31)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F33%2F68%2F9eadc96f9899caebd98f55f942d6a8f3fb2b8f8e69ba81a0f771269897e9%2Fpython_dateutil-2.5.3-py2.py3-none-any.whl Downloading/unpacking pandas (from -r requirements-dev.txt (line 33)) Using download cache from raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F11%2F09%2Fe66eb844daba8680ddff26335d5b4fead77f60f957678243549a8dd4830d%2Fpandas-0.18.1.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/pandas/setup.py) egg_info for package pandas Running from numpy source directory. /tmp/easy_install-vLLc62/numpy-1.11.1/setup.py:327: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command, proceeding with " /bin/sh: 1: svnversion: not found /bin/sh: 1: svnversion: not found /tmp/easy_install-vLLc62/numpy-1.11.1/temp/tmpOtPqeZ/source.c:1:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] void zungqr(); ^ /tmp/easy_install-vLLc62/numpy-1.11.1/temp/tmpOtPqeZ/source.c: In function ‘main’: /tmp/easyinstall-vLLc62/numpy-1.11.1/temp/tmpOtPqeZ/source.c:4:13: warning: implicit declaration of function ‘zungqr’ [-Wimplicit-function-declaration] zungqr_(); ^ /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros' warnings.warn(msg) _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’ int exp (void); ^ _configtest.o: In function main': /tmp/easy_install-vLLc62/numpy-1.11.1/_configtest.c:6: undefined reference toexp' collect2: error: ld returned 1 exit status _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’ int exp (void); ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 4)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 8)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 8)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 16)]; ^ _configtest.c: In function ‘main’: _configtest.c:7:12: error: ‘SIZEOF_LONGDOUBLE’ undeclared (first use in this function) (void) SIZEOF_LONGDOUBLE; ^ _configtest.c:7:12: note: each undeclared identifier is reported only once for each function it appears in _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 16)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 32)]; ^ _configtest.c: In function ‘main’: _configtest.c:7:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:7:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 8)]; ^ _configtest.c: In function ‘main’: _configtest.c:7:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:7:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 8)]; ^ _configtest.c: In function ‘main’: _configtest.c:7:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:7:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 8)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) >= 0)]; ^ _configtest.c: In function ‘main’: _configtest.c:5:16: warning: variable ‘test_array’ set but not used [-Wunused-but-set-variable] static int test_array [1 - 2 * !(((long) (sizeof (npy_check_sizeof_type))) == 8)]; ^ _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’ int exp (void); ^ _configtest.o: In function main': /tmp/easy_install-vLLc62/numpy-1.11.1/_configtest.c:6: undefined reference toexp' collect2: error: ld returned 1 exit status _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’ int exp (void); ^ _configtest.c:1:5: warning: conflicting types for built-in function ‘asin’ int asin (void); ^ _configtest.c:2:5: warning: conflicting types for built-in function ‘cos’ int cos (void); ^ _configtest.c:3:5: warning: conflicting types for built-in function ‘log’ int log (void); ^ _configtest.c:4:5: warning: conflicting types for built-in function ‘fabs’ int fabs (void); ^ _configtest.c:5:5: warning: conflicting types for built-in function ‘tanh’ int tanh (void); ^ _configtest.c:6:5: warning: conflicting types for built-in function ‘atan’ int atan (void); ^ _configtest.c:7:5: warning: conflicting types for built-in function ‘acos’ int acos (void); ^ _configtest.c:8:5: warning: conflicting types for built-in function ‘floor’ int floor (void); ^ _configtest.c:9:5: warning: conflicting types for built-in function ‘fmod’ int fmod (void); ^ _configtest.c:10:5: warning: conflicting types for built-in function ‘sqrt’ int sqrt (void); ^ _configtest.c:11:5: warning: conflicting types for built-in function ‘cosh’ int cosh (void); ^ _configtest.c:12:5: warning: conflicting types for built-in function ‘modf’ int modf (void); ^ _configtest.c:13:5: warning: conflicting types for built-in function ‘sinh’ int sinh (void); ^ _configtest.c:14:5: warning: conflicting types for built-in function ‘frexp’ int frexp (void); ^ _configtest.c:15:5: warning: conflicting types for built-in function ‘exp’ int exp (void); ^ _configtest.c:16:5: warning: conflicting types for built-in function ‘tan’ int tan (void); ^ _configtest.c:17:5: warning: conflicting types for built-in function ‘ceil’ int ceil (void); ^ _configtest.c:18:5: warning: conflicting types for built-in function ‘log10’ int log10 (void); ^ _configtest.c:19:5: warning: conflicting types for built-in function ‘sin’ int sin (void); ^ _configtest.c:20:5: warning: conflicting types for built-in function ‘ldexp’ int ldexp (void); ^ _configtest.c:1:5: warning: conflicting types for built-in function ‘log2’ int log2 (void); ^ _configtest.c:2:5: warning: conflicting types for built-in function ‘pow’ int pow (void); ^ _configtest.c:4:5: warning: conflicting types for built-in function ‘exp2’ int exp2 (void); ^ _configtest.c:5:5: warning: conflicting types for built-in function ‘atan2’ int atan2 (void); ^ _configtest.c:7:5: warning: conflicting types for built-in function ‘rint’ int rint (void); ^ _configtest.c:10:5: warning: conflicting types for built-in function ‘cbrt’ int cbrt (void); ^ _configtest.c:11:5: warning: conflicting types for built-in function ‘nextafter’ int nextafter (void); ^ _configtest.c:12:5: warning: conflicting types for built-in function ‘trunc’ int trunc (void); ^ _configtest.c: In function ‘main’: _configtest.c:5:3: warning: statement with no effect [-Wunused-value] builtin_isnan(5.); ^ _configtest.c: In function ‘main’: _configtest.c:5:3: warning: statement with no effect [-Wunused-value] __builtin_isinf(5.); ^ _configtest.c: In function ‘main’: _configtest.c:5:3: warning: statement with no effect [-Wunused-value] builtin_isfinite(5.); ^ _configtest.c: In function ‘main’: _configtest.c:5:3: warning: statement with no effect [-Wunused-value] builtin_bswap32(5u); ^ _configtest.c: In function ‘main’: _configtest.c:5:3: warning: statement with no effect [-Wunused-value] __builtin_bswap64(5u); ^ _configtest.c: In function ‘main’: _configtest.c:5:3: warning: statement with no effect [-Wunused-value] builtin_expect(5, 0); ^ _configtest.c:3:0: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]

pragma clang diagnostic error "-Wattributes"

