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omegacen / conda-depgraph

A command-line utility to plot the dependency graph of a Conda environment.
GNU Lesser General Public License v3.0
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Exceptions msgpack.exceptions.ExtraData: unpack(b) received extra data. #1

Closed wl2776 closed 5 years ago

wl2776 commented 5 years ago

Any command produces the following traceback:

$ conda depgraph --name=base out --distance=1 conda
Traceback (most recent call last):
  File "/opt/anaconda/bin/conda-depgraph", line 10, in <module>
    sys.exit(main())
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1164, in invoke
    return _process_result(rv)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1102, in _process_result
    **ctx.params)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/conda_depgraph/cli.py", line 48, in process_subcommands
    print(graph_to_ascii(g))
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 108, in graph_to_ascii
    return _asciigraph.graph_to_ascii(graph, timeout=timeout).decode(encoding='UTF-8')
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 84, in graph_to_ascii
    return loads(response.content)
  File "msgpack/_unpacker.pyx", line 209, in msgpack._cmsgpack.unpackb
msgpack.exceptions.ExtraData: unpack(b) received extra data.
~$ conda --version
conda 4.6.13

Installed from https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh

teake commented 5 years ago

Sorry, I can't reproduce this (yet). Could you post the output of conda info and of conda list of the environment you've installed conda-depgraph in? Also, could you try to reproduce it in a freshly installed Miniconda and post the exact steps you took?

wl2776 commented 5 years ago

Sorry for delay, I was on vacation. Here are the outputs of conda info and conda list

~$ conda info

     active environment : None
       user config file : /home/user/.condarc
 populated config files : /opt/anaconda/.condarc
                          /home/user/.condarc
          conda version : 4.6.13
    conda-build version : not installed
         python version : 3.6.7.final.0
       base environment : /opt/anaconda  (read only)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/anaconda/pkgs
                          /home/user/.conda/pkgs
       envs directories : /home/user/.conda/envs
                          /opt/anaconda/envs
               platform : linux-64
             user-agent : conda/4.6.13 requests/2.21.0 CPython/3.6.7 Linux/4.15.0-47-generic ubuntu/18.04.2 glibc/2.27
                UID:GID : 4007:4007
             netrc file : None
           offline mode : False

$ cat /home/user/.condarc
channel_priority: flexible

~$ cat /opt/anaconda/.condarc
channels:
  - conda-forge
  - defaults
auto_update_conda: false
show_channel_urls: true

