Anaconda broken after trying to install matplotlib 2.0 beta (ubuntu) #7325
Description
Yesterday I installed matplotlib 2.00 b4 in windows 10 using:
conda install -c conda-forge/label/rc -c conda-forge matplotlib
(which by the way looks great) but I am trying to do the same in ubuntu 15.10 and I end up breaking anaconda (it cannot longer find the python installation or recognize the conda commands).
I can replicate the errors by installing anaconda:
Current conda install:
platform : linux-64
conda version : 4.2.9
conda is private : False
conda-env version : 4.2.9
conda-build version : 2.0.2
python version : 2.7.12.final.0
requests version : 2.11.1
root environment : /home/vital/anaconda/python2 (writable)
default environment : /home/vital/anaconda/python2
envs directories : /home/vital/anaconda/python2/envs
package cache : /home/vital/anaconda/python2/pkgs
channel URLs : https://conda.anaconda.org/sherpa/linux-64/
https://conda.anaconda.org/sherpa/noarch/
https://repo.continuum.io/pkgs/free/linux-64/
https://repo.continuum.io/pkgs/free/noarch/
https://repo.continuum.io/pkgs/pro/linux-64/
https://repo.continuum.io/pkgs/pro/noarch/
config file : /home/vital/.condarc
offline mode : False
And the error occurs after running the previous command:
vital@foreshadowing:~$ conda install -c conda-forge/label/rc -c conda-forge matplotlib
Fetching package metadata .............
Solving package specifications: ..........
Package plan for installation in environment /home/vital/anaconda/python2:
The following packages will be downloaded:
package | build
---------------------------|-----------------
jpeg-9b | 0 918 KB conda-forge
libiconv-1.14 | 3 2.0 MB conda-forge
libtiff-4.0.6 | 6 507 KB conda-forge
anaconda-custom | py27_0 3 KB
conda-env-2.5.2 | py27_0 26 KB conda-forge
freetype-2.6.3 | 1 2.8 MB conda-forge
subprocess32-3.2.7 | py27_0 55 KB conda-forge
conda-4.1.12 | py27_0 200 KB conda-forge
fontconfig-2.11.1 | 3 874 KB conda-forge
pillow-3.4.1 | py27_1 925 KB conda-forge
cairo-1.12.18 | 8 1.1 MB conda-forge
pango-1.40.1 | 0 912 KB conda-forge
qt-4.8.7 | 4 32.7 MB
pyqt-4.11.4 | py27_0 3.5 MB conda-forge
anaconda-navigator-1.2.3 | py27_0 3.0 MB
matplotlib-2.0.0b4 | np111py27_1 9.2 MB conda-forge/label/rc
qtconsole-4.2.1 | py27_0 132 KB conda-forge
spyder-2.3.9 | py27_1 2.1 MB conda-forge
------------------------------------------------------------
Total: 60.8 MB
The following NEW packages will be INSTALLED:
libiconv: 1.14-3 conda-forge
pango: 1.40.1-0 conda-forge
subprocess32: 3.2.7-py27_0 conda-forge
The following packages will be UPDATED:
anaconda: 4.2.0-np111py27_0 --> custom-py27_0
cairo: 1.12.18-6 --> 1.12.18-8 conda-forge
freetype: 2.5.5-1 --> 2.6.3-1 conda-forge
icu: 54.1-0 --> 56.1-4 conda-forge
jpeg: 8d-2 --> 9b-0 conda-forge
libtiff: 4.0.6-2 --> 4.0.6-6 conda-forge
matplotlib: 1.5.3-np111py27_0 --> 2.0.0b4-np111py27_1 conda-forge/label/rc
pillow: 3.3.1-py27_0 --> 3.4.1-py27_1 conda-forge
The following packages will be SUPERCEDED by a higher-priority channel:
conda: 4.2.9-py27_0 --> 4.1.12-py27_0 conda-forge
conda-env: 2.6.0-0 --> 2.5.2-py27_0 conda-forge
fontconfig: 2.11.1-6 --> 2.11.1-3 conda-forge
pyqt: 5.6.0-py27_0 --> 4.11.4-py27_0 conda-forge
qtconsole: 4.2.1-py27_1 --> 4.2.1-py27_0 conda-forge
spyder: 3.0.0-py27_0 --> 2.3.9-py27_1 conda-forge
The following packages will be DOWNGRADED due to dependency conflicts:
anaconda-navigator: 1.3.1-py27_0 --> 1.2.3-py27_0
qt: 5.6.0-0 --> 4.8.7-4
Proceed ([y]/n)? y
Fetching packages ...