 ^
_configtest.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 main()
 ^
_configtest.c:3:0: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
 #pragma clang diagnostic error "-Wattributes"
 ^
_configtest.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 main()
 ^
_configtest.c:3:0: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
 #pragma clang diagnostic error "-Wattributes"
 ^
_configtest.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 main()
 ^
_configtest.c:3:0: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
 #pragma clang diagnostic error "-Wattributes"
 ^
_configtest.c:8:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 main()
 ^
_configtest.c:3:0: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
 #pragma clang diagnostic error "-Wattributes"
 ^
_configtest.c:5:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int __declspec(thread) foo;
     ^
_configtest.c: In function ‘__declspec’:
_configtest.c:5:24: error: expected declaration specifiers before ‘foo’
 int __declspec(thread) foo;
                        ^
_configtest.c:9:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘{’ token
 {
 ^
_configtest.c:5:5: warning: type of ‘thread’ defaults to ‘int’ [-Wimplicit-int]
 int __declspec(thread) foo;
     ^
_configtest.c:11:1: error: expected ‘{’ at end of input
 }
 ^
_configtest.c:11:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
_configtest.c:1:5: warning: conflicting types for built-in function ‘cosf’
 int cosf (void);
     ^
_configtest.c:2:5: warning: conflicting types for built-in function ‘coshf’
 int coshf (void);
     ^
_configtest.c:3:5: warning: conflicting types for built-in function ‘rintf’
 int rintf (void);
     ^
_configtest.c:4:5: warning: conflicting types for built-in function ‘fabsf’
 int fabsf (void);
     ^
_configtest.c:5:5: warning: conflicting types for built-in function ‘floorf’
 int floorf (void);
     ^
_configtest.c:6:5: warning: conflicting types for built-in function ‘nextafterf’
 int nextafterf (void);
     ^
_configtest.c:7:5: warning: conflicting types for built-in function ‘tanhf’
 int tanhf (void);
     ^
_configtest.c:8:5: warning: conflicting types for built-in function ‘log10f’
 int log10f (void);
     ^
_configtest.c:9:5: warning: conflicting types for built-in function ‘logf’
 int logf (void);
     ^
_configtest.c:10:5: warning: conflicting types for built-in function ‘sinhf’
 int sinhf (void);
     ^
_configtest.c:11:5: warning: conflicting types for built-in function ‘acosf’
 int acosf (void);
     ^
_configtest.c:12:5: warning: conflicting types for built-in function ‘sqrtf’
 int sqrtf (void);
     ^
_configtest.c:13:5: warning: conflicting types for built-in function ‘ldexpf’
 int ldexpf (void);
     ^
_configtest.c:14:5: warning: conflicting types for built-in function ‘hypotf’
 int hypotf (void);
     ^
_configtest.c:15:5: warning: conflicting types for built-in function ‘log2f’
 int log2f (void);
     ^
_configtest.c:16:5: warning: conflicting types for built-in function ‘exp2f’
 int exp2f (void);
     ^
_configtest.c:17:5: warning: conflicting types for built-in function ‘atanf’
 int atanf (void);
     ^
_configtest.c:18:5: warning: conflicting types for built-in function ‘fmodf’
 int fmodf (void);
     ^
_configtest.c:19:5: warning: conflicting types for built-in function ‘atan2f’
 int atan2f (void);
     ^
_configtest.c:20:5: warning: conflicting types for built-in function ‘cbrtf’
 int cbrtf (void);
     ^
_configtest.c:21:5: warning: conflicting types for built-in function ‘modff’
 int modff (void);
     ^
_configtest.c:22:5: warning: conflicting types for built-in function ‘ceilf’
 int ceilf (void);
     ^
_configtest.c:23:5: warning: conflicting types for built-in function ‘log1pf’
 int log1pf (void);
     ^
_configtest.c:24:5: warning: conflicting types for built-in function ‘asinf’
 int asinf (void);
     ^
_configtest.c:25:5: warning: conflicting types for built-in function ‘copysignf’
 int copysignf (void);
     ^
_configtest.c:26:5: warning: conflicting types for built-in function ‘acoshf’
 int acoshf (void);
     ^
_configtest.c:27:5: warning: conflicting types for built-in function ‘sinf’
 int sinf (void);
     ^
_configtest.c:28:5: warning: conflicting types for built-in function ‘tanf’
 int tanf (void);
     ^
_configtest.c:29:5: warning: conflicting types for built-in function ‘atanhf’
 int atanhf (void);
     ^
_configtest.c:30:5: warning: conflicting types for built-in function ‘truncf’
 int truncf (void);
     ^
_configtest.c:31:5: warning: conflicting types for built-in function ‘asinhf’
 int asinhf (void);
     ^
_configtest.c:32:5: warning: conflicting types for built-in function ‘frexpf’
 int frexpf (void);
     ^
_configtest.c:33:5: warning: conflicting types for built-in function ‘powf’
 int powf (void);
     ^
_configtest.c:34:5: warning: conflicting types for built-in function ‘expf’
 int expf (void);
     ^
_configtest.c:35:5: warning: conflicting types for built-in function ‘expm1f’
 int expm1f (void);
     ^
_configtest.c:1:5: warning: conflicting types for built-in function ‘tanhl’
 int tanhl (void);
     ^
_configtest.c:2:5: warning: conflicting types for built-in function ‘log10l’
 int log10l (void);
     ^
_configtest.c:3:5: warning: conflicting types for built-in function ‘nextafterl’
 int nextafterl (void);
     ^
_configtest.c:4:5: warning: conflicting types for built-in function ‘coshl’
 int coshl (void);
     ^
_configtest.c:5:5: warning: conflicting types for built-in function ‘cosl’
 int cosl (void);
     ^
_configtest.c:6:5: warning: conflicting types for built-in function ‘floorl’
 int floorl (void);
     ^
_configtest.c:7:5: warning: conflicting types for built-in function ‘rintl’
 int rintl (void);
     ^
_configtest.c:8:5: warning: conflicting types for built-in function ‘fabsl’
 int fabsl (void);
     ^
_configtest.c:9:5: warning: conflicting types for built-in function ‘acosl’
 int acosl (void);
     ^
_configtest.c:10:5: warning: conflicting types for built-in function ‘ldexpl’
 int ldexpl (void);
     ^
_configtest.c:11:5: warning: conflicting types for built-in function ‘sqrtl’
 int sqrtl (void);
     ^
_configtest.c:12:5: warning: conflicting types for built-in function ‘logl’
 int logl (void);
     ^
_configtest.c:13:5: warning: conflicting types for built-in function ‘expm1l’
 int expm1l (void);
     ^
_configtest.c:14:5: warning: conflicting types for built-in function ‘hypotl’
 int hypotl (void);
     ^
_configtest.c:15:5: warning: conflicting types for built-in function ‘log2l’
 int log2l (void);
     ^
_configtest.c:16:5: warning: conflicting types for built-in function ‘copysignl’
 int copysignl (void);
     ^
_configtest.c:17:5: warning: conflicting types for built-in function ‘exp2l’
 int exp2l (void);
     ^
_configtest.c:18:5: warning: conflicting types for built-in function ‘atanl’
 int atanl (void);
     ^
_configtest.c:19:5: warning: conflicting types for built-in function ‘frexpl’
 int frexpl (void);
     ^
_configtest.c:20:5: warning: conflicting types for built-in function ‘atan2l’
 int atan2l (void);
     ^
_configtest.c:21:5: warning: conflicting types for built-in function ‘sinhl’
 int sinhl (void);
     ^
_configtest.c:22:5: warning: conflicting types for built-in function ‘fmodl’
 int fmodl (void);
     ^
_configtest.c:23:5: warning: conflicting types for built-in function ‘log1pl’
 int log1pl (void);
     ^
_configtest.c:24:5: warning: conflicting types for built-in function ‘asinl’
 int asinl (void);
     ^
_configtest.c:25:5: warning: conflicting types for built-in function ‘ceill’
 int ceill (void);
     ^
_configtest.c:26:5: warning: conflicting types for built-in function ‘sinl’
 int sinl (void);
     ^
_configtest.c:27:5: warning: conflicting types for built-in function ‘cbrtl’
 int cbrtl (void);
     ^
_configtest.c:28:5: warning: conflicting types for built-in function ‘acoshl’
 int acoshl (void);
     ^
_configtest.c:29:5: warning: conflicting types for built-in function ‘atanhl’
 int atanhl (void);
     ^
_configtest.c:30:5: warning: conflicting types for built-in function ‘tanl’
 int tanl (void);
     ^
_configtest.c:31:5: warning: conflicting types for built-in function ‘truncl’
 int truncl (void);
     ^
_configtest.c:32:5: warning: conflicting types for built-in function ‘powl’
 int powl (void);
     ^
_configtest.c:33:5: warning: conflicting types for built-in function ‘expl’
 int expl (void);
     ^
_configtest.c:34:5: warning: conflicting types for built-in function ‘modfl’
 int modfl (void);
     ^
_configtest.c:35:5: warning: conflicting types for built-in function ‘asinhl’
 int asinhl (void);
     ^
_configtest.c: In function ‘main’:
_configtest.c:8:12: error: ‘HAVE_DECL_SIGNBIT’ undeclared (first use in this function)
     (void) HAVE_DECL_SIGNBIT;
            ^
_configtest.c:8:12: note: each undeclared identifier is reported only once for each function it appears in
_configtest.c:1:5: warning: conflicting types for built-in function ‘clog’
 int clog (void);
     ^
_configtest.c:2:5: warning: conflicting types for built-in function ‘ctan’
 int ctan (void);
     ^
_configtest.c:3:5: warning: conflicting types for built-in function ‘casinh’
 int casinh (void);
     ^
_configtest.c:4:5: warning: conflicting types for built-in function ‘cacosh’
 int cacosh (void);
     ^
_configtest.c:5:5: warning: conflicting types for built-in function ‘cabs’
 int cabs (void);
     ^
_configtest.c:6:5: warning: conflicting types for built-in function ‘conj’
 int conj (void);
     ^
_configtest.c:7:5: warning: conflicting types for built-in function ‘csqrt’
 int csqrt (void);
     ^
_configtest.c:8:5: warning: conflicting types for built-in function ‘creal’
 int creal (void);
     ^
_configtest.c:9:5: warning: conflicting types for built-in function ‘cproj’
 int cproj (void);
     ^
_configtest.c:10:5: warning: conflicting types for built-in function ‘cpow’
 int cpow (void);
     ^
_configtest.c:11:5: warning: conflicting types for built-in function ‘csinh’
 int csinh (void);
     ^
_configtest.c:12:5: warning: conflicting types for built-in function ‘catan’
 int catan (void);