$ conda list
# packages in environment at /opt/anaconda:
#
# Name                    Version                   Build  Channel
_tflow_select             2.1.0                       gpu    defaults
absl-py                   0.7.1                    py36_0    conda-forge
alabaster                 0.7.12                   pypi_0    pypi
alembic                   1.0.8                      py_0    conda-forge
arxiv                     0.3.1                    pypi_0    pypi
asciinet                  0.4.pre.cec4d1f               0    omegacen
asn1crypto                0.24.0                py36_1003    conda-forge
astor                     0.7.1                      py_0    conda-forge
async_generator           1.10                       py_0    conda-forge
atari-py                  0.1.7                    pypi_0    pypi
atomicwrites              1.3.0                      py_0    conda-forge
attrs                     19.1.0                     py_0    conda-forge
audioread                 2.1.6                    py36_0    conda-forge
auto-sklearn              0.5.0                    pypi_0    pypi
babel                     2.6.0                    pypi_0    pypi
backcall                  0.1.0                      py_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.os              0.1.1                 py36_1000    conda-forge
bash-kernel               0.7.1                    pypi_0    pypi
beautifulsoup4            4.7.1                    pypi_0    pypi
binutils_impl_linux-64    2.31.1               h6176602_1    defaults
binutils_linux-64         2.31.1               h6176602_3    defaults
bkcharts                  0.2                      py36_0    conda-forge
blas                      2.5                    openblas    conda-forge
bleach                    3.1.0                      py_0    conda-forge
blinker                   1.4                        py_1    conda-forge
bokeh                     1.1.0                    py36_0    conda-forge
boto                      2.49.0                     py_0    conda-forge
box2d-py                  2.3.8                    pypi_0    pypi
bs4                       0.0.1                    pypi_0    pypi
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
c-ares                    1.15.0            h14c3975_1001    conda-forge
ca-certificates           2019.3.9             hecc5488_0    conda-forge
certifi                   2019.3.9                 py36_0    conda-forge
cffi                      1.12.2           py36hf0e25f4_1    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
cite2c                    0.2.1                    pypi_0    pypi
click                     7.0                      pypi_0    pypi
cloudpickle               0.8.1                      py_0    conda-forge
colorama                  0.4.1                    pypi_0    pypi
colorlover                0.3.0                      py_0    conda-forge
conda                     4.6.13                   py36_0    conda-forge
conda-depgraph            1.0.1                         0    omegacen
conda-env                 2.6.0                         1    conda-forge
configspace               0.4.9                    pypi_0    pypi
configurable-http-proxy   1.3.0                         0    conda-forge
coverage                  4.5.3            py36h14c3975_0    conda-forge
cryptography              2.6.1            py36h72c5cf5_0    conda-forge
cudatoolkit               9.0                  h13b8566_0    defaults
cudnn                     7.3.1                 cuda9.0_0    defaults
cufflinks                 0.14.6                   pypi_0    pypi
cupti                     9.0.176                       0    defaults
curl                      7.64.1               hf8cf82a_0    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cython                    0.29.7           py36he1b5a44_0    conda-forge
cytoolz                   0.9.0.1         py36h14c3975_1001    conda-forge
dask-core                 1.2.0                      py_0    conda-forge
dbus                      1.13.0            h4e0c4b3_1000    conda-forge
decorator                 4.4.0                      py_0    conda-forge
defusedxml                0.5.0                      py_1    conda-forge
dill                      0.2.9                    py36_0    conda-forge
docutils                  0.14                  py36_1001    conda-forge
entrypoints               0.3                   py36_1000    conda-forge
expat                     2.2.5             hf484d3e_1002    conda-forge
faker                     1.0.2                    pypi_0    pypi
fastcache                 1.0.2           py36h14c3975_1001    conda-forge
feedparser                5.2.1                    pypi_0    pypi
ffmpeg                    4.1.1                h167e202_0    conda-forge
filelock                  3.0.10                   pypi_0    pypi
finance-enums             0.1.0                    pypi_0    pypi
flatbuffers               1.10                     pypi_0    pypi
fontconfig                2.13.1            he4413a7_1000    conda-forge
freeglut                  3.0.0             hf484d3e_1005    conda-forge
freetype                  2.10.0               he983fc9_0    conda-forge
fribidi                   1.0.5             h14c3975_1000    conda-forge
funcsigs                  1.0.2                    pypi_0    pypi
future                    0.17.1                py36_1000    conda-forge
gast                      0.2.2                      py_0    conda-forge
gcc_impl_linux-64         7.3.0                habb00fd_1    conda-forge
gcc_linux-64              7.3.0                h553295d_3    conda-forge
gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
glib                      2.58.3            hf63aee3_1001    conda-forge
gmp                       6.1.2             hf484d3e_1000    conda-forge
gmpy2                     2.0.8           py36hb20f59a_1002    conda-forge
gnutls                    3.6.5             hd3a4fd2_1002    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
grpcio                    1.16.1           py36hf8bcb03_1    defaults
gstreamer                 1.14.4            h66beb1c_1001    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1    conda-forge
