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Installation error in last version when compiling from source in python2

See original GitHub issue

When compiling from source in python2 I get the following error:

$python -c "import datashader"
Segmentation fault (core dumped)

When using the conda recipe or python3 everthing is ok

Issue Analytics

State:
Created 7 years ago
Comments:8 (3 by maintainers)

Top GitHub Comments

1reaction

huhai463127310commented, Jul 1, 2017

I resloved this problem by use pip uninstall scipy. I found scipy was mentioned in core file. So I tried to uninstall the scipy, and then it the segment fault gone away. My scipy version is 0.18.1. @jbednar

0reactions

huhai463127310commented, Jun 25, 2017

How did you solve it ? I meet the same problem. @miguelgfierro Do you have any suggestion to sovle it ? @jbednar

error infomation

(tensorflow) bigdata@iZuf6istfz0zvzaadgdwhhZ:~$ python
Python 2.7.13 |Continuum Analytics, Inc.| (default, Dec 20 2016, 23:09:15) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import datashader
Segmentation fault (core dumped)

installation method

conda install -c bokeh datashader

os version

Linux iZuf6istfz0zvzaadgdwhhZ 3.13.0-86-generic #131-Ubuntu SMP Thu May 12 23:33:13 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

cond list

#packages in environment at /home/bigdata/bin/anaconda2/envs/tensorflow:
#
appdirs                   1.4.1                     <pip>
backports                 1.0                      py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
backports-abc             0.5                       <pip>
backports.shutil-get-terminal-size 1.0.0                     <pip>
backports_abc             0.5                      py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bkcharts                  0.2                       <pip>
bleach                    1.5.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
bleach                    1.5.0                     <pip>
bokeh                     0.12.6                    <pip>
bokeh                     0.12.4                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
certifi                   2017.4.17                 <pip>
chainer                   1.21.0                    <pip>
chardet                   3.0.4                     <pip>
cloudpickle               0.2.2                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
colorcet                  0.9.1                    py27_0    bokeh
colorcet                  0.9.1                     <pip>
configparser              3.5.0                     <pip>
configparser              3.5.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
dask                      0.14.3                   py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
datashader                0.5.0                    py27_0    bokeh
datashape                 0.5.4                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
dbus                      1.10.10                       0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
decorator                 4.0.11                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
decorator                 4.0.11                    <pip>
entrypoints               0.2.2                     <pip>
entrypoints               0.2.2                    py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
enum34                    1.1.6                     <pip>
enum34                    1.1.6                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
expat                     2.1.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
filelock                  2.0.7                     <pip>
fontconfig                2.12.1                        3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
freetype                  2.5.5                         2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
funcsigs                  1.0.2                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
funcsigs                  1.0.2                     <pip>
functools32               3.2.3.2                  py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
functools32               3.2.3.post2               <pip>
futures                   3.1.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
futures                   3.1.1                     <pip>
get_terminal_size         1.0.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
glib                      2.50.2                        1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
gst-plugins-base          1.8.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
gstreamer                 1.8.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
html5lib                  0.9999999                 <pip>
html5lib                  0.999                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
icu                       54.1                          0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
idna                      2.5                       <pip>
ipykernel                 4.5.2                     <pip>
ipykernel                 4.5.2                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipython                   5.2.2                     <pip>
ipython                   5.2.2                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipython-genutils          0.1.0                     <pip>
ipython-genutils          0.2.0                     <pip>
ipython_genutils          0.1.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ipywidgets                5.2.2                    py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jbig                      2.1                           0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jinja2                    2.9.4                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
Jinja2                    2.9.6                     <pip>
jpeg                      9b                            0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jsonschema                2.6.0                     <pip>
jsonschema                2.5.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jupyter                   1.0.0                    py27_3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jupyter-client            4.4.0                     <pip>
jupyter-client            5.0.0                     <pip>
jupyter-contrib-core      0.3.0                     <pip>
jupyter-contrib-nbextensions 0.2.4                     <pip>
jupyter-core              4.3.0                     <pip>
jupyter-highlight-selected-word 0.0.8                     <pip>
jupyter-latex-envs        1.3.7.2                   <pip>
jupyter-nbextensions-configurator 0.2.3                     <pip>
jupyter_client            4.4.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jupyter_console           5.1.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
jupyter_core              4.3.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libffi                    3.2.1                         1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libgcc                    5.2.0                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libiconv                  1.14                          0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libpng                    1.6.27                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libsodium                 1.0.10                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libtiff                   4.0.6                         3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libxcb                    1.12                          1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
libxml2                   2.9.4                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
llvmlite                  0.18.0                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
locket                    0.2.0                    py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
MarkupSafe                0.23                      <pip>
markupsafe                0.23                     py27_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
MarkupSafe                1.0                       <pip>
mistune                   0.7.3                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