     ^
_configtest.c:13:5: warning: conflicting types for built-in function ‘ctanh’
 int ctanh (void);
     ^
_configtest.c:14:5: warning: conflicting types for built-in function ‘ccosh’
 int ccosh (void);
     ^
_configtest.c:15:5: warning: conflicting types for built-in function ‘cimag’
 int cimag (void);
     ^
_configtest.c:16:5: warning: conflicting types for built-in function ‘casin’
 int casin (void);
     ^
_configtest.c:17:5: warning: conflicting types for built-in function ‘carg’
 int carg (void);
     ^
_configtest.c:18:5: warning: conflicting types for built-in function ‘csin’
 int csin (void);
     ^
_configtest.c:19:5: warning: conflicting types for built-in function ‘cexp’
 int cexp (void);
     ^
_configtest.c:20:5: warning: conflicting types for built-in function ‘ccos’
 int ccos (void);
     ^
_configtest.c:21:5: warning: conflicting types for built-in function ‘cacos’
 int cacos (void);
     ^
_configtest.c:22:5: warning: conflicting types for built-in function ‘catanh’
 int catanh (void);
     ^
_configtest.c:1:5: warning: conflicting types for built-in function ‘ctanhf’
 int ctanhf (void);
     ^
_configtest.c:2:5: warning: conflicting types for built-in function ‘csinhf’
 int csinhf (void);
     ^
_configtest.c:3:5: warning: conflicting types for built-in function ‘cprojf’
 int cprojf (void);
     ^
_configtest.c:4:5: warning: conflicting types for built-in function ‘cacoshf’
 int cacoshf (void);
     ^
_configtest.c:5:5: warning: conflicting types for built-in function ‘cacosf’
 int cacosf (void);
     ^
_configtest.c:6:5: warning: conflicting types for built-in function ‘cargf’
 int cargf (void);
     ^
_configtest.c:7:5: warning: conflicting types for built-in function ‘cpowf’
 int cpowf (void);
     ^
_configtest.c:8:5: warning: conflicting types for built-in function ‘csinf’
 int csinf (void);
     ^
_configtest.c:9:5: warning: conflicting types for built-in function ‘clogf’
 int clogf (void);
     ^
_configtest.c:10:5: warning: conflicting types for built-in function ‘ccoshf’
 int ccoshf (void);
     ^
_configtest.c:11:5: warning: conflicting types for built-in function ‘conjf’
 int conjf (void);
     ^
_configtest.c:12:5: warning: conflicting types for built-in function ‘casinhf’
 int casinhf (void);
     ^
_configtest.c:13:5: warning: conflicting types for built-in function ‘ccosf’
 int ccosf (void);
     ^
_configtest.c:14:5: warning: conflicting types for built-in function ‘ctanf’
 int ctanf (void);
     ^
_configtest.c:15:5: warning: conflicting types for built-in function ‘cexpf’
 int cexpf (void);
     ^
_configtest.c:16:5: warning: conflicting types for built-in function ‘cimagf’
 int cimagf (void);
     ^
_configtest.c:17:5: warning: conflicting types for built-in function ‘catanhf’
 int catanhf (void);
     ^
_configtest.c:18:5: warning: conflicting types for built-in function ‘casinf’
 int casinf (void);
     ^
_configtest.c:19:5: warning: conflicting types for built-in function ‘catanf’
 int catanf (void);
     ^
_configtest.c:20:5: warning: conflicting types for built-in function ‘csqrtf’
 int csqrtf (void);
     ^
_configtest.c:21:5: warning: conflicting types for built-in function ‘crealf’
 int crealf (void);
     ^
_configtest.c:22:5: warning: conflicting types for built-in function ‘cabsf’
 int cabsf (void);
     ^
_configtest.c:1:5: warning: conflicting types for built-in function ‘csinhl’
 int csinhl (void);
     ^
_configtest.c:2:5: warning: conflicting types for built-in function ‘ctanhl’
 int ctanhl (void);
     ^
_configtest.c:3:5: warning: conflicting types for built-in function ‘cacosl’
 int cacosl (void);
     ^
_configtest.c:4:5: warning: conflicting types for built-in function ‘cacoshl’
 int cacoshl (void);
     ^
_configtest.c:5:5: warning: conflicting types for built-in function ‘cprojl’
 int cprojl (void);
     ^
_configtest.c:6:5: warning: conflicting types for built-in function ‘cargl’
 int cargl (void);
     ^
_configtest.c:7:5: warning: conflicting types for built-in function ‘ccoshl’
 int ccoshl (void);
     ^
_configtest.c:8:5: warning: conflicting types for built-in function ‘conjl’
 int conjl (void);
     ^
_configtest.c:9:5: warning: conflicting types for built-in function ‘csinl’
 int csinl (void);
     ^
_configtest.c:10:5: warning: conflicting types for built-in function ‘clogl’
 int clogl (void);
     ^
_configtest.c:11:5: warning: conflicting types for built-in function ‘cexpl’
 int cexpl (void);
     ^
_configtest.c:12:5: warning: conflicting types for built-in function ‘ccosl’
 int ccosl (void);
     ^
_configtest.c:13:5: warning: conflicting types for built-in function ‘ctanl’
 int ctanl (void);
     ^
_configtest.c:14:5: warning: conflicting types for built-in function ‘cpowl’
 int cpowl (void);
     ^
_configtest.c:15:5: warning: conflicting types for built-in function ‘casinhl’
 int casinhl (void);
     ^
_configtest.c:16:5: warning: conflicting types for built-in function ‘csqrtl’
 int csqrtl (void);
     ^
_configtest.c:17:5: warning: conflicting types for built-in function ‘casinl’
 int casinl (void);
     ^
_configtest.c:18:5: warning: conflicting types for built-in function ‘catanl’
 int catanl (void);
     ^
_configtest.c:19:5: warning: conflicting types for built-in function ‘catanhl’
 int catanhl (void);
     ^
_configtest.c:20:5: warning: conflicting types for built-in function ‘creall’
 int creall (void);
     ^
_configtest.c:21:5: warning: conflicting types for built-in function ‘cabsl’
 int cabsl (void);
     ^
_configtest.c:22:5: warning: conflicting types for built-in function ‘cimagl’
 int cimagl (void);
     ^
_configtest.c:2:12: warning: ‘static_func’ defined but not used [-Wunused-function]
 static int static_func (char \* restrict a)
            ^
non-existing path in 'numpy/distutils': 'site.cfg'
_configtest.o: In function `main':
/tmp/easy_install-vLLc62/numpy-1.11.1/_configtest.c:6: undefined reference to`exp'
collect2: error: ld returned 1 exit status
_configtest.c: In function ‘main’:
_configtest.c:7:12: error: ‘SIZEOF_LONGDOUBLE’ undeclared (first use in this function)
     (void) SIZEOF_LONGDOUBLE;
            ^
_configtest.c:7:12: note: each undeclared identifier is reported only once for each function it appears in
_configtest.o: In function `main':
/tmp/easy_install-vLLc62/numpy-1.11.1/_configtest.c:6: undefined reference to`exp'
collect2: error: ld returned 1 exit status
_configtest.c:3:0: warning: ignoring #pragma clang diagnostic [-Wunknown-pragmas]
 #pragma clang diagnostic error "-Wattributes"
 ^
_configtest.c:5:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 int __declspec(thread) foo;
     ^
_configtest.c: In function ‘__declspec’:
_configtest.c:5:24: error: expected declaration specifiers before ‘foo’
 int __declspec(thread) foo;
                        ^
_configtest.c:9:1: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘{’ token
 {
 ^
_configtest.c:5:5: warning: type of ‘thread’ defaults to ‘int’ [-Wimplicit-int]
 int __declspec(thread) foo;
     ^
_configtest.c:11:1: error: expected ‘{’ at end of input
 }
 ^
_configtest.c:11:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
_configtest.c: In function ‘main’:
_configtest.c:8:12: error: ‘HAVE_DECL_SIGNBIT’ undeclared (first use in this function)
     (void) HAVE_DECL_SIGNBIT;
            ^
_configtest.c:8:12: note: each undeclared identifier is reported only once for each function it appears in
File: build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h
#define HAVE_ENDIAN_H 1
#define SIZEOF_PY_INTPTR_T 8
#define SIZEOF_OFF_T 8
#define SIZEOF_PY_LONG_LONG 8
#define MATHLIB m
#define HAVE_SIN 1
#define HAVE_COS 1
#define HAVE_TAN 1
#define HAVE_SINH 1
#define HAVE_COSH 1
#define HAVE_TANH 1
#define HAVE_FABS 1
#define HAVE_FLOOR 1
#define HAVE_CEIL 1
#define HAVE_SQRT 1
#define HAVE_LOG10 1
#define HAVE_LOG 1
#define HAVE_EXP 1
#define HAVE_ASIN 1
#define HAVE_ACOS 1
#define HAVE_ATAN 1
#define HAVE_FMOD 1
#define HAVE_MODF 1
#define HAVE_FREXP 1
#define HAVE_LDEXP 1
#define HAVE_RINT 1
#define HAVE_TRUNC 1
#define HAVE_EXP2 1
#define HAVE_LOG2 1
#define HAVE_ATAN2 1
#define HAVE_POW 1
#define HAVE_NEXTAFTER 1
#define HAVE_STRTOLL 1
#define HAVE_STRTOULL 1
#define HAVE_CBRT 1
#define HAVE_STRTOLD_L 1
#define HAVE_FALLOCATE 1
#define HAVE_XMMINTRIN_H 1
#define HAVE_EMMINTRIN_H 1
#define HAVE_FEATURES_H 1
#define HAVE___BUILTIN_ISNAN 1
#define HAVE___BUILTIN_ISINF 1
#define HAVE___BUILTIN_ISFINITE 1
#define HAVE___BUILTIN_BSWAP32 1
#define HAVE___BUILTIN_BSWAP64 1
#define HAVE___BUILTIN_EXPECT 1
#define HAVE___BUILTIN_MUL_OVERFLOW 1
#define HAVE__MM_LOAD_PS 1
#define HAVE__MM_PREFETCH 1
#define HAVE__MM_LOAD_PD 1
#define HAVE___BUILTIN_PREFETCH 1
#define HAVE_ATTRIBUTE_OPTIMIZE_UNROLL_LOOPS 1
#define HAVE_ATTRIBUTE_OPTIMIZE_OPT_3 1
#define HAVE_ATTRIBUTE_NONNULL 1
#define HAVE___THREAD 1
#define HAVE_SINF 1
#define HAVE_COSF 1
#define HAVE_TANF 1
#define HAVE_SINHF 1
#define HAVE_COSHF 1
#define HAVE_TANHF 1
#define HAVE_FABSF 1
#define HAVE_FLOORF 1
#define HAVE_CEILF 1
#define HAVE_RINTF 1
#define HAVE_TRUNCF 1
#define HAVE_SQRTF 1
#define HAVE_LOG10F 1
#define HAVE_LOGF 1
#define HAVE_LOG1PF 1
#define HAVE_EXPF 1
#define HAVE_EXPM1F 1
#define HAVE_ASINF 1
#define HAVE_ACOSF 1
#define HAVE_ATANF 1
#define HAVE_ASINHF 1
#define HAVE_ACOSHF 1
#define HAVE_ATANHF 1
#define HAVE_HYPOTF 1
#define HAVE_ATAN2F 1
#define HAVE_POWF 1
#define HAVE_FMODF 1
#define HAVE_MODFF 1
#define HAVE_FREXPF 1
#define HAVE_LDEXPF 1
#define HAVE_EXP2F 1
#define HAVE_LOG2F 1
#define HAVE_COPYSIGNF 1
#define HAVE_NEXTAFTERF 1
#define HAVE_CBRTF 1
#define HAVE_SINL 1
#define HAVE_COSL 1
#define HAVE_TANL 1
#define HAVE_SINHL 1
#define HAVE_COSHL 1
#define HAVE_TANHL 1
#define HAVE_FABSL 1_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
 int exp (void);
     ^
_configtest.o: In function `main':
/tmp/easy_install-vLLc62/numpy-1.11.1/_configtest.c:6: undefined reference to`exp'
collect2: error: ld returned 1 exit status
_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
 int exp (void);
     ^
_configtest.c:3:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
 main()
 ^