gxx_linux-64              7.3.0                h553295d_3    conda-forge
gym                       0.12.0                   pypi_0    pypi
h5py                      2.9.0           nompi_py36hf008753_1102    conda-forge
hdf4                      4.2.13            h9a582f1_1002    conda-forge
hdf5                      1.10.4          nompi_h3c11f04_1106    conda-forge
html5lib                  1.0.1                      py_0    conda-forge
hyperas                   0.4.1                    pypi_0    pypi
hyperopt                  0.1.2                    pypi_0    pypi
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.8                   py36_1000    conda-forge
imageio                   2.5.0                    py36_0    conda-forge
imagesize                 1.1.0                    pypi_0    pypi
intel-openmp              2019.3                      199    defaults
ipydatawidgets            4.0.0                    pypi_0    pypi
ipykernel                 5.1.0           py36h24bf2e0_1002    conda-forge
ipysheet                  0.3.1                    pypi_0    pypi
ipython                   7.4.0            py36h24bf2e0_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipyvolume                 0.5.1                    pypi_0    pypi
ipywebrtc                 0.4.3                    pypi_0    pypi
ipywidgets                7.4.2                      py_0    conda-forge
isort                     4.3.17                   py36_0    conda-forge
jasper                    2.0.14               h07fcdf6_0    conda-forge
jbig                      2.1               h14c3975_2001    conda-forge
jedi                      0.13.3                   py36_0    conda-forge
jinja2                    2.10.1                     py_0    conda-forge
jmespath                  0.9.4                      py_0    conda-forge
joblib                    0.13.2                     py_0    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsoncpp                   1.8.4             h6bb024c_1001    conda-forge
jsonschema                3.0.1                    py36_0    conda-forge
jupyter-conda             2.4.1                    pypi_0    pypi
jupyter-tensorboard       0.1.9                    pypi_0    pypi
jupyter_client            5.2.4                      py_3    conda-forge
jupyter_cms               0.7.0                 py36_1000    conda-forge
jupyter_console           6.0.0                      py_0    conda-forge
jupyter_contrib_core      0.3.3                      py_2    conda-forge
jupyter_contrib_nbextensions 0.5.1                    py36_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyter_highlight_selected_word 0.2.0                 py36_1000    conda-forge
jupyter_latex_envs        1.4.4                 py36_1000    conda-forge
jupyter_nbextensions_configurator 0.4.1                    py36_0    conda-forge
jupyterhub                0.9.6                    py36_0    conda-forge
jupyterhub-ldap-authenticator 0.3.1                    pypi_0    pypi
jupyterhub-ldapauthenticator 1.2.2                   py_1000    conda-forge
jupyterhub-systemdspawner 0.11                     pypi_0    pypi
jupyterlab                0.35.4                   py36_0    conda-forge
jupyterlab-git            0.5.0                    pypi_0    pypi
jupyterlab-iframe         0.0.11                   pypi_0    pypi
jupyterlab-latex          0.4.1                    pypi_0    pypi
jupyterlab-quickopen      0.1.0                    pypi_0    pypi
jupyterlab_server         0.2.0                      py_0    conda-forge
keras                     2.1.6                    py36_0    conda-forge
keras-applications        1.0.7                      py_0    conda-forge
keras-preprocessing       1.0.9                      py_0    conda-forge
kiwisolver                1.0.1           py36h6bb024c_1002    conda-forge
krb5                      1.16.3            h05b26f9_1001    conda-forge
lame                      3.100             h14c3975_1001    conda-forge
ldap3                     2.6                        py_0    conda-forge
liac-arff                 2.4.0                    pypi_0    pypi
libblas                   3.8.0                5_openblas    conda-forge
libcblas                  3.8.0                5_openblas    conda-forge
libcurl                   7.64.1               hda55be3_0    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgfortran               3.0.0                         1    conda-forge
libgfortran-ng            7.3.0                hdf63c60_0    anaconda
libglu                    9.0.0             hf484d3e_1000    conda-forge
libgpuarray               0.7.6             h14c3975_1003    conda-forge
libiconv                  1.15              h516909a_1005    conda-forge
liblapack                 3.8.0                5_openblas    conda-forge
liblapacke                3.8.0                5_openblas    conda-forge
libnetcdf                 4.6.2             hbdf4f91_1001    conda-forge
libogg                    1.3.2             h14c3975_1001    conda-forge
libopenblas               0.2.20               h9ac9557_7    defaults
libopus                   1.3                  h7b6447c_0    anaconda
libpng                    1.6.37               hed695b0_0    conda-forge
libprotobuf               3.7.1                h8b12597_0    conda-forge
libsodium                 1.0.16            h14c3975_1001    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtheora                 1.1.1             h14c3975_1001    conda-forge
libtiff                   4.0.10            h9022e91_1002    conda-forge
libtool                   2.4.6             h14c3975_1002    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libvorbis                 1.3.5             h14c3975_1001    conda-forge
libvpx                    1.7.0                h439df22_0    anaconda
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
libxslt                   1.1.32            h4785a14_1002    conda-forge
lineup-widget             1.0.7                    pypi_0    pypi
llvmlite                  0.28.0           py36hdbcaa40_0    conda-forge
lockfile                  0.12.2                   pypi_0    pypi
lxml                      4.3.3            py36h7ec2d77_0    conda-forge
lz4                       2.1.6                    pypi_0    pypi
