PyPlot not working on 0.4.0

Linus Härenstam-Nielsen

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Jun 18, 2015, 10:27:51 AM6/18/15

to julia...@googlegroups.com

I am having problems with using PyPlot in the nightly build (version 0.4.0). Typing 'using PyPlot' followed by 'plot([sin(a) for a=linspace(0,2*pi)])' yields the following:

               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "help()" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.4.0-dev+5416 (2015-06-17 00:39 UTC)
 _/ |\__'_|_|_|\__'_|  |  Commit 0bb31a0 (1 day old master)
|__/                   |  x86_64-w64-mingw32

julia> using PyPlot
Warning: New definition
    call(Type{PyCall.PyDict}, Base.Associative{#K<:Any, Any}) at C:\Users\Linus\.julia\v0.4\PyCall
rc\conversions.jl:464
is ambiguous with:
    call(Type{PyCall.PyDict}, Base.Associative{Any, #V<:Any}) at C:\Users\Linus\.julia\v0.4\PyCall
rc\conversions.jl:463.
To fix, define
    call(Type{PyCall.PyDict}, Base.Associative{Any, Any})
before the new definition.
WARNING: No working GUI backend found for matplotlib.
C:\Anaconda\lib\site-packages\matplotlib\__init__.py:1318: UserWarning:  This call to matplotlib.u
() has no effect
because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

  warnings.warn(_use_error_msg)
WARNING: ntuple(n::Integer,f::Function) is deprecated, use ntuple(f,n) instead.
 in depwarn at deprecated.jl:62
 in ntuple at deprecated.jl:49
 in convert at C:\Users\Linus\.julia\v0.4\PyCall\src\conversions.jl:222
 in py2array at C:\Users\Linus\.julia\v0.4\PyCall\src\conversions.jl:73
 in convert at C:\Users\Linus\.julia\v0.4\PyCall\src\conversions.jl:429
 in pywrap at C:\Users\Linus\.julia\v0.4\PyCall\src\PyCall.jl:305
 in pywrap at C:\Users\Linus\.julia\v0.4\PyCall\src\PyCall.jl:304
 in __init__ at C:\Users\Linus\.julia\v0.4\PyPlot\src\PyPlot.jl:149
 in include at boot.jl:254
 in include_from_node1 at loading.jl:133
 in reload_path at loading.jl:157
 in _require at loading.jl:69
 in require at loading.jl:52
while loading C:\Users\Linus\.julia\v0.4\PyPlot\src\PyPlot.jl, in expression starting on line 560

julia> plot([sin(a) for a=linspace(0,2*pi)])
WARNING: ntuple(n::Integer,f::Function) is deprecated, use ntuple(f,n) instead.
 in depwarn at deprecated.jl:62
 in ntuple at deprecated.jl:49
 in convert at C:\Users\Linus\.julia\v0.4\PyCall\src\conversions.jl:222
 in convert at C:\Users\Linus\.julia\v0.4\PyCall\src\conversions.jl:846
 in jl_Function_call at C:\Users\Linus\.julia\v0.4\PyCall\src\callback.jl:36
 in pycall at C:\Users\Linus\.julia\v0.4\PyCall\src\PyCall.jl:73
 in plot at C:\Users\Linus\.julia\v0.4\PyPlot\src\PyPlot.jl:371
 in anonymous at no file
while loading no file, in expression starting on line 0
1-element Array{Any,1}:
 PyObject <matplotlib.lines.Line2D object at 0x000000001555D080>

julia> plot([sin(a) for a=linspace(0,2*pi)])
1-element Array{Any,1}:
 PyObject <matplotlib.lines.Line2D object at 0x000000001555D2B0>

As you can see importing PyPlot produces several warnings, one of them is 'WARNING: No working GUI backend found for matplotlib' which led me to believe there is a problem with loading matplotlib? I am using python 2.7.9 on windows 8.1 with the Anaconda 2.2.0 distribution and matplotlib version 1.4.3.