jpeg-9b-0.tar. 100% |##################################################################################################################| Time: 0:00:02 463.35 kB/s
libiconv-1.14- 100% |##################################################################################################################| Time: 0:00:02 898.08 kB/s
libtiff-4.0.6- 100% |##################################################################################################################| Time: 0:00:02 252.28 kB/s
anaconda-custo 100% |##################################################################################################################| Time: 0:00:00 3.21 MB/s
conda-env-2.5. 100% |##################################################################################################################| Time: 0:00:00 92.31 kB/s
freetype-2.6.3 100% |##################################################################################################################| Time: 0:00:02 1.10 MB/s
subprocess32-3 100% |##################################################################################################################| Time: 0:00:00 145.39 kB/s
conda-4.1.12-p 100% |##################################################################################################################| Time: 0:00:00 210.43 kB/s
fontconfig-2.1 100% |##################################################################################################################| Time: 0:00:01 559.46 kB/s
pillow-3.4.1-p 100% |##################################################################################################################| Time: 0:00:01 504.22 kB/s
cairo-1.12.18- 100% |##################################################################################################################| Time: 0:00:02 442.60 kB/s
pango-1.40.1-0 100% |##################################################################################################################| Time: 0:00:02 447.25 kB/s
qt-4.8.7-4.tar 100% |##################################################################################################################| Time: 0:00:26 1.28 MB/s
pyqt-4.11.4-py 100% |##################################################################################################################| Time: 0:00:10 338.20 kB/s
anaconda-navig 100% |##################################################################################################################| Time: 0:00:03 885.30 kB/s
matplotlib-2.0 100% |##################################################################################################################| Time: 0:00:05 1.77 MB/s
qtconsole-4.2. 100% |##################################################################################################################| Time: 0:00:00 194.23 kB/s
spyder-2.3.9-p 100% |##################################################################################################################| Time: 0:00:03 716.27 kB/s
Extracting packages ...
[ COMPLETE ]|#####################################################################################################################################| 100%
Unlinking packages ...
[ COMPLETE ]|#####################################################################################################################################| 100%
Linking packages ...
CondaOSError: OS error: failed to link (src=u'/home/vital/anaconda/python2/pkgs/icu-56.1-4/lib/icu/current', dst='/home/vital/anaconda/python2/lib/icu/current', type=3, error=OSError(17, 'File exists'))
Incidentally, if I try to run the pip upgrade I get:
vital@foreshadowing:~$ pip install --pre matplotlib
Requirement already satisfied (use --upgrade to upgrade): matplotlib in ./anaconda/python2/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.6 in ./anaconda/python2/lib/python2.7/site-packages (from matplotlib)
Requirement already satisfied (use --upgrade to upgrade): python-dateutil in ./anaconda/python2/lib/python2.7/site-packages (from matplotlib)
Requirement already satisfied (use --upgrade to upgrade): pytz in ./anaconda/python2/lib/python2.7/site-packages (from matplotlib)
Requirement already satisfied (use --upgrade to upgrade): cycler in ./anaconda/python2/lib/python2.7/site-packages (from matplotlib)
Requirement already satisfied (use --upgrade to upgrade): pyparsing!=2.0.4,!=2.1.2,>=1.5.6 in ./anaconda/python2/lib/python2.7/site-packages (from matplotlib)
Requirement already satisfied (use --upgrade to upgrade): six>=1.5 in ./anaconda/python2/lib/python2.7/site-packages (from python-dateutil->matplotlib)
vital@foreshadowing:~$ pip install --upgrade matplotlib
Requirement already up-to-date: matplotlib in ./anaconda/python2/lib/python2.7/site-packages
Collecting numpy>=1.6 (from matplotlib)
Using cached numpy-1.11.2-cp27-cp27mu-manylinux1_x86_64.whl
Requirement already up-to-date: python-dateutil in ./anaconda/python2/lib/python2.7/site-packages (from matplotlib)
Collecting pytz (from matplotlib)
Using cached pytz-2016.7-py2.py3-none-any.whl
Requirement already up-to-date: cycler in ./anaconda/python2/lib/python2.7/site-packages (from matplotlib)
Collecting pyparsing!=2.0.4,!=2.1.2,>=1.5.6 (from matplotlib)
Using cached pyparsing-2.1.10-py2.py3-none-any.whl
Requirement already up-to-date: six>=1.5 in ./anaconda/python2/lib/python2.7/site-packages (from python-dateutil->matplotlib)
Installing collected packages: numpy, pytz, pyparsing
Found existing installation: numpy 1.11.1
Uninstalling numpy-1.11.1:
Successfully uninstalled numpy-1.11.1
Found existing installation: pytz 2016.6.1
DEPRECATION: Uninstalling a distutils installed project (pytz) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
Uninstalling pytz-2016.6.1:
Successfully uninstalled pytz-2016.6.1
Found existing installation: pyparsing 2.1.4
Uninstalling pyparsing-2.1.4:
Successfully uninstalled pyparsing-2.1.4
Successfully installed numpy-1.11.2 pyparsing-2.1.10 pytz-2016.7
But I still have the 1.5.4 version
Thanks for all the work.