lz4-c                     1.8.3             hf484d3e_1001    conda-forge
mako                      1.0.7                      py_1    conda-forge
markdown                  2.6.11                     py_0    conda-forge
markupsafe                1.1.1            py36h14c3975_0    conda-forge
matplotlib                3.0.3                    py36_0    conda-forge
matplotlib-base           3.0.3            py36h167e16e_0    conda-forge
mimesis                   3.1.0                    pypi_0    pypi
mistune                   0.8.4           py36h14c3975_1000    conda-forge
mkl                       2018.0.3                      1    defaults
mkl_fft                   1.0.10                   py36_0    conda-forge
mkl_random                1.0.2                    py36_0    conda-forge
mock                      2.0.0                 py36_1001    conda-forge
more-itertools            4.3.0                 py36_1000    conda-forge
mpc                       1.1.0             hb20f59a_1006    conda-forge
mpfr                      4.0.2                ha14ba45_0    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
msgpack-python            0.6.1            py36h6bb024c_0    conda-forge
natsort                   6.0.0                      py_0    conda-forge
nb_conda_kernels          2.2.1                    py36_0    conda-forge
nb_sciserver              0.1.1                    py36_0    sciserver
nbconvert                 5.4.1                      py_2    conda-forge
nbformat                  4.4.0                      py_1    conda-forge
nbresuse                  0.3.0                    pypi_0    pypi
nccl                      1.3.5                 cuda9.0_0    defaults
nccl2                     1.0                           0    pytorch
ncurses                   6.1               hf484d3e_1002    conda-forge
neo                       0.7.1                    pypi_0    pypi
nettle                    3.4.1             h1bed415_1002    conda-forge
networkx                  2.3                        py_0    conda-forge
nibabel                   2.3.3                    pypi_0    pypi
ninja                     1.9.0                h6bb024c_0    conda-forge
niwidgets                 0.2.1                    pypi_0    pypi
nodejs                    11.11.0              hf484d3e_0    conda-forge
nose                      1.3.7                 py36_1002    conda-forge
notebook                  5.7.8                    py36_0    conda-forge
numba                     0.43.1           py36he1b5a44_0    conda-forge
numexpr                   2.6.9           py36h637b7d7_1000    conda-forge
numpy                     1.15.4          py36h8b7e671_1002    conda-forge
numpy-base                1.14.3           py36h2b20989_0    defaults
oauthlib                  3.0.1                      py_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openblas                  0.3.5             h9ac9557_1001    conda-forge
opencv-python             4.0.0.21                 pypi_0    pypi
openh264                  1.8.0             hdbcaa40_1000    conda-forge
openjdk                   11.0.1            h516909a_1015    conda-forge
openssl                   1.1.1b               h14c3975_1    conda-forge
packaging                 19.0                       py_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandas                    0.24.2           py36hf484d3e_0    conda-forge
pandoc                    2.7.2                         0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.4.0                      py_0    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pbr                       5.1.3                      py_0    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
perspective-python        0.1.4                    pypi_0    pypi
pexpect                   4.7.0                    py36_0    conda-forge
pickleshare               0.7.5                 py36_1000    conda-forge
pillow                    6.0.0            py36he7afcd5_0    conda-forge
pip                       19.0.3                   py36_0    conda-forge
pixman                    0.38.0            h516909a_1003    conda-forge
plotly                    3.8.0                      py_0    conda-forge
pluggy                    0.9.0                      py_0    conda-forge
prometheus_client         0.6.0                      py_0    conda-forge
prompt_toolkit            2.0.9                      py_0    conda-forge
protobuf                  3.7.1            py36he1b5a44_0    conda-forge
psutil                    5.6.1            py36h14c3975_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
py                        1.8.0                      py_0    conda-forge
pyarrow                   0.12.1                   pypi_0    pypi
pyasn1                    0.4.4                      py_1    conda-forge
pycosat                   0.6.3           py36h14c3975_1001    conda-forge
pycparser                 2.19                     py36_1    conda-forge
pycurl                    7.43.0.2         py36h1ba5d50_0    defaults
pydocstyle                2.1.1                 py36_1000    conda-forge
pygments                  2.3.1                      py_0    conda-forge
pygpu                     0.7.6           py36h3010b51_1000    conda-forge
pyjwt                     1.7.1                      py_0    conda-forge
pylantern                 0.1.2                    pypi_0    pypi
pymatbridge               0.5.2                      py_0    conda-forge
pynisher                  0.5.0                    pypi_0    pypi
pyopengl                  3.1.0                    pypi_0    pypi
pyopenssl                 19.0.0                   py36_0    conda-forge
pyparsing                 2.4.0                      py_0    conda-forge
pypdf2                    1.26.0                     py_2    conda-forge
pyqt                      4.11.4                   py36_3    conda-forge
pyrfr                     0.7.4                    pypi_0    pypi
pyrsistent                0.14.11          py36h14c3975_0    conda-forge
pysocks                   1.6.8                 py36_1002    conda-forge
pytest                    4.4.1                    py36_0    conda-forge
pytest-cov                2.6.1                      py_0    conda-forge
pytest-faulthandler       1.5.0                 py36_1000    conda-forge
