Error in Pkg.add("IJulia")

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Michael Churchill

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Sep 13, 2013, 4:24:05 PM9/13/13
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I'm trying to install the iJulia notebook locally on a RHEL 6.4 box. I've updated my iPython installation, and julia is up to date, compiled from source. When I run Pkg.add("IJulia"), I get the following error:

make[1]: Leaving directory `/home/rmchurch/.julia/Nettle/deps/builds/nettle/examples'
WARNING: An exception occured while building binary dependencies.
You may have to take manual steps to complete the installation, see the error message below.
To reattempt the installation, run Pkg.fixup("Nettle").


 in build at pkg.jl:362
ERROR: Provider BuildProcess failed to satisfy dependency nettle
 in error at error.jl:21
 in satisfy! at /home/rmchurch/.julia/BinDeps/src/dependencies.jl:416
 in satisfy! at /home/rmchurch/.julia/BinDeps/src/dependencies.jl:402
 in anonymous at /home/rmchurch/.julia/BinDeps/src/dependencies.jl:430
 in include at boot.jl:238
at /home/rmchurch/.julia/Nettle/deps/build.jl:37

 I tried adding the "Nettle" package directly: Pkg.add("Nettle"), which worked, then Pkg.add("IJulia") ran through. However, when I ran the iPython notebook (ipython notebook --profile julia), the browswer comes up, I can upload a notebook, but when I open the notebook, the Kernel dies constantly. The terminal window has the following error:
ERROR: Could not load library nettle. Try running Pkg2.fixup() to install missing dependencies!
 in error at error.jl:21
 in include at boot.jl:238
at /home/rmchurch/.julia/Nettle/src/Nettle.jl:542
at /home/rmchurch/.julia/IJulia/src/hmac.jl:1
at /home/rmchurch/.julia/IJulia/src/IJulia.jl:39
at /home/rmchurch/.julia/IJulia/src/kernel.jl:4

Pkg2.fixup() throws the same error.

Any guidance would be appreciated. Not sure where to start...

Julia information:
Version 0.2.0-prerelease+3705
Commit 766bc6f 2013-09-12 17:16:48 UTC
x86_64-redhat-linux

Elliot Saba

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Sep 17, 2013, 1:18:23 PM9/17/13
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Hey there Michael, sorry to hear you're having trouble.

You've posted the very end of the actual build error, so I can't see what comes before it, which will likely include the cause.  Can you post the full output of `Pkg.fixup("Nettle")`?  Thanks!

Sven Mesecke

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Sep 18, 2013, 8:44:05 AM9/18/13
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Hi,

just to add another data point as the same happens to me (same version as well:

Julia Version 0.2.0-prerelease+3754
Commit 349c336 2013-09-17 04:57:44 UTC
Platform Info:
  System: Darwin (x86_64-apple-darwin12.4.0)
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY)
  LAPACK: libopenblas
  LIBM: libopenlibm

I get an error using tornado after starting the ipython notebook:

2013-09-18 14:39:58.273 [tornado.application] ERROR | Uncaught exception POST /kernels?notebook=3ba49d4f-7abc-47e4-9324-c6ef12d92bde (127.0.0.1)
HTTPRequest(protocol='http', host='127.0.0.1:8998', method='POST', uri='/kernels?notebook=3ba49d4f-7abc-47e4-9324-c6ef12d92bde', version='HTTP/1.1', remote_ip='127.0.0.1', body='', headers={'Content-Length': '0', 'Accept-Language': 'en-US,en;q=0.5', 'Accept-Encoding': 'gzip, deflate', 'Host': '127.0.0.1:8998', 'Accept': 'application/json, text/javascript, */*; q=0.01', 'User-Agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:23.0) Gecko/20100101 Firefox/23.0', 'Dnt': '1', 'Connection': 'keep-alive', 'X-Requested-With': 'XMLHttpRequest', 'Pragma': 'no-cache', 'Cache-Control': 'no-cache', 'Referer': 'http://127.0.0.1:8998/3ba49d4f-7abc-47e4-9324-c6ef12d92bde'})
Traceback (most recent call last):
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/tornado/web.py", line 1077, in _execute
    *self.path_args, **self.path_kwargs)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/tornado/web.py", line 1892, in wrapper
    return method(self, *args, **kwargs)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/html/services/kernels/handlers.py", line 46, in post
    kernel_id = km.start_kernel(notebook_id, cwd=nbm.notebook_dir)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/html/services/kernels/kernelmanager.py", line 86, in start_kernel
    kernel_id = super(MappingKernelManager, self).start_kernel(**kwargs)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/kernel/multikernelmanager.py", line 115, in start_kernel
    km.start_kernel(**kwargs)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/kernel/manager.py", line 205, in start_kernel
    **kw)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/kernel/manager.py", line 161, in _launch_kernel
    return launch_kernel(kernel_cmd, **kw)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/kernel/launcher.py", line 251, in launch_kernel
    stdin=_stdin, stdout=_stdout, stderr=_stderr, cwd=cwd, env=os.environ)
  File "/usr/local/Cellar/python/2.7.4/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/local/Cellar/python/2.7.4/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
ERROR:tornado.application:Uncaught exception POST /kernels?notebook=3ba49d4f-7abc-47e4-9324-c6ef12d92bde (127.0.0.1)
HTTPRequest(protocol='http', host='127.0.0.1:8998', method='POST', uri='/kernels?notebook=3ba49d4f-7abc-47e4-9324-c6ef12d92bde', version='HTTP/1.1', remote_ip='127.0.0.1', body='', headers={'Content-Length': '0', 'Accept-Language': 'en-US,en;q=0.5', 'Accept-Encoding': 'gzip, deflate', 'Host': '127.0.0.1:8998', 'Accept': 'application/json, text/javascript, */*; q=0.01', 'User-Agent': 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:23.0) Gecko/20100101 Firefox/23.0', 'Dnt': '1', 'Connection': 'keep-alive', 'X-Requested-With': 'XMLHttpRequest', 'Pragma': 'no-cache', 'Cache-Control': 'no-cache', 'Referer': 'http://127.0.0.1:8998/3ba49d4f-7abc-47e4-9324-c6ef12d92bde'})
Traceback (most recent call last):
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/tornado/web.py", line 1077, in _execute
    *self.path_args, **self.path_kwargs)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/tornado/web.py", line 1892, in wrapper
    return method(self, *args, **kwargs)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/html/services/kernels/handlers.py", line 46, in post
    kernel_id = km.start_kernel(notebook_id, cwd=nbm.notebook_dir)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/html/services/kernels/kernelmanager.py", line 86, in start_kernel
    kernel_id = super(MappingKernelManager, self).start_kernel(**kwargs)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/kernel/multikernelmanager.py", line 115, in start_kernel
    km.start_kernel(**kwargs)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/kernel/manager.py", line 205, in start_kernel
    **kw)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/kernel/manager.py", line 161, in _launch_kernel
    return launch_kernel(kernel_cmd, **kw)
  File "/Users/mesecke/.virtualenvs/science/lib/python2.7/site-packages/IPython/kernel/launcher.py", line 251, in launch_kernel
    stdin=_stdin, stdout=_stdout, stderr=_stderr, cwd=cwd, env=os.environ)
  File "/usr/local/Cellar/python/2.7.4/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)
  File "/usr/local/Cellar/python/2.7.4/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
2013-09-18 14:39:58.281 [tornado.access] ERROR | 500 POST /kernels?notebook=3ba49d4f-7abc-47e4-9324-c6ef12d92bde (127.0.0.1) 34.62ms
ERROR:tornado.access:500 POST /kernels?notebook=3ba49d4f-7abc-47e4-9324-c6ef12d92bde (127.0.0.1) 34.62ms