The plot function returns a PyObject properly but no plot window is opened. In Julia 0.3.9 everything works as you would expect with no warnings.

Any ideas?

Scott T

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Jun 18, 2015, 11:58:43 AM6/18/15

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Hi Linus,

This is due to a change in Julia master which altered the way timers work. It's broken PyCall and therefore PyPlot in this particular case.

There are pending pull requests on PyCall which should fix this, but they haven't been merged yet. You could check this one out locally by doing the following (at the command line):

go to your Julia package directory - not sure what it is on Windows
go to v0.4/PyCall
git fetch origin pull/155/head:fix-timer-api

this will make a copy of the pull request on your machine in a branch called "fix-timer-api"

git checkout fix-timer-api

this will switch to that branch

This got PyPlot working again for me. Note that it will freeze your version of PyCall so, once these fixes are actually merged into the package itself, you can swap to the latest version by doing Pkg.checkout("PyCall") from within Julia.

Cheers,

Scott

Scott T

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Jun 18, 2015, 12:24:57 PM6/18/15

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Oh and of course you could always revert Julia to an earlier version, like the parent commit (29d8c650). Using the nightlies, it's pretty much guaranteed that things will break occasionally.

Cheers,

Scott

On Thursday, 18 June 2015 15:27:51 UTC+1, Linus Härenstam-Nielsen wrote:

Linus Härenstam-Nielsen

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Jun 19, 2015, 2:54:47 PM6/19/15

to julia...@googlegroups.com

This fixed it! Thanks

jda

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Nov 4, 2015, 10:03:38 AM11/4/15

to julia-users

I'm new to both julia and git. Trying to follow this thread because I am having problems with using Plots in 0.4.0 (and 0.3.8). I downloaded Git Desktop (https://desktop.github.com/) and tried the following from the Git Shell:

C:\Users\user\.julia\v0.4\PyCall [master]> git fetch origin pull/155/head:fix-timer-api
From git://github.com/stevengj/PyCall.jl
 * [new ref]         refs/pull/155/head -> fix-timer-api

C:\Users\user\.julia\v0.4\PyCall [master]> git checkout fix-timer-api
Switched to branch 'fix-timer-api'

C:\Users\user\.julia\v0.4\PyCall [fix-timer-api +1 ~0 -0 !]>

After this I tried opening Julia 0.4.0 repl and running the Plots package with no luck.

I am not sure what do to next, or if I am missing some crucial step.

julia> using Plots
ERROR: ArgumentError: Docile not found in path
 in require at loading.jl:233
 in stale_cachefile at loading.jl:439
 in recompile_stale at loading.jl:457
 in _require_from_serialized at loading.jl:83
 in _require_from_serialized at loading.jl:109
 in require at loading.jl:219

Tom Breloff

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Nov 4, 2015, 10:11:53 AM11/4/15

to julia-users

This issue is several months old, and I don't think it applies anymore. Can you run both "versioninfo()" and "Pkg.status()" at your Julia prompt? Then we might be able to help you get back to a working install.

jda

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Nov 4, 2015, 2:01:46 PM11/4/15

to julia-users

Could very much use the help! Here is the info:

               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org


   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.4.0 (2015-10-08 06:20 UTC)
 _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
|__/                   |  x86_64-w64-mingw32


julia> versioninfo()
Julia Version 0.4.0
Commit 0ff703b* (2015-10-08 06:20 UTC)
Platform Info:
  System: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM)2 Duo CPU     E8400  @ 3.00GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Penryn)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.3