python                    3.6.7             h381d211_1004    conda-forge
python-crfsuite           0.9.6           py36h6bb024c_1000    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
python-editor             1.0.4                      py_0    conda-forge
python-levenshtein        0.12.0                   pypi_0    pypi
python-oauth2             1.0.1                    py36_0    conda-forge
python-picard             0.4                      pypi_0    pypi
pythreejs                 2.0.2                    pypi_0    pypi
pytorch                   0.4.0            py36hdf912b8_0    defaults
pytz                      2019.1                     py_0    conda-forge
pywavelets                1.0.3            py36hd352d35_1    conda-forge
pyyaml                    5.1              py36h14c3975_0    conda-forge
pyzmq                     18.0.1           py36h0e1adb2_0    conda-forge
qgrid                     1.1.1                    pypi_0    pypi
qt                        4.8.7                         2    defaults
quantities                0.12.3                   pypi_0    pypi
rauth                     0.7.3                    pypi_0    pypi
ray                       0.6.4                    pypi_0    pypi
readline                  7.0               hf8c457e_1001    conda-forge
redis                     3.2.0                    pypi_0    pypi
requests                  2.21.0                py36_1000    conda-forge
requests-oauthlib         1.2.0                      py_0    conda-forge
resampy                   0.2.1                      py_1    conda-forge
retrying                  1.3.3                      py_2    conda-forge
rlgraph                   0.3.3                    pypi_0    pypi
ruamel_yaml               0.15.71         py36h14c3975_1000    conda-forge
scikit-learn              0.19.2                   pypi_0    pypi
scipy                     1.2.1            py36h09a28d5_1    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                41.0.0                   py36_0    conda-forge
sidecar                   0.2.0                    pypi_0    pypi
simplegeneric             0.8.1                      py_1    conda-forge
sip                       4.18                     py36_1    conda-forge
six                       1.12.0                py36_1000    conda-forge
sklearn                   0.0                      pypi_0    pypi
smac                      0.8.0                    pypi_0    pypi
snowballstemmer           1.2.1                      py_1    conda-forge
socketio-client-nexus     0.7.6                    pypi_0    pypi
soupsieve                 1.8                      pypi_0    pypi
sphinx                    1.8.5                    pypi_0    pypi
sphinx-rtd-theme          0.4.3                    pypi_0    pypi
sphinxcontrib-websupport  1.1.0                    pypi_0    pypi
sqlalchemy                1.3.3            py36h516909a_0    conda-forge
sqlite                    3.26.0            h67949de_1001    conda-forge
statsmodels               0.9.0           py36h3010b51_1000    conda-forge
sympy                     1.4                      py36_0    conda-forge
tabulate                  0.8.3                      py_0    conda-forge
tbb                       2019.5               hc9558a2_0    conda-forge
tensorboard               1.13.1                   py36_0    conda-forge
tensorboardx              1.6                        py_0    conda-forge
tensorflow                1.13.1          gpu_py36h26cf82e_0    defaults
tensorflow-base           1.13.1          gpu_py36h8f37b9b_0    defaults
tensorflow-estimator      1.13.0                     py_0    defaults
tensorflow-gpu            1.13.1               h0d30ee6_0    defaults
termcolor                 1.1.0                      py_2    conda-forge
terminado                 0.8.2                    py36_0    conda-forge
testpath                  0.4.2                   py_1001    conda-forge
text-unidecode            1.2                      pypi_0    pypi
tflearn                   0.3.2                    pypi_0    pypi
theano                    1.0.4           py36hf484d3e_1000    conda-forge
tk                        8.6.9             h84994c4_1001    conda-forge
toolz                     0.9.0                      py_1    conda-forge
torchvision               0.2.1                 py36_1000    conda-forge
tornado                   6.0.2            py36h516909a_0    conda-forge
tqdm                      4.31.1                     py_0    conda-forge
traitlets                 4.3.2                 py36_1000    conda-forge
traits                    5.1.1            py36h516909a_0    conda-forge
traittypes                0.2.1                    pypi_0    pypi
typing                    3.6.6                    pypi_0    pypi
ujson                     1.35            py36h14c3975_1001    conda-forge
urllib3                   1.24.2                   py36_0    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          0.55.0                   pypi_0    pypi
websockets                7.0                      pypi_0    pypi
werkzeug                  0.15.2                     py_0    conda-forge
wheel                     0.33.1                   py36_0    conda-forge
whoosh                    2.7.4                      py_1    conda-forge
widgetsnbextension        3.4.2                 py36_1000    conda-forge
x264                      1!152.20180806       h14c3975_0    conda-forge
xorg-fixesproto           5.0               h14c3975_1002    conda-forge
xorg-inputproto           2.3.2             h14c3975_1002    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.3                h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxfixes            5.0.3             h516909a_1004    conda-forge
xorg-libxi                1.7.9             h516909a_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
yaml                      0.1.7             h14c3975_1001    conda-forge
yapf                      0.27.0                     py_0    conda-forge
zeromq                    4.2.5             hf484d3e_1006    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge
zstd                      1.3.3                         1    conda-forge
teake commented 5 years ago