#define HAVE_FLOORL 1
#define HAVE_CEILL 1
#define HAVE_RINTL 1
#define HAVE_TRUNCL 1
#define HAVE_SQRTL 1
#define HAVE_LOG10L 1
#define HAVE_LOGL 1
#define HAVE_LOG1PL 1
#define HAVE_EXPL 1
#define HAVE_EXPM1L 1
#define HAVE_ASINL 1
#define HAVE_ACOSL 1
#define HAVE_ATANL 1
#define HAVE_ASINHL 1
#define HAVE_ACOSHL 1
#define HAVE_ATANHL 1
#define HAVE_HYPOTL 1
#define HAVE_ATAN2L 1
#define HAVE_POWL 1
#define HAVE_FMODL 1
#define HAVE_MODFL 1
#define HAVE_FREXPL 1
#define HAVE_LDEXPL 1
#define HAVE_EXP2L 1
#define HAVE_LOG2L 1
#define HAVE_COPYSIGNL 1
#define HAVE_NEXTAFTERL 1
#define HAVE_CBRTL 1
#define HAVE_DECL_SIGNBIT
#define HAVE_COMPLEX_H 1
#define HAVE_CABS 1
#define HAVE_CACOS 1
#define HAVE_CACOSH 1
#define HAVE_CARG 1
#define HAVE_CASIN 1
#define HAVE_CASINH 1
#define HAVE_CATAN 1
#define HAVE_CATANH 1
#define HAVE_CCOS 1
#define HAVE_CCOSH 1
#define HAVE_CEXP 1
#define HAVE_CIMAG 1
#define HAVE_CLOG 1
#define HAVE_CONJ 1
#define HAVE_CPOW 1
#define HAVE_CPROJ 1
#define HAVE_CREAL 1
#define HAVE_CSIN 1
#define HAVE_CSINH 1
#define HAVE_CSQRT 1
#define HAVE_CTAN 1
#define HAVE_CTANH 1
#define HAVE_CABSF 1
#define HAVE_CACOSF 1
#define HAVE_CACOSHF 1
#define HAVE_CARGF 1
#define HAVE_CASINF 1
#define HAVE_CASINHF 1
#define HAVE_CATANF 1
#define HAVE_CATANHF 1
#define HAVE_CCOSF 1
#define HAVE_CCOSHF 1
#define HAVE_CEXPF 1
#define HAVE_CIMAGF 1
#define HAVE_CLOGF 1
#define HAVE_CONJF 1
#define HAVE_CPOWF 1
#define HAVE_CPROJF 1
#define HAVE_CREALF 1
#define HAVE_CSINF 1
#define HAVE_CSINHF 1
#define HAVE_CSQRTF 1
#define HAVE_CTANF 1
#define HAVE_CTANHF 1
#define HAVE_CABSL 1
#define HAVE_CACOSL 1
#define HAVE_CACOSHL 1
#define HAVE_CARGL 1
#define HAVE_CASINL 1
#define HAVE_CASINHL 1
#define HAVE_CATANL 1
#define HAVE_CATANHL 1
#define HAVE_CCOSL 1
#define HAVE_CCOSHL 1
#define HAVE_CEXPL 1
#define HAVE_CIMAGL 1
#define HAVE_CLOGL 1
#define HAVE_CONJL 1
#define HAVE_CPOWL 1
#define HAVE_CPROJL 1
#define HAVE_CREALL 1
#define HAVE_CSINL 1
#define HAVE_CSINHL 1
#define HAVE_CSQRTL 1
#define HAVE_CTANL 1
#define HAVE_CTANHL 1
#define NPY_RESTRICT restrict
#define HAVE_LDOUBLE_INTEL_EXTENDED_16_BYTES_LE 1
#ifndef __cplusplus
/* #undef inline */
#endif