julia> Pkg.status()
4 required packages:
 - MAT                           0.2.14
 - Plots                         0.4.2
 - PyCall                        0.8.2-             fix-timer-api
 - PyPlot                        2.1.1
20 additional packages:
 - BinDeps                       0.3.19
 - Blosc                         0.1.4
 - ColorTypes                    0.2.0
 - Colors                        0.6.0
 - Compat                        0.7.7
 - Conda                         0.1.7
 - Dates                         0.4.4
 - FixedPointNumbers             0.1.0
 - HDF5                          0.5.6
 - HTTPClient                    0.2.0
 - JSON                          0.5.0
 - LaTeXStrings                  0.1.6
 - LibCURL                       0.2.0
 - LibExpat                      0.1.0
 - Plotly                        0.0.3+             master
 - Reexport                      0.0.3
 - SHA                           0.1.2
 - URIParser                     0.1.1
 - WinRPM                        0.1.13
 - Zlib                          0.1.12

Scott T

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Nov 4, 2015, 2:20:52 PM11/4/15

to julia-users

My reply disappeared - I may have sent it directly to jda instead of the group. Anyway, try

julia> Pkg.checkout("PyCall")

julia> Pkg.update()

since the instructions above are outdated and will give you an old version of PyCall. Then let us know what error you're getting.

Steven G. Johnson

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Nov 5, 2015, 9:59:13 AM11/5/15

to julia-users

On Wednesday, November 4, 2015 at 2:20:52 PM UTC-5, Scott T wrote:

My reply disappeared - I may have sent it directly to jda instead of the group. Anyway, try

julia> Pkg.checkout("PyCall")
julia> Pkg.update()

since the instructions above are outdated and will give you an old version of PyCall. Then let us know what error you're getting.

You need to manually run Pkg.build("PyCall") if you do Pkg.checkout.

jda

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Nov 5, 2015, 2:21:16 PM11/5/15

to julia-users

I have two windows computers that I am trying to get working. On one of them a couple of un/re-installations fixed the problem. But the second computer is still not working. Here is my session on a fresh install on the second computer:

               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.4.0 (2015-10-08 06:20 UTC)
 _/ |\__'_|_|_|\__'_|  |  Official http://julialang.org/ release
|__/                   |  x86_64-w64-mingw32

julia> versioninfo()
Julia Version 0.4.0
Commit 0ff703b* (2015-10-08 06:20 UTC)
Platform Info:
  System: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM)2 Duo CPU     E8400  @ 3.00GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Penryn)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.3

julia> Pkg.add("PyCall")
INFO: Cloning cache of BinDeps from git://github.com/JuliaLang/BinDeps.jl.git
INFO: Cloning cache of Compat from git://github.com/JuliaLang/Compat.jl.git
INFO: Cloning cache of Conda from git://github.com/Luthaf/Conda.jl.git
INFO: Cloning cache of Dates from git://github.com/quinnj/Dates.jl.git
INFO: Cloning cache of JSON from git://github.com/JuliaLang/JSON.jl.git
INFO: Cloning cache of PyCall from git://github.com/stevengj/PyCall.jl.git
INFO: Cloning cache of SHA from git://github.com/staticfloat/SHA.jl.git
INFO: Cloning cache of URIParser from git://github.com/JuliaWeb/URIParser.jl.git

INFO: Installing BinDeps v0.3.19
INFO: Installing Compat v0.7.7
INFO: Installing Conda v0.1.8
INFO: Installing Dates v0.4.4
INFO: Installing JSON v0.5.0
INFO: Installing PyCall v1.1.2
INFO: Installing SHA v0.1.2
INFO: Installing URIParser v0.1.1
INFO: Building PyCall
INFO: Precompiling module Compat...
INFO: Precompiling module Conda...
INFO: No system-wide Python was found; got the following error:
could not spawn `python -c "import distutils.sysconfig; print(distutils.sysconfi
g.get_config_var('VERSION'))"`: no such file or directory (ENOENT)
using the Python distribution in the Conda package
INFO: Downloading miniconda installer ...
INFO: Installing miniconda ...
Fetching package metadata: ....
Solving package specifications: .
Package plan for installation in environment C:\Users\user\.julia\v0.4\Con
da\deps\usr:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    msvc_runtime-1.0.1         |            vc9_0         1.1 MB
    conda-env-2.4.4            |           py27_0          64 KB
    numpy-1.10.1               |           py27_0        23.6 MB
    pyyaml-3.11                |           py27_2         167 KB
    requests-2.8.1             |           py27_0         609 KB
    setuptools-18.4            |           py27_0         647 KB
    wheel-0.26.0               |           py27_1         116 KB
    conda-3.18.3               |           py27_0         218 KB
    pip-7.1.2                  |           py27_0         1.4 MB
    ------------------------------------------------------------
                                           Total:        28.0 MB