Sorry, I still can't reproduce it. When I create a new environment with

conda create -n depgraph -c conda-forge -c omegacen conda-depgraph "msgpack-python=0.6.1" "python=3.6.7"

I get a subset of your packages with almost exactly the same versions (except for libgcc-ng and libstdcxx-ng, which for me come from defaults), but still conda-depgraph works normally.

My best bet would be that the versions you have for libgcc-ng and libstdcxx-ng are causing trouble, since those are listed as broken: https://anaconda.org/conda-forge/libgcc-ng/files and https://anaconda.org/conda-forge/libstdcxx-ng/files.

Try upgrading them with 

conda update libgcc-ng libstdcxx-ng

Both should update to 8.2.0 from the defaults channel.

wl2776 commented 5 years ago

Upgraded to 8.2.0, anyway the same error.

$ sudo /opt/anaconda/bin/conda update libgcc-ng libstdcxx-ng -c defaults
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /opt/anaconda

  added / updated specs:
    - libgcc-ng
    - libstdcxx-ng

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ca-certificates-2019.1.23  |                0         126 KB  defaults
    certifi-2019.3.9           |           py36_0         155 KB  defaults
    libgcc-ng-8.2.0            |       hdf63c60_1         7.6 MB  defaults
    libstdcxx-ng-8.2.0         |       hdf63c60_1         2.9 MB  defaults
    openssl-1.1.1b             |       h7b6447c_1         4.0 MB  defaults
    ------------------------------------------------------------
                                           Total:        14.8 MB

The following packages will be UPDATED:

  libgcc-ng          conda-forge::libgcc-ng-7.3.0-hdf63c60~ --> pkgs/main::libgcc-ng-8.2.0-hdf63c60_1
  libstdcxx-ng       conda-forge::libstdcxx-ng-7.3.0-hdf63~ --> pkgs/main::libstdcxx-ng-8.2.0-hdf63c60_1

The following packages will be SUPERSEDED by a higher-priority channel:

  ca-certificates    conda-forge::ca-certificates-2019.3.9~ --> pkgs/main::ca-certificates-2019.1.23-0
  certifi                                       conda-forge --> pkgs/main
  openssl            conda-forge::openssl-1.1.1b-h14c3975_1 --> pkgs/main::openssl-1.1.1b-h7b6447c_1

Proceed ([y]/n)?

Downloading and Extracting Packages
ca-certificates-2019 | 126 KB    | ################################################################################################################################################ | 100%
openssl-1.1.1b       | 4.0 MB    | ################################################################################################################################################ | 100%
libgcc-ng-8.2.0      | 7.6 MB    | ################################################################################################################################################ | 100%
libstdcxx-ng-8.2.0   | 2.9 MB    | ################################################################################################################################################ | 100%
certifi-2019.3.9     | 155 KB    | ################################################################################################################################################ | 100%
Preparing transaction: done
Verifying transaction: done

~$ CONDA_EXE=/opt/anaconda/bin/conda sudo -E /opt/anaconda/bin/conda depgraph --name=base out --distance=1 pytorch
Traceback (most recent call last):
  File "/opt/anaconda/bin/conda-depgraph", line 10, in <module>
    sys.exit(main())
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1164, in invoke
    return _process_result(rv)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1102, in _process_result
    **ctx.params)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/conda_depgraph/cli.py", line 48, in process_subcommands
    print(graph_to_ascii(g))
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 108, in graph_to_ascii
    return _asciigraph.graph_to_ascii(graph, timeout=timeout).decode(encoding='UTF-8')
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 84, in graph_to_ascii
    return loads(response.content)
  File "msgpack/_unpacker.pyx", line 209, in msgpack._cmsgpack.unpackb
msgpack.exceptions.ExtraData: unpack(b) received extra data.

~$ CONDA_EXE=/opt/anaconda/bin/conda sudo -E /opt/anaconda/bin/conda depgraph --name=base out --distance=1 conda
Traceback (most recent call last):
  File "/opt/anaconda/bin/conda-depgraph", line 10, in <module>
    sys.exit(main())
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1164, in invoke
    return _process_result(rv)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1102, in _process_result
    **ctx.params)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/conda_depgraph/cli.py", line 48, in process_subcommands
    print(graph_to_ascii(g))
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 108, in graph_to_ascii
    return _asciigraph.graph_to_ascii(graph, timeout=timeout).decode(encoding='UTF-8')
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 84, in graph_to_ascii
    return loads(response.content)
  File "msgpack/_unpacker.pyx", line 209, in msgpack._cmsgpack.unpackb
msgpack.exceptions.ExtraData: unpack(b) received extra data.

Error persists without sudo too.