#ifndef _NPY_NPY_CONFIG_H_
#error config.h should never be included directly, include npy_config.h instead
#endif

EOF
_configtest.o: In function `main':
/tmp/easy_install-vLLc62/numpy-1.11.1/_configtest.c:6: undefined reference to `exp'
collect2: error: ld returned 1 exit status
File: build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h
#define NPY_HAVE_ENDIAN_H 1
#define NPY_SIZEOF_SHORT SIZEOF_SHORT
#define NPY_SIZEOF_INT SIZEOF_INT
#define NPY_SIZEOF_LONG SIZEOF_LONG
#define NPY_SIZEOF_FLOAT 4
#define NPY_SIZEOF_COMPLEX_FLOAT 8
#define NPY_SIZEOF_DOUBLE 8
#define NPY_SIZEOF_COMPLEX_DOUBLE 16
#define NPY_SIZEOF_LONGDOUBLE 16
#define NPY_SIZEOF_COMPLEX_LONGDOUBLE 32
#define NPY_SIZEOF_PY_INTPTR_T 8
#define NPY_SIZEOF_OFF_T 8
#define NPY_SIZEOF_PY_LONG_LONG 8
#define NPY_SIZEOF_LONGLONG 8
#define NPY_NO_SMP 0
#define NPY_HAVE_DECL_ISNAN
#define NPY_HAVE_DECL_ISINF
#define NPY_HAVE_DECL_ISFINITE
#define NPY_HAVE_DECL_SIGNBIT
#define NPY_USE_C99_COMPLEX 1
#define NPY_HAVE_COMPLEX_DOUBLE 1
#define NPY_HAVE_COMPLEX_FLOAT 1
#define NPY_HAVE_COMPLEX_LONG_DOUBLE 1
#define NPY_USE_C99_FORMATS 1
#define NPY_VISIBILITY_HIDDEN __attribute__((visibility("hidden")))
#define NPY_ABI_VERSION 0x01000009
#define NPY_API_VERSION 0x0000000A

#ifndef __STDC_FORMAT_MACROS
#define __STDC_FORMAT_MACROS 1
#endif

EOF
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '*.pyd' found anywhere in distribution

[demis001]

It seems you haven't activated the virtual environment on this one. Are you sure you did in the following sequences:

Would you please remove the folder and install in the following sequence? rm -rf raslpipe-1.2-alpha

1. System dependencies:

sudo apt-get install python-dev g++ libjpeg-dev pkg-config ghostscript git gfortran zlib1g-dev build-essential libopenblas-base libopenblas-dev liblapack-dev python-sphinx libncurses5 libncurses5-dev libpng12-dev libfreetype6-dev

1. Clone repos:

wget https://github.com/demis001/raslpipe/archive/v1.2-alpha.tar.gz -O- | tar xzf - cd raslpipe-1.2-alpha

1. Initialize Virtualenv:

wget --no-check-certificate https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.11.6.tar.gz -O- | tar xzf - python virtualenv-1.11.6/virtualenv.py raslpipe

1. Activate virtualenv

source raslpipe/bin/activate pip install paver sphinx_rtd_theme

1. Install the application

python setup.py install

The manual page are optional.

[akadrhouse]

I am at work. Running Ubuntu 15, and all went fine until the end.