The following NEW packages will be INSTALLED:

    msvc_runtime: 1.0.1-vc9_0   [vc9]
    numpy:        1.10.1-py27_0
    pip:          7.1.2-py27_0
    setuptools:   18.4-py27_0
    wheel:        0.26.0-py27_1

The following packages will be UPDATED:

    conda:        3.9.1-py27_0 --> 3.18.3-py27_0
    conda-env:    2.1.3-py27_0 --> 2.4.4-py27_0
    pyyaml:       3.11-py27_0  --> 3.11-py27_2
    requests:     2.5.3-py27_0 --> 2.8.1-py27_0

Fetching packages ...
msvc_runtime-1 100% |###############################| Time: 0:00:00   2.95 MB/s
conda-env-2.4. 100% |###############################| Time: 0:00:00   2.03 MB/s
numpy-1.10.1-p 100% |###############################| Time: 0:00:03   7.28 MB/s
pyyaml-3.11-py 100% |###############################| Time: 0:00:00   2.76 MB/s
requests-2.8.1 100% |###############################| Time: 0:00:00   4.99 MB/s
setuptools-18. 100% |###############################| Time: 0:00:00   4.70 MB/s
wheel-0.26.0-p 100% |###############################| Time: 0:00:00   2.54 MB/s
conda-3.18.3-p 100% |###############################| Time: 0:00:00   2.41 MB/s
pip-7.1.2-py27 100% |###############################| Time: 0:00:00   5.61 MB/s
Extracting packages ...
[      COMPLETE      ] |#################################################| 100%
Unlinking packages ...
[      COMPLETE      ] |#################################################| 100%
Linking packages ...
[      COMPLETE      ] |#################################################| 100%
INFO: PyCall is using C:\Users\user\.julia\v0.4\Conda\deps\usr\python.exe
(Python 2.7.9) at C:\Users\user\.julia\v0.4\Conda\deps\usr\python.exe, lib
python = C:\Users\user\.julia\v0.4\Conda\deps\usr\python27.dll
INFO: Package database updated

julia> Pkg.checkout("PyCall")
INFO: Checking out PyCall master...
INFO: Pulling PyCall latest master...
INFO: No packages to install, update or remove

julia> Pkg.build("PyCall")
INFO: Building PyCall
Fetching package metadata: ....
Solving package specifications: .................
Package plan for installation in environment C:\Users\user\.julia\v0.4\Con
da\deps\usr:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    python-2.7.10              |                3        17.9 MB

The following packages will be UPDATED:

    python: 2.7.9-1 --> 2.7.10-3

Fetching packages ...
python-2.7.10- 100% |###############################| Time: 0:00:02   7.22 MB/s
Extracting packages ...
[      COMPLETE      ]|##################################################| 100%
Unlinking packages ...
[      COMPLETE      ]|##################################################| 100%
Linking packages ...
[      COMPLETE      ]|##################################################| 100%
INFO: PyCall is using C:\Users\user\.julia\v0.4\Conda\deps\usr\python.exe
(Python 2.7.9) at C:\Users\user\.julia\v0.4\Conda\deps\usr\python.exe, lib
python = C:\Users\user\.julia\v0.4\Conda\deps\usr\python27.dll