~$ conda depgraph --name=base out --distance=1 conda
Traceback (most recent call last):
  File "/opt/anaconda/bin/conda-depgraph", line 10, in <module>
    sys.exit(main())
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1164, in invoke
    return _process_result(rv)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1102, in _process_result
    **ctx.params)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/conda_depgraph/cli.py", line 48, in process_subcommands
    print(graph_to_ascii(g))
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 108, in graph_to_ascii
    return _asciigraph.graph_to_ascii(graph, timeout=timeout).decode(encoding='UTF-8')
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 84, in graph_to_ascii
    return loads(response.content)
  File "msgpack/_unpacker.pyx", line 209, in msgpack._cmsgpack.unpackb
msgpack.exceptions.ExtraData: unpack(b) received extra data.
wl2776 commented 5 years ago

I've also tried to install mgspack-python from default channel. Still the same error

$ sudo /opt/anaconda/bin/conda update msgpack-python -c defaults
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /opt/anaconda

  added / updated specs:
    - msgpack-python

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    msgpack-python-0.6.1       |   py36hfd86e86_1          92 KB  defaults
    ------------------------------------------------------------
                                           Total:          92 KB

The following packages will be UPDATED:

  msgpack-python     conda-forge::msgpack-python-0.6.1-py3~ --> pkgs/main::msgpack-python-0.6.1-py36hfd86e86_1

Proceed ([y]/n)?

Downloading and Extracting Packages
msgpack-python-0.6.1 | 92 KB     | ################################################################################################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
~$ conda depgraph --name=base out --distance=1 conda
Traceback (most recent call last):
  File "/opt/anaconda/bin/conda-depgraph", line 10, in <module>
    sys.exit(main())
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1164, in invoke
    return _process_result(rv)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1102, in _process_result
    **ctx.params)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/conda_depgraph/cli.py", line 48, in process_subcommands
    print(graph_to_ascii(g))
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 108, in graph_to_ascii
    return _asciigraph.graph_to_ascii(graph, timeout=timeout).decode(encoding='UTF-8')
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 84, in graph_to_ascii
    return loads(response.content)
  File "msgpack/_unpacker.pyx", line 209, in msgpack._cmsgpack.unpackb
msgpack.exceptions.ExtraData: unpack(b) received extra data.

I've attached current conda list. conda_list.txt

teake commented 5 years ago

Huh, then I don't know what's going on. Perhaps your environment got a bit messed up from some of the pip-installed packages, or perhaps it's the non-standard way you're invoking conda. Did you activate the environment ($ conda activate base) before running conda depgraph?

All I can think of now is to install conda-depgraph in a separate environment:

$ conda create -n depgraph -c omegacen conda-depgraph
$ conda activate depgraph
$ conda depgraph out --distance=1 conda
$ conda depgraph --name=base out --distance=1 conda

If that also fails, try re-installing conda (latest I think is (https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh) and do a conda init after installation.

teake commented 5 years ago

Btw, could you also send the output of conda list --explicit? Then I can re-create your environment exactly.

wl2776 commented 5 years ago

  1. Tried to activate base environment before running depgraph - same error

    ~$ conda activate
(base) ~$ conda depgraph out --distance=1 conda
Traceback (most recent call last):
File "/opt/anaconda/bin/conda-depgraph", line 10, in <module>
sys.exit(main())
File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1164, in invoke
return _process_result(rv)
File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1102, in _process_result
**ctx.params)
File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/opt/anaconda/lib/python3.6/site-packages/conda_depgraph/cli.py", line 48, in process_subcommands
print(graph_to_ascii(g))
File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 108, in graph_to_ascii
return _asciigraph.graph_to_ascii(graph, timeout=timeout).decode(encoding='UTF-8')
File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 84, in graph_to_ascii
return loads(response.content)
File "msgpack/_unpacker.pyx", line 209, in msgpack._cmsgpack.unpackb
msgpack.exceptions.ExtraData: unpack(b) received extra data.

  2. I've tried to install conda-depgraph in separate environment. Third command conda depgraph out --distance=1 conda fails with the same error.

(depgraph) ~$ conda activate depgraph
(depgraph) ~$ conda depgraph out --distance=1 conda
Traceback (most recent call last):
  File "/opt/anaconda/bin/conda-depgraph", line 10, in <module>
    sys.exit(main())
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1164, in invoke
    return _process_result(rv)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 1102, in _process_result
    **ctx.params)
  File "/opt/anaconda/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/opt/anaconda/lib/python3.6/site-packages/conda_depgraph/cli.py", line 48, in process_subcommands
    print(graph_to_ascii(g))
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 108, in graph_to_ascii
    return _asciigraph.graph_to_ascii(graph, timeout=timeout).decode(encoding='UTF-8')
  File "/opt/anaconda/lib/python3.6/site-packages/asciinet/__init__.py", line 84, in graph_to_ascii
    return loads(response.content)
  File "msgpack/_unpacker.pyx", line 209, in msgpack._cmsgpack.unpackb
msgpack.exceptions.ExtraData: unpack(b) received extra data.