Running setup.py install for MarkupSafe

building 'markupsafe._speedups' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c markupsafe/_speedups.c -o build/temp.linux-x86_64-2.7/markupsafe/_speedups.o
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/markupsafe/_speedups.o -o build/lib.linux-x86_64-2.7/markupsafe/_speedups.so

Successfully installed paver sphinx-rtd-theme sphinx babel snowballstemmer six Pygments docutils Jinja2 imagesize alabaster pytz MarkupSafe Cleaning up... john@john-VirtualBox:~/raslpipe-1.2-alpha$ python virtualenv-1.11.6/virtualenv.py raslpipe New python executable in raslpipe/bin/python Installing setuptools, pip...done. john@john-VirtualBox:~/raslpipe-1.2-alpha$ python setup.py install ---> pavement.install ---> pavement.prepare ---> pavement.install_dependencies ---> pavement.install_python_dependencies pip install -r requirements-dev.txt --download-cache raslpipe/download/.pip_cache Downloading/unpacking pytest==2.5.1 (from -r requirements-dev.txt (line 5)) Creating supposed download cache at raslpipe/download/.pip_cache Downloading pytest-2.5.1.tar.gz (577kB): 577kB downloaded Storing download in cache at ./raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F2c%2Fe8%2F28d5668bb1d81cab9aa28b715a2c3a6bfdae5b56789f3d5ebc49b8b9fdbd%2Fpytest-2.5.1.tar.gz Cleaning up... Exception: Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 122, in main status = self.run(options, args) File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 304, in run requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle) File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1198, in prepare_files do_download, File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1376, in unpack_url self.session, File "/usr/lib/python2.7/dist-packages/pip/download.py", line 586, in unpack_http_url cache_download(cache_file, temp_location, content_type) File "/usr/lib/python2.7/dist-packages/pip/util.py", line 628, in cache_download fp = open(target_file+'.content-type', 'w') IOError: [Errno 36] File name too long: 'raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F2c%2Fe8%2F28d5668bb1d81cab9aa28b715a2c3a6bfdae5b56789f3d5ebc49b8b9fdbd%2Fpytest-2.5.1.tar.gz.content-type'

Storing debug log for failure in /home/john/.pip/pip.log

Captured Task Output:

---> pavement.install ---> pavement.prepare ---> pavement.install_dependencies ---> pavement.install_python_dependencies pip install -r requirements-dev.txt --download-cache raslpipe/download/.pip_cache

Build failed running pavement.install: Subprocess return code: 2 john@john-VirtualBox:~/raslpipe-1.2-alpha$

[demis001]

You forgot to activate the virtualenv: The bash status line should have to changed from john@john-VirtualBox:~/raslpipe-1.2-alpha$ to (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$.

It seems you forgot to do this.

source raslpipe/bin/activate

Make sure your bash status line looks like (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ after you activate the virtualenv

Then,

pip install paver sphinx_rtd_theme

Followed by:

python setup.py install

[akadrhouse]

john@john-VirtualBox:~/raslpipe-1.2-alpha$ source raslpipe/bin/activate (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ pip install paver sphinx_rtd_theme Downloading/unpacking paver Downloading Paver-1.2.4-py2.py3-none-any.whl (295kB): 295kB downloaded Downloading/unpacking sphinx-rtd-theme Downloading sphinx_rtd_theme-0.1.9-py2-none-any.whl (693kB): 693kB downloaded Downloading/unpacking sphinx>=1.3 (from sphinx-rtd-theme) Downloading Sphinx-1.4.4-py2.py3-none-any.whl (1.6MB): 1.6MB downloaded Downloading/unpacking babel>=1.3,!=2.0 (from sphinx>=1.3->sphinx-rtd-theme) Downloading Babel-2.3.4-py2.py3-none-any.whl (7.1MB): 7.1MB downloaded Downloading/unpacking Jinja2>=2.3 (from sphinx>=1.3->sphinx-rtd-theme) Downloading Jinja2-2.8-py2.py3-none-any.whl (263kB): 263kB downloaded Downloading/unpacking alabaster>=0.7,<0.8 (from sphinx>=1.3->sphinx-rtd-theme) Downloading alabaster-0.7.8-py2.py3-none-any.whl Downloading/unpacking imagesize (from sphinx>=1.3->sphinx-rtd-theme) Downloading imagesize-0.7.1-py2.py3-none-any.whl Downloading/unpacking six>=1.4 (from sphinx>=1.3->sphinx-rtd-theme) Downloading six-1.10.0-py2.py3-none-any.whl Downloading/unpacking Pygments>=2.0 (from sphinx>=1.3->sphinx-rtd-theme) Downloading Pygments-2.1.3-py2.py3-none-any.whl (755kB): 755kB downloaded Downloading/unpacking snowballstemmer>=1.1 (from sphinx>=1.3->sphinx-rtd-theme) Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB): 64kB downloaded Downloading/unpacking docutils>=0.11 (from sphinx>=1.3->sphinx-rtd-theme) Downloading docutils-0.12.tar.gz (1.6MB): 1.6MB downloaded Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/docutils/setup.py) egg_info for package docutils

warning: no files found matching 'MANIFEST'
warning: no files found matching '*' under directory 'extras'
warning: no previously-included files matching '.cvsignore' found under

directory '' warning: no previously-included files matching '.pyc' found under directory '' warning: no previously-included files matching '~' found under directory '_' warning: no previously-included files matching '.DSStore' found under directory '' Downloading/unpacking pytz>=0a (from babel>=1.3,!=2.0->sphinx>=1.3->sphinx-rtd-theme) Downloading pytz-2016.4-py2.py3-none-any.whl (480kB): 480kB downloaded Downloading/unpacking MarkupSafe (from Jinja2>=2.3->sphinx>=1.3->sphinx-rtd-theme) Downloading MarkupSafe-0.23.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/MarkupSafe/setup.py) egg_info for package MarkupSafe

Installing collected packages: paver, sphinx-rtd-theme, sphinx, babel, Jinja2, alabaster, imagesize, six, Pygments, snowballstemmer, docutils, pytz, MarkupSafe Running setup.py install for docutils changing mode of build/scripts-2.7/rst2html.py from 664 to 775 changing mode of build/scripts-2.7/rst2s5.py from 664 to 775 changing mode of build/scripts-2.7/rst2latex.py from 664 to 775 changing mode of build/scripts-2.7/rst2xetex.py from 664 to 775 changing mode of build/scripts-2.7/rst2man.py from 664 to 775 changing mode of build/scripts-2.7/rst2xml.py from 664 to 775 changing mode of build/scripts-2.7/rst2pseudoxml.py from 664 to 775 changing mode of build/scripts-2.7/rstpep2html.py from 664 to 775 changing mode of build/scripts-2.7/rst2odt.py from 664 to 775 changing mode of build/scripts-2.7/rst2odt_prepstyles.py from 664 to 775

warning: no files found matching 'MANIFEST'
warning: no files found matching '*' under directory 'extras'
warning: no previously-included files matching '.cvsignore' found under

directory '' warning: no previously-included files matching '.pyc' found under directory '' warning: no previously-included files matching '~' found under directory '_' warning: no previously-included files matching '.DSStore' found under directory '' changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2odt.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2latex.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2man.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2xml.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rstpep2html.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2xetex.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2pseudoxml.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2s5.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2odt_prepstyles.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2html.py to 775 Running setup.py install for MarkupSafe

building 'markupsafe._speedups' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall

-Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c markupsafe/_speedups.c -o build/temp.linux-x86_64-2.7/markupsafe/_speedups.o x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/markupsafe/_speedups.o -o build/lib.linux-x86_64-2.7/markupsafe/_speedups.so Successfully installed paver sphinx-rtd-theme sphinx babel Jinja2 alabaster imagesize six Pygments snowballstemmer docutils pytz MarkupSafe Cleaning up... (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ python setup.py install ---> pavement.install ---> pavement.prepare ---> pavement.install_dependencies ---> pavement.install_python_dependencies pip install -r requirements-dev.txt --download-cache raslpipe/download/.pip_cache Downloading/unpacking pytest==2.5.1 (from -r requirements-dev.txt (line 5)) Downloading pytest-2.5.1.tar.gz (577kB): 577kB downloaded Storing download in cache at ./raslpipe/download/.pip_cache/https%3A%2F% 2Fpypi.python.org %2Fpackages%2F2c%2Fe8%2F28d5668bb1d81cab9aa28b715a2c3a6bfdae5b56789f3d5ebc49b8b9fdbd%2Fpytest-2.5.1.tar.gz Cleaning up... Exception: Traceback (most recent call last): File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/basecommand.py", line 122, in main status = self.run(options, args) File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/commands/install.py", line 278, in run requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle) File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/req.py", line 1197, in prepare_files do_download, File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/req.py", line 1375, in unpack_url self.session, File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/download.py", line 586, in unpack_http_url cache_download(cache_file, temp_location, content_type) File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/util.py", line 609, in cache_download fp = open(target_file+'.content-type', 'w') IOError: [Errno 36] File name too long: 'raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org %2Fpackages%2F2c%2Fe8%2F28d5668bb1d81cab9aa28b715a2c3a6bfdae5b56789f3d5ebc49b8b9fdbd%2Fpytest-2.5.1.tar.gz.content-type'

Storing debug log for failure in /home/john/.pip/pip.log

Captured Task Output:

---> pavement.install ---> pavement.prepare ---> pavement.install_dependencies ---> pavement.install_python_dependencies pip install -r requirements-dev.txt --download-cache raslpipe/download/.pip_cache

Build failed running pavement.install: Subprocess return code: 2 (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$

---

John S. House PhD 919-515-1919 Bioinformatics Research Center https://brc.ncsu.edu/ 1 Lampe Drive, Ricks Hall #301 Campus Box 7566 Raleigh NC, 27695 North Carolina State University https://www.ncsu.edu/

On Wed, Jul 6, 2016 at 10:23 AM, Dereje Jima notifications@github.com wrote:

You forgot to activate the virtualenv: The bash status line should have to changed from john@john-VirtualBox:~/raslpipe-1.2-alpha$ to (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$.

It seems you forgot to do this.

source raslpipe/bin/activate

Make sure your bash status line looks like (raslpipe)john@john-VirtualBox :~/raslpipe-1.2-alpha$ after you activate the virtualenv

Then,

pip install paver sphinx_rtd_theme

Followed by:

python setup.py install

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/demis001/raslpipe/issues/11#issuecomment-230787200, or mute the thread https://github.com/notifications/unsubscribe/ATTloh51lsOCHFt5mNAMaKBuC9hTdNIcks5qS7pSgaJpZM4JFq6V .

[akadrhouse]

_IOError: [Errno 36] File name too long: 'raslpipe/download/.pipcache/https%3A%2F%2Fpypi.python.org http://2fpypi.python.org/%2Fpackages%2F2c%2Fe8%2F28d5668bb1d81cab9aa28b715a2c3a6bfdae5b56789f3d5ebc49b8b9fdbd%2Fpytest-2.5.1.tar.gz.content-type'

---

John S. House PhD 919-515-1919 Bioinformatics Research Center https://brc.ncsu.edu/ 1 Lampe Drive, Ricks Hall #301 Campus Box 7566 Raleigh NC, 27695 North Carolina State University https://www.ncsu.edu/

On Wed, Jul 6, 2016 at 10:25 AM, John House jshouse@ncsu.edu wrote:

john@john-VirtualBox:~/raslpipe-1.2-alpha$ source raslpipe/bin/activate (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ pip install paver sphinx_rtd_theme Downloading/unpacking paver Downloading Paver-1.2.4-py2.py3-none-any.whl (295kB): 295kB downloaded Downloading/unpacking sphinx-rtd-theme Downloading sphinx_rtd_theme-0.1.9-py2-none-any.whl (693kB): 693kB downloaded Downloading/unpacking sphinx>=1.3 (from sphinx-rtd-theme) Downloading Sphinx-1.4.4-py2.py3-none-any.whl (1.6MB): 1.6MB downloaded Downloading/unpacking babel>=1.3,!=2.0 (from sphinx>=1.3->sphinx-rtd-theme) Downloading Babel-2.3.4-py2.py3-none-any.whl (7.1MB): 7.1MB downloaded Downloading/unpacking Jinja2>=2.3 (from sphinx>=1.3->sphinx-rtd-theme) Downloading Jinja2-2.8-py2.py3-none-any.whl (263kB): 263kB downloaded Downloading/unpacking alabaster>=0.7,<0.8 (from sphinx>=1.3->sphinx-rtd-theme) Downloading alabaster-0.7.8-py2.py3-none-any.whl Downloading/unpacking imagesize (from sphinx>=1.3->sphinx-rtd-theme) Downloading imagesize-0.7.1-py2.py3-none-any.whl Downloading/unpacking six>=1.4 (from sphinx>=1.3->sphinx-rtd-theme) Downloading six-1.10.0-py2.py3-none-any.whl Downloading/unpacking Pygments>=2.0 (from sphinx>=1.3->sphinx-rtd-theme) Downloading Pygments-2.1.3-py2.py3-none-any.whl (755kB): 755kB downloaded Downloading/unpacking snowballstemmer>=1.1 (from sphinx>=1.3->sphinx-rtd-theme) Downloading snowballstemmer-1.2.1-py2.py3-none-any.whl (64kB): 64kB downloaded Downloading/unpacking docutils>=0.11 (from sphinx>=1.3->sphinx-rtd-theme) Downloading docutils-0.12.tar.gz (1.6MB): 1.6MB downloaded Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/docutils/setup.py) egg_info for package docutils

warning: no files found matching 'MANIFEST'
warning: no files found matching '*' under directory 'extras'
warning: no previously-included files matching '.cvsignore' found

under directory '' warning: no previously-included files matching '.pyc' found under directory '' warning: no previously-included files matching '~' found under directory '_' warning: no previously-included files matching '.DSStore' found under directory '' Downloading/unpacking pytz>=0a (from babel>=1.3,!=2.0->sphinx>=1.3->sphinx-rtd-theme) Downloading pytz-2016.4-py2.py3-none-any.whl (480kB): 480kB downloaded Downloading/unpacking MarkupSafe (from Jinja2>=2.3->sphinx>=1.3->sphinx-rtd-theme) Downloading MarkupSafe-0.23.tar.gz Running setup.py (path:/home/john/raslpipe-1.2-alpha/raslpipe/build/MarkupSafe/setup.py) egg_info for package MarkupSafe

