i get error when build using conda
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joseph morgan
Jan 13, 2016, 11:15:30 AM1/13/16
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(astropy35)joseph-3537 ~/astropy $ python setup.py build
running build
running build_py
running pre_hook from astropy._erfa.setup_package for build_py command
running pre_hook from astropy.modeling.setup_package for build_py command
running build_ext
running pre_hook from astropy._erfa.setup_package for build_ext command
running pre_hook from astropy.modeling.setup_package for build_ext command
building 'astropy._compiler' extension
gcc -pthread -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/joseph/anaconda3/envs/astropy35/include/python3.5m -c astropy/_compiler.c -o build/temp.linux-x86_64-3.5/astropy/_compiler.o
In file included from /usr/lib/gcc/x86_64-linux-gnu/4.8/include-fixed/syslimits.h:7:0,
from /usr/lib/gcc/x86_64-linux-gnu/4.8/include-fixed/limits.h:34,
from /home/joseph/anaconda3/envs/astropy35/include/python3.5m/Python.h:11,
from astropy/_compiler.c:1:
/usr/lib/gcc/x86_64-linux-gnu/4.8/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory
#include_next <limits.h> /* recurse down to the real one */
^
compilation terminated.
error: command 'gcc' failed with exit status 1
Dominik Klaes
Jan 13, 2016, 11:19:29 AM1/13/16
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Hi Joseph,
can you try to execute 'gcc' on your terminal? It looks like this compiler is not installed on your machine. Depending on your os, you can install it with e.g. 'sudo apt-get install gcc'.
Cheers,
Dominik
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Erik Bray
Jan 13, 2016, 11:22:28 AM1/13/16
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Hi Joseph,
What OS are you on? It looks like you're missing some system headers.
It's possible you need to install additional development packages.
For example, on Ubuntu there's a build-essentials package that should
have most of what you need.
What OS are you on? It looks like you're missing some system headers.
It's possible you need to install additional development packages.
For example, on Ubuntu there's a build-essentials package that should
have most of what you need.
joseph morgan
Jan 13, 2016, 11:23:53 AM1/13/16
to astropy-dev
in my linux os.. i have already 'gcc'.
joseph morgan
Jan 13, 2016, 11:25:09 AM1/13/16
to astropy-dev
thanks for reply me. i reinstall 'gcc' but i get same error
joseph morgan
Jan 13, 2016, 11:28:33 AM1/13/16
to astropy-dev
(astropy35)joseph ~ $ conda list
# packages in environment at /home/joseph/anaconda3/envs/astropy35:
#
_license 1.1 py35_1
abstract-rendering 0.5.1 np110py35_0
alabaster 0.7.6 py35_0
anaconda 2.4.1 np110py35_0
anaconda-client 1.2.1 py35_0
argcomplete 1.0.0 py35_1
astropy 1.0.6 np110py35_0
babel 2.1.1 py35_0
beautifulsoup4 4.4.1 py35_0
bitarray 0.8.1 py35_0