Attached two files, obtained with following commands

~$ conda list --explicit > conda_list_base.txt
~$ conda list --explicit -n depgraph > conda_list_depgraph.txt

conda_list_depgraph.txt conda_list_base.txt

teake commented 5 years ago

Ugh, I still can't reproduce the error, even after installing the exact list of packages you have. There is probably something wrong with your conda install. As a last ditch effort, could you send the output of the following?

$ python
>>> import msgpack
>>> msgpack.version
>>> msgpack.__file__

I get:

$ python
Python 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import msgpack
>>> msgpack.version
(0, 6, 1)
>>> msgpack.__file__
'/root/miniconda3/lib/python3.6/site-packages/msgpack/__init__.py'
wl2776 commented 5 years ago

I see exactly the same output

~$ python
Python 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import msgpack
>>> msgpack.version
(0, 6, 1)
>>> msgpack.__file__
'/opt/anaconda/lib/python3.6/site-packages/msgpack/__init__.py'
>>>
teake commented 5 years ago

Ok, I think I have to give up. If you want, you could remove and re-install conda and then re-create your current environment with

$ conda install --name base --file conda_list_base.txt

You will miss out on all the pip installed packages. If you want to install those as well, you can do

$ pip install alabaster=="0.7.12" arxiv=="0.3.1" atari-py=="0.1.7" auto-sklearn=="0.5.0" babel=="2.6.0" bash-kernel=="0.7.1" beautifulsoup4=="4.7.1" box2d-py=="2.3.8" bs4=="0.0.1" cite2c=="0.2.1" click=="7.0" colorama=="0.4.1" configspace=="0.4.9" cufflinks=="0.14.6" faker=="1.0.2" feedparser=="5.2.1" filelock=="3.0.10" finance-enums=="0.1.0" flatbuffers=="1.10" funcsigs=="1.0.2" gym=="0.12.0" hyperas=="0.4.1" hyperopt=="0.1.2" imagesize=="1.1.0" ipydatawidgets=="4.0.0" ipysheet=="0.3.1" ipyvolume=="0.5.1" ipywebrtc=="0.4.3" jupyter-conda=="2.4.1" jupyter-tensorboard=="0.1.9" jupyterhub-ldap-authenticator=="0.3.1" jupyterhub-systemdspawner=="0.11" jupyterlab-git=="0.5.0" jupyterlab-iframe=="0.0.11" jupyterlab-latex=="0.4.1" jupyterlab-quickopen=="0.1.0" liac-arff=="2.4.0" lineup-widget=="1.0.7" lockfile=="0.12.2" lz4=="2.1.6" mimesis=="3.1.0" nbresuse=="0.3.0" neo=="0.7.1" nibabel=="2.3.3" niwidgets=="0.2.1" opencv-python=="4.0.0.21" perspective-python=="0.1.4" pyarrow=="0.12.1" pylantern=="0.1.2" pynisher=="0.5.0" pyopengl=="3.1.0" pyrfr=="0.7.4" python-levenshtein=="0.12.0" python-picard=="0.4" pythreejs=="2.0.2" qgrid=="1.1.1" quantities=="0.12.3" rauth=="0.7.3" ray=="0.6.4" redis=="3.2.0" rlgraph=="0.3.3" scikit-learn=="0.19.2" sidecar=="0.2.0" sklearn=="0.0" smac=="0.8.0" socketio-client-nexus=="0.7.6" soupsieve=="1.8" sphinx=="1.8.5" sphinx-rtd-theme=="0.4.3" sphinxcontrib-websupport=="1.1.0" text-unidecode=="1.2" tflearn=="0.3.2" traittypes=="0.2.1" typing=="3.6.6" websocket-client=="0.55.0" websockets=="7.0"

This will give some install errors, so your environment will not be 100% the same as it is now. But then the error should really be gone.

wl2776 commented 5 years ago

Is it possible to run the code from command line or IDE directly without conda?

teake commented 5 years ago

Yes, that's possible (although a bit clunky because I didn't design the interface for this purpose):

from conda_depgraph.conda_facade import channelcache_graph
from conda_depgraph.algorithms import outgraph
from asciinet import graph_to_ascii

g = channelcache_graph()
s = outgraph(g, "conda", 1)
print(graph_to_ascii(s))

Btw, since I can't reproduce your problem and I because I suspect it's an issue with you conda installation, I'm afraid I'm going to close this issue. But feel free to re-open if you can reproduce it in a clean conda installation.