mistune                   0.7.3                     <pip>
mkl                       2017.0.1                      0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
mock                      2.0.0                     <pip>
multipledispatch          0.4.9                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nbconvert                 5.1.1                     <pip>
nbconvert                 5.1.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nbformat                  4.3.0                     <pip>
nbformat                  4.2.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nbformat                  4.2.0                     <pip>
networkx                  1.11                     py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
nose                      1.3.7                     <pip>
notebook                  4.4.1                     <pip>
notebook                  4.3.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
numba                     0.33.0              np111py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
numpy                     1.11.3                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
numpy                     1.13.0                    <pip>
odo                       0.5.0                    py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
olefile                   0.44                     py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
openssl                   1.0.2k                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
packaging                 16.8                      <pip>
pandas                    0.19.2              np111py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pandocfilters             1.4.1                     <pip>
pandocfilters             1.4.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
partd                     0.3.8                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
path.py                   10.1                     py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pathlib2                  2.2.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pathlib2                  2.2.1                     <pip>
pbr                       1.10.0                    <pip>
pcre                      8.39                          1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pexpect                   4.2.1                     <pip>
pexpect                   4.2.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pickleshare               0.7.4                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pickleshare               0.7.4                     <pip>
Pillow                    4.0.0                     <pip>
pillow                    4.1.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pip                       9.0.1                    py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
plotly                    2.0.11                    <pip>
prompt-toolkit            1.0.13                    <pip>
prompt_toolkit            1.0.9                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
protobuf                  3.2.0                     <pip>
psutil                    5.1.3                     <pip>
ptyprocess                0.5.1                     <pip>
ptyprocess                0.5.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pygments                  2.1.3                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
Pygments                  2.2.0                     <pip>
pyparsing                 2.1.10                    <pip>
pyqt                      5.6.0                    py27_2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
python                    2.7.13                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
python-dateutil           2.6.0                     <pip>
python-dateutil           2.6.0                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pytz                      2017.2                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pytz                      2017.2                    <pip>
PyYAML                    3.12                      <pip>
pyyaml                    3.12                     py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
pyzmq                     16.0.2                    <pip>
pyzmq                     16.0.2                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
qt                        5.6.2                         3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
qtconsole                 4.2.1                    py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
readline                  6.2                           2    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
requests                  2.18.1                    <pip>
requests                  2.14.2                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
scandir                   1.4                       <pip>
scandir                   1.4                      py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
scikit-learn              0.18.1                    <pip>
scipy                     0.18.1                    <pip>
seaborn                   0.7.1                     <pip>
setuptools                27.2.0                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
setuptools                34.3.0                    <pip>
simplegeneric             0.8.1                    py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
simplegeneric             0.8.1                     <pip>
singledispatch            3.4.0.3                   <pip>
singledispatch            3.4.0.3                  py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sip                       4.18                     py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
six                       1.10.0                    <pip>
six                       1.10.0                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
sklearn                   0.0                       <pip>
sqlite                    3.13.0                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
ssl_match_hostname        3.4.0.2                  py27_1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tensorflow                0.12.1                    <pip>
terminado                 0.6                      py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
terminado                 0.6                       <pip>
testpath                  0.3                       <pip>
testpath                  0.3                      py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tk                        8.5.18                        0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
toolz                     0.8.2                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
tornado                   4.4.2                     <pip>
tornado                   4.5.1                     <pip>
tornado                   4.4.2                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
traitlets                 4.3.1                     <pip>
traitlets                 4.3.1                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
traitlets                 4.3.2                     <pip>
urllib3                   1.21.1                    <pip>
wcwidth                   0.1.7                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
wcwidth                   0.1.7                     <pip>
wheel                     0.29.0                    <pip>
wheel                     0.29.0                   py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
widgetsnbextension        1.2.6                     <pip>
widgetsnbextension        1.2.6                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xarray                    0.9.5                    py27_0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
xz                        5.2.2                         1    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
yaml                      0.1.6                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zeromq                    4.1.5                         0    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
zlib                      1.2.8                         3    https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free