blaze 0.8.3 <pip>
blaze-core 0.8.3 py35_0
bokeh 0.10.0 py35_0
boto 2.38.0 py35_0
bottleneck 1.0.0 np110py35_0
cffi 1.2.1 py35_0
clyent 1.2.0 py35_0
colorama 0.3.3 py35_0
configobj 5.0.6 py35_0
cryptography 1.0.2 py35_0
curl 7.45.0 0
cycler 0.9.0 py35_0
cython 0.23.4 py35_0
cytoolz 0.7.4 py35_0
datashape 0.4.7 np110py35_1
decorator 4.0.4 py35_0
docutils 0.12 py35_0
dynd 9b63882 <pip>
dynd-python 0.7.0 py35_0
fastcache 1.0.2 py35_0
flask 0.10.1 py35_1
fontconfig 2.11.1 5
freetype 2.5.5 0
greenlet 0.4.9 py35_0
h5py 2.5.0 np110py35_4
hdf5 1.8.15.1 2
idna 2.0 py35_0
ipykernel 4.1.1 py35_0
ipython 4.0.1 py35_0
ipython-genutils 0.1.0 <pip>
ipython-notebook 4.0.4 py35_0
ipython-qtconsole 4.0.1 py35_0
ipython_genutils 0.1.0 py35_0
ipywidgets 4.1.0 py35_0
itsdangerous 0.24 py35_0
jbig 2.1 0
jdcal 1.0 py35_0
jedi 0.9.0 py35_0
jinja2 2.8 py35_0
jpeg 8d 0
jsonschema 2.4.0 py35_0
jupyter 1.0.0 py35_1
jupyter-client 4.1.1 <pip>
jupyter-console 4.0.3 <pip>
jupyter-core 4.0.6 <pip>
jupyter_client 4.1.1 py35_0
jupyter_console 4.0.3 py35_0
jupyter_core 4.0.6 py35_0
libdynd 0.7.0 0
libffi 3.0.13 0
libgfortran 1.0 0
libpng 1.6.17 0
libsodium 1.0.3 0
libtiff 4.0.6 1
libxml2 2.9.2 0
libxslt 1.1.28 0
llvmlite 0.8.0 py35_0
lxml 3.4.4 py35_0
markupsafe 0.23 py35_0
matplotlib 1.5.0 np110py35_0
mistune 0.7.1 py35_0
multipledispatch 0.4.8 py35_0
nbconvert 4.0.0 py35_0
nbformat 4.0.1 py35_0
networkx 1.10 py35_0
nltk 3.1 py35_0
nose 1.3.7 py35_0
notebook 4.0.6 py35_0
numba 0.22.1 np110py35_0
numexpr 2.4.4 np110py35_0
numpy 1.10.1 py35_0
odo 0.3.4 py35_0
openblas 0.2.14 3
openpyxl 2.2.6 py35_0
openssl 1.0.2d 0
pandas 0.17.1 np110py35_0
patchelf 0.6 0
path.py 8.1.2 py35_1
patsy 0.4.0 np110py35_0
pep8 1.6.2 py35_0
pexpect 3.3 py35_0
pickleshare 0.5 py35_0
pillow 3.0.0 py35_1
pip 7.1.2 py35_0
ply 3.8 py35_0
psutil 3.3.0 py35_0
ptyprocess 0.5 py35_0
py 1.4.30 py35_0
pyasn1 0.1.9 py35_0
pycosat 0.6.1 py35_0
pycparser 2.14 py35_0
pycrypto 2.6.1 py35_0
pycurl 7.19.5.1 py35_3
pyflakes 1.0.0 py35_0
pygments 2.0.2 py35_0
pyopenssl 0.15.1 py35_1
pyparsing 2.0.3 py35_0
pyqt 4.11.4 py35_1
pytables 3.2.2 np110py35_0
pytest 2.8.1 py35_0
python 3.5.1 0
python-dateutil 2.4.2 py35_0
pytz 2015.7 py35_0
pyyaml 3.11 py35_1
pyzmq 14.7.0 py35_1
qt 4.8.7 1
qtconsole 4.1.1 py35_0
readline 6.2 2
redis 2.6.9 0
redis-py 2.10.3 py35_0
requests 2.8.1 py35_0
rope 0.9.4 py35_1
rope-py3k-0.9.4 1 <pip>
scikit-image 0.11.3 np110py35_0
scikit-learn 0.17 np110py35_1
scipy 0.16.0 np110py35_1
setuptools 18.5 py35_0
simplegeneric 0.8.1 py35_0
sip 4.16.9 py35_0
six 1.10.0 py35_0
snowballstemmer 1.2.0 py35_0
sockjs-tornado 1.0.1 py35_0
sphinx 1.3.1 py35_0
sphinx-rtd-theme 0.1.7 <pip>
sphinx_rtd_theme 0.1.7 py35_0
spyder 2.3.8 py35_0
spyder-app 2.3.8 py35_0
sqlalchemy 1.0.9 py35_0
sqlite 3.8.4.1 1
statsmodels 0.6.1 np110py35_0
sympy 0.7.6.1 py35_0
tables 3.2.2 <pip>
terminado 0.5 py35_1
theano 0.7.0 np110py35_0
tk 8.5.18 0