Installing collected packages: paver, sphinx-rtd-theme, sphinx, babel, Jinja2, alabaster, imagesize, six, Pygments, snowballstemmer, docutils, pytz, MarkupSafe Running setup.py install for docutils changing mode of build/scripts-2.7/rst2html.py from 664 to 775 changing mode of build/scripts-2.7/rst2s5.py from 664 to 775 changing mode of build/scripts-2.7/rst2latex.py from 664 to 775 changing mode of build/scripts-2.7/rst2xetex.py from 664 to 775 changing mode of build/scripts-2.7/rst2man.py from 664 to 775 changing mode of build/scripts-2.7/rst2xml.py from 664 to 775 changing mode of build/scripts-2.7/rst2pseudoxml.py from 664 to 775 changing mode of build/scripts-2.7/rstpep2html.py from 664 to 775 changing mode of build/scripts-2.7/rst2odt.py from 664 to 775 changing mode of build/scripts-2.7/rst2odt_prepstyles.py from 664 to 775

warning: no files found matching 'MANIFEST'
warning: no files found matching '*' under directory 'extras'
warning: no previously-included files matching '.cvsignore' found

under directory '' warning: no previously-included files matching '.pyc' found under directory '' warning: no previously-included files matching '~' found under directory '_' warning: no previously-included files matching '.DSStore' found under directory '' changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2odt.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2latex.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2man.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2xml.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rstpep2html.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2xetex.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2pseudoxml.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2s5.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2odt_prepstyles.py to 775 changing mode of /home/john/raslpipe-1.2-alpha/raslpipe/bin/rst2html.py to 775 Running setup.py install for MarkupSafe

building 'markupsafe._speedups' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall

-Wstrict-prototypes -fno-strict-aliasing -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/usr/include/python2.7 -c markupsafe/_speedups.c -o build/temp.linux-x86_64-2.7/markupsafe/_speedups.o x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/markupsafe/_speedups.o -o build/lib.linux-x86_64-2.7/markupsafe/_speedups.so Successfully installed paver sphinx-rtd-theme sphinx babel Jinja2 alabaster imagesize six Pygments snowballstemmer docutils pytz MarkupSafe Cleaning up... (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ python setup.py install ---> pavement.install ---> pavement.prepare ---> pavement.install_dependencies ---> pavement.install_python_dependencies pip install -r requirements-dev.txt --download-cache raslpipe/download/.pip_cache Downloading/unpacking pytest==2.5.1 (from -r requirements-dev.txt (line 5)) Downloading pytest-2.5.1.tar.gz (577kB): 577kB downloaded Storing download in cache at ./raslpipe/download/.pip_cache/https%3A%2F% 2Fpypi.python.org %2Fpackages%2F2c%2Fe8%2F28d5668bb1d81cab9aa28b715a2c3a6bfdae5b56789f3d5ebc49b8b9fdbd%2Fpytest-2.5.1.tar.gz Cleaning up... Exception: Traceback (most recent call last): File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/basecommand.py", line 122, in main status = self.run(options, args) File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/commands/install.py", line 278, in run requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle) File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/req.py", line 1197, in prepare_files do_download, File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/req.py", line 1375, in unpack_url self.session, File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/download.py", line 586, in unpack_http_url cache_download(cache_file, temp_location, content_type) File "/home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages/pip/util.py", line 609, in cache_download fp = open(target_file+'.content-type', 'w') IOError: [Errno 36] File name too long: 'raslpipe/download/.pip_cache/https%3A%2F%2Fpypi.python.org %2Fpackages%2F2c%2Fe8%2F28d5668bb1d81cab9aa28b715a2c3a6bfdae5b56789f3d5ebc49b8b9fdbd%2Fpytest-2.5.1.tar.gz.content-type'

Storing debug log for failure in /home/john/.pip/pip.log

Captured Task Output:

---> pavement.install ---> pavement.prepare ---> pavement.install_dependencies ---> pavement.install_python_dependencies pip install -r requirements-dev.txt --download-cache raslpipe/download/.pip_cache

Build failed running pavement.install: Subprocess return code: 2 (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$

---

John S. House PhD 919-515-1919 Bioinformatics Research Center https://brc.ncsu.edu/ 1 Lampe Drive, Ricks Hall #301 Campus Box 7566 Raleigh NC, 27695 North Carolina State University https://www.ncsu.edu/

On Wed, Jul 6, 2016 at 10:23 AM, Dereje Jima notifications@github.com wrote:

You forgot to activate the virtualenv: The bash status line should have to changed from john@john-VirtualBox:~/raslpipe-1.2-alpha$ to (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$.

It seems you forgot to do this.

source raslpipe/bin/activate

Make sure your bash status line looks like (raslpipe)john@john-VirtualBox :~/raslpipe-1.2-alpha$ after you activate the virtualenv

Then,

pip install paver sphinx_rtd_theme

Followed by:

python setup.py install

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/demis001/raslpipe/issues/11#issuecomment-230787200, or mute the thread https://github.com/notifications/unsubscribe/ATTloh51lsOCHFt5mNAMaKBuC9hTdNIcks5qS7pSgaJpZM4JFq6V .

[demis001]

It seems your home directory has encryption setup that limit the file name length to 144.

Can you do this and paste the result

pip -V

[akadrhouse]

(raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ pip -V pip 1.5.6 from /home/john/raslpipe-1.2-alpha/raslpipe/local/lib/python2.7/site-packages (python 2.7)

[demis001]

Let us upgrade the pip to 1.6 and see if that solves the problem. Got the information from here

https://github.com/pypa/pip/issues/2002

Do this: To exit the vertualenv do this (deactivate ) on terminal. This will convert (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ to john@john-VirtualBox:~/raslpipe-1.2-alpha$

deactivate

Then, remove the bin directory rm -rf raslpipe/bin

Get new virtualenv

wget --no-check-certificate https://pypi.python.org/packages/source/v/virtualenv/virtualenv-12.0.tar.gz -O- | tar xzf -

Install and Activate:

python virtualenv-12.0/virtualenv.py raslpipe source raslpipe/bin/activate

See the version:

pip -V

Install:

pip install paver sphinx_rtd_theme python setup.py install

[akadrhouse]

It is currently working on the install. [image: Inline image 1]

---

John S. House PhD 919-515-1919 Bioinformatics Research Center https://brc.ncsu.edu/ 1 Lampe Drive, Ricks Hall #301 Campus Box 7566 Raleigh NC, 27695 North Carolina State University https://www.ncsu.edu/

On Wed, Jul 6, 2016 at 11:02 AM, Dereje Jima notifications@github.com wrote:

Let us upgrade the pip to 1.6 and see if that solves the problem. Got the information from here

https://github.com/pypa/pip/issues/2002 http://url

Do this: To exit the vertualenv do this on terminal. This will convert (raslpipe)john@john-VirtualBox:~/raslpipe-1.2-alpha$ to john@john-VirtualBox:~/raslpipe-1.2-alpha$

deactivate

Then, remove the bin directory rm -rf raslpip/bin

Get new virtualenv

wget --no-check-certificate https://pypi.python.org/packages/source/v/virtualenv/virtualenv-12.0.tar.gz -O- | tar xzf -

Install and Activate:

python virtualenv-12.0/virtualenv.py raslpipe source raslpipe/bin/activate

See the version:

pip -V

Install:

python setup.py install

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/demis001/raslpipe/issues/11#issuecomment-230800068, or mute the thread https://github.com/notifications/unsubscribe/ATTlolmiL840O28Vu3wGnyV9L9g4yg5Dks5qS8N4gaJpZM4JFq6V .

[demis001]

Excellent! let me know when it finish. The 'scipy` module take sometimes. Get a cup of coffee. It will take sometime.