julia> Pkg.add("PyPlot")
INFO: Cloning cache of ColorTypes from git://github.com/JuliaGraphics/ColorTypes
.jl.git
INFO: Cloning cache of Colors from git://github.com/JuliaGraphics/Colors.jl.git
INFO: Cloning cache of FixedPointNumbers from git://github.com/JeffBezanson/Fixe
dPointNumbers.jl.git
INFO: Cloning cache of LaTeXStrings from git://github.com/stevengj/LaTeXStrings.
jl.git
INFO: Cloning cache of PyPlot from git://github.com/stevengj/PyPlot.jl.git
INFO: Cloning cache of Reexport from git://github.com/simonster/Reexport.jl.git
INFO: Installing ColorTypes v0.2.0
INFO: Installing Colors v0.6.0
INFO: Installing FixedPointNumbers v0.1.1
INFO: Installing LaTeXStrings v0.1.6
INFO: Installing PyPlot v2.1.1
INFO: Installing Reexport v0.0.3
INFO: Building PyCall
Fetching package metadata: ....
Solving package specifications: .................
# All requested packages already installed.
# packages in environment at C:\Users\user\.julia\v0.4\Conda\deps\usr:
#
numpy                     1.10.1                   py27_0
INFO: PyCall is using C:\Users\user\.julia\v0.4\Conda\deps\usr\python.exe
(Python 2.7.9) at C:\Users\user\.julia\v0.4\Conda\deps\usr\python.exe, lib
python = C:\Users\user\.julia\v0.4\Conda\deps\usr\python27.dll
INFO: Package database updated

julia> using PyPlot
INFO: Precompiling module PyPlot...
INFO: Installing matplotlib via the Conda package...
Fetching package metadata: ....
Solving package specifications: .....................
Package plan for installation in environment C:\Users\user\.julia\v0.4\Con
da\deps\usr:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    jpeg-8d                    |            vc9_0         175 KB
    libpng-1.6.17              |            vc9_1         461 KB
    openssl-1.0.2d             |            vc9_0         3.3 MB
    tk-8.5.18                  |            vc9_0         2.2 MB
    zlib-1.2.8                 |            vc9_2         107 KB
    libtiff-4.0.6              |            vc9_0         464 KB
    pyparsing-2.0.3            |           py27_0          63 KB
    pytz-2015.7                |           py27_0         169 KB
    qt-4.8.7                   |            vc9_4        50.8 MB
    sip-4.16.9                 |           py27_1         249 KB
    six-1.10.0                 |           py27_0          16 KB
    pyqt-4.11.4                |           py27_2         3.9 MB
    python-dateutil-2.4.2      |           py27_0         219 KB
    matplotlib-1.4.3           |      np110py27_3        40.8 MB
    ------------------------------------------------------------
                                           Total:       102.8 MB

The following NEW packages will be INSTALLED:

    jpeg:            8d-vc9_0          [vc9]
    libpng:          1.6.17-vc9_1      [vc9]
    libtiff:         4.0.6-vc9_0       [vc9]
    matplotlib:      1.4.3-np110py27_3
    openssl:         1.0.2d-vc9_0      [vc9]
    pyparsing:       2.0.3-py27_0
    pyqt:            4.11.4-py27_2
    python-dateutil: 2.4.2-py27_0
    pytz:            2015.7-py27_0
    qt:              4.8.7-vc9_4       [vc9]
    sip:             4.16.9-py27_1
    six:             1.10.0-py27_0
    tk:              8.5.18-vc9_0      [vc9]
    zlib:            1.2.8-vc9_2       [vc9]