toolz 0.7.4 py35_0
tornado 4.3 py35_0
traitlets 4.0.0 py35_0
ujson 1.33 py35_0
unicodecsv 0.14.1 py35_0
util-linux 2.21 0
werkzeug 0.11.2 py35_0
wheel 0.26.0 py35_1
xlrd 0.9.4 py35_0
xlsxwriter 0.7.7 py35_0
xlwt 1.0.0 py35_0
xz 5.0.5 0
yaml 0.1.6 0
zeromq 4.1.3 0
zlib 1.2.8 0
Erik Bray
Jan 13, 2016, 11:36:14 AM1/13/16
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On Wed, Jan 13, 2016 at 11:23 AM, joseph morgan
<josephm...@gmail.com> wrote:
> in my linux os.. i have already 'gcc'.
Yes, but what Linux distribution are you on? Just "linux" doesn't
<josephm...@gmail.com> wrote:
> in my linux os.. i have already 'gcc'.
tell much. You're probably missing system packages for OS, not conda
packages.
joseph morgan
Jan 13, 2016, 12:21:12 PM1/13/16
to astropy-dev
@Erik my os is linux mint17 ...build-essentials package working but finally i test then i get this error
>>> python setup.py test
============================= test session starts ==============================
platform linux -- Python 3.5.1 -- py-1.4.30 -- pytest-2.7.3
rootdir: /tmp/astropy-test-57eaa8la, inifile: setup.cfg
Running tests with Astropy version 1.1.dev14329.
Running tests in lib.linux-x86_64-3.5/astropy docs.
Date: 2016-01-13T10:38:57
Platform: Linux-3.13.0-24-generic-x86_64-with-debian-jessie-sid
Executable: /home/joseph/anaconda3/envs/astropy35/bin/python
Full Python Version:
3.5.1 |Anaconda 2.4.1 (64-bit)| (default, Dec 7 2015, 11:16:01)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
encodings: sys: utf-8, locale: UTF-8, filesystem: utf-8
byteorder: little
float info: dig: 15, mant_dig: 15
Numpy: 1.10.1
Scipy: 0.16.0
Matplotlib: 1.5.0
h5py: 2.5.0
Pandas: 0.17.1
collected 7583 items
astropy/_erfa/tests/test_erfa.py .....
astropy/analytic_functions/tests/test_blackbody.py .....
astropy/config/configuration.py .
...............
../docs/whatsnew/index.rst .
====== 7417 passed, 125 skipped, 39 xfailed, 2 xpassed in 199.79 seconds =======
sys:1: ResourceWarning: unclosed file <_io.TextIOWrapper name='/dev/null' mode='w' encoding='UTF-8'>
Erik Bray
Jan 13, 2016, 12:27:21 PM1/13/16
to astro...@googlegroups.com
On Wed, Jan 13, 2016 at 12:21 PM, joseph morgan
<josephm...@gmail.com> wrote:
> @Erik my os is linux mint17 ...build-essentials package working but finally
> i test then i get this error
That's just a warning from Python. Nothing to worry about. I've
<josephm...@gmail.com> wrote:
> @Erik my os is linux mint17 ...build-essentials package working but finally
> i test then i get this error
tried tracking it down but not very hard--there's lots of code that
could be opening /dev/null, so it could be coming form almost
anywhere. I don't think it's even from anything in Astropy. More
likely from py.test, or one of Astropy's dependencies.
joseph morgan
Jan 13, 2016, 12:34:58 PM1/13/16
to astropy-dev
thanks a lot @Erik Bray
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