pip freeze

appdirs==1.4.1
backports-abc==0.5
backports.shutil-get-terminal-size==1.0.0
backports.ssl-match-hostname==3.4.0.2
bkcharts==0.2
bleach==1.5.0
bokeh==0.12.6
certifi==2017.4.17
chainer==1.21.0
chardet==3.0.4
cloudpickle==0.2.2
colorcet==0.9.1
configparser==3.5.0
cycler==0.10.0
dask==0.14.3
datashader==0.5.0
datashape==0.5.4
decorator==4.0.11
entrypoints==0.2.2
enum34==1.1.6
et-xmlfile==1.0.1
filelock==2.0.7
funcsigs==1.0.2
functools32==3.2.3.post2
futures==3.1.1
html5lib==0.9999999
idna==2.5
ipykernel==4.5.2
ipython==5.2.2
ipython-genutils==0.2.0
ipywidgets==5.2.2
jdcal==1.3
Jinja2==2.9.6
jsonschema==2.6.0
jupyter==1.0.0
jupyter-client==5.0.0
jupyter-console==5.1.0
jupyter-contrib-core==0.3.0
jupyter-contrib-nbextensions==0.2.4
jupyter-core==4.3.0
jupyter-highlight-selected-word==0.0.8
jupyter-latex-envs==1.3.7.2
jupyter-nbextensions-configurator==0.2.3
llvmlite==0.18.0
locket==0.2.0
MarkupSafe==1.0
matplotlib==2.0.0
mistune==0.7.3
mock==2.0.0
multipledispatch==0.4.9
nbconvert==5.1.1
nbformat==4.3.0
networkx==1.11
nose==1.3.7
notebook==4.4.1
numba==0.33.0+0.ge79330a.dirty
numpy==1.13.0
odo==0.5.0
olefile==0.44
openpyxl==2.4.2
packaging==16.8
pandas==0.19.2
pandocfilters==1.4.1
partd==0.3.8
pathlib2==2.2.1
pbr==1.10.0
pexpect==4.2.1
pickleshare==0.7.4
Pillow==4.1.1
plotly==2.0.11
prompt-toolkit==1.0.13
protobuf==3.2.0
psutil==5.1.3
ptyprocess==0.5.1
Pygments==2.2.0
pyparsing==2.1.10
python-dateutil==2.6.0
pytz==2017.2
PyYAML==3.12
pyzmq==16.0.2
qtconsole==4.2.1
requests==2.18.1
scandir==1.4
scikit-learn==0.18.1
scipy==0.18.1
seaborn==0.7.1
simplegeneric==0.8.1
singledispatch==3.4.0.3
six==1.10.0
sklearn==0.0
subprocess32==3.2.7
tensorflow==0.12.1
terminado==0.6
testpath==0.3
toolz==0.8.2
tornado==4.5.1
traitlets==4.3.2
urllib3==1.21.1
wcwidth==0.1.7
widgetsnbextension==1.2.6
xarray==0.9.5

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