Fetching packages ...
jpeg-8d-vc9_0. 100% |###############################| Time: 0:00:00   2.30 MB/s
libpng-1.6.17- 100% |###############################| Time: 0:00:00   3.77 MB/s
openssl-1.0.2d 100% |###############################| Time: 0:00:00   8.45 MB/s
tk-8.5.18-vc9_ 100% |###############################| Time: 0:00:00   7.68 MB/s
zlib-1.2.8-vc9 100% |###############################| Time: 0:00:00   2.33 MB/s
libtiff-4.0.6- 100% |###############################| Time: 0:00:00   4.36 MB/s
pyparsing-2.0. 100% |###############################| Time: 0:00:00   2.09 MB/s
pytz-2015.7-py 100% |###############################| Time: 0:00:00   2.74 MB/s
qt-4.8.7-vc9_4 100% |###############################| Time: 0:00:03  14.66 MB/s
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matplotlib-1.4 100% |###############################| Time: 0:00:04  10.47 MB/s
Extracting packages ...
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C:\Users\user\.julia\v0.4\Conda\deps\usr\lib\site-packages\matplotlib\__in
it__.py:1318: UserWarning:  This call to matplotlib.use() has no effect

because the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.

  warnings.warn(_use_error_msg)

WARNING: No working GUI backend found for matplotlib.

ERROR: InitError: PyError (:PyImport_ImportModule) <type 'exceptions.ImportError
'>
ImportError('DLL load failed: The specified module could not be found.',)
  File "C:\Users\user\.julia\v0.4\Conda\deps\usr\lib\site-packages\matplot
lib\pyplot.py", line 27, in <module>
    import matplotlib.colorbar
  File "C:\Users\user\.julia\v0.4\Conda\deps\usr\lib\site-packages\matplot
lib\colorbar.py", line 34, in <module>
    import matplotlib.collections as collections
  File "C:\Users\user\.julia\v0.4\Conda\deps\usr\lib\site-packages\matplot
lib\collections.py", line 27, in <module>
    import matplotlib.backend_bases as backend_bases
  File "C:\Users\user\.julia\v0.4\Conda\deps\usr\lib\site-packages\matplot
lib\backend_bases.py", line 56, in <module>
    import matplotlib.textpath as textpath
  File "C:\Users\user\.julia\v0.4\Conda\deps\usr\lib\site-packages\matplot
lib\textpath.py", line 22, in <module>
    from matplotlib.mathtext import MathTextParser
  File "C:\Users\user\.julia\v0.4\Conda\deps\usr\lib\site-packages\matplot
lib\mathtext.py", line 63, in <module>
    import matplotlib._png as _png

 [inlined code] from C:\Users\user\.julia\v0.4\PyCall\src\exception.jl:81
 in pyimport at C:\Users\user\.julia\v0.4\PyCall\src\PyCall.jl:79
 in __init__ at C:\Users\user\.julia\v0.4\PyPlot\src\PyPlot.jl:250
 in _require_from_serialized at loading.jl:84
 in require at loading.jl:251
during initialization of module PyPlot

julia> Pkg.status()
2 required packages:
 - PyCall                        1.1.2+             master
 - PyPlot                        2.1.1
12 additional packages:
 - BinDeps                       0.3.19

 - ColorTypes                    0.2.0
 - Colors                        0.6.0
 - Compat                        0.7.7

 - Conda                         0.1.8
 - Dates                         0.4.4
 - FixedPointNumbers             0.1.1

 - JSON                          0.5.0
 - LaTeXStrings                  0.1.6

Daniel Høegh

unread,

Nov 5, 2015, 3:19:03 PM11/5/15

to julia-users

This has also been seen https://github.com/stevengj/PyCall.jl/issues/209 which is actually an upstream problem with the Continuum Analytics conda package manager, see https://github.com/conda/conda/issues/1753#issuecomment-153550914. I can fix it locally by:

using Conda
Conda.add("matplotlib=1.4.0")
Conda.add("pyqt=4.10")

jda

unread,

Nov 5, 2015, 3:58:41 PM11/5/15

to julia-users

Fixed now, great many thanks !!

Very happy to have my code start running before the weekend starts.

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