When hitting shift-enter in an ipython cell simply nothing happens (though I experienced a similar behavior as the parent, before doing some changes the kernel constantly died and automatically restarted).

Any ideas?

Thanks,

Sven

Steven G. Johnson

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Sep 18, 2013, 10:56:28 AM9/18/13
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Try deleting your .ipython/profile_julia directory and re-running Pkg.fixup("IJulia")

Adam Hesterberg

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Sep 18, 2013, 5:20:09 PM9/18/13
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Same error for me. I don't see a profile_julia directory. The entire Julia session is below. IJulia opens, but gives kernel errors.

               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "help()" to list help topics
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.2.0-prerelease+3768
 _/ |\__'_|_|_|\__'_|  |  Commit d6f7c7c 2013-09-18 04:01:51 UTC
|__/                   |  x86_64-w64-mingw32

julia> Pkg.add("IJulia")
INFO: Initializing package repository C:\Users\achesterberg\AppData\Roaming\Juli
a\packages.
INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl
INFO: Cloning cache of BinDeps from git://github.com/loladiro/BinDeps.jl.git
INFO: Cloning cache of IJulia from git://github.com/JuliaLang/IJulia.jl.git
INFO: Cloning cache of JSON from git://github.com/JuliaLang/JSON.jl.git
INFO: Cloning cache of Nettle from git://github.com/staticfloat/Nettle.jl.git
INFO: Cloning cache of REPLCompletions from git://github.com/loladiro/REPLComple
tions.jl.git
INFO: Cloning cache of URIParser from git://github.com/loladiro/URIParser.jl.git

INFO: Cloning cache of ZMQ from git://github.com/JuliaLang/ZMQ.jl.git
INFO: Installing BinDeps v0.2.6
INFO: Installing IJulia v0.0.0
INFO: Installing JSON v0.2.2
INFO: Installing Nettle v0.0.0
INFO: Installing REPLCompletions v0.0.0
INFO: Installing URIParser v0.0.0
INFO: Installing ZMQ v0.1.2
INFO: Running build script for package IJulia
Found IPython version 1.1.0 ... ok.
Creating julia profile in IPython...
[ProfileCreate] Generating default config file: u'C:\\Users\\achesterberg\\.ipyt
hon\\profile_julia\\ipython_config.py'
[ProfileCreate] Generating default config file: u'C:\\Users\\achesterberg\\.ipyt
hon\\profile_julia\\ipython_qtconsole_config.py'
[ProfileCreate] Generating default config file: u'C:\\Users\\achesterberg\\.ipyt
hon\\profile_julia\\ipython_notebook_config.py'
[ProfileCreate] Generating default config file: u'C:\\Users\\achesterberg\\.ipyt
hon\\profile_julia\\ipython_nbconvert_config.py'
Adding KernelManager.kernel_cmd = ["C:\\Users\\achesterberg\\julia-d6f7c7c781\\b
in\\julia.bat", "C:\\Users\\achesterberg\\AppData\\Roaming\\Julia\\packages\\IJu
lia\\src\\kernel.jl", "{connection_file}"] to ipython_config.py...
Adding IPythonWidget.execute_on_complete_input = False to ipython_qtconsole_conf
ig.py...
Adding NotebookApp.port = 8998 to ipython_notebook_config.py...
Copying IJulia png logo to Julia IPython profile.
Copying IJulia svg logo to Julia IPython profile.
Copying tooltip.js to Julia IPython profile.
Copying custom.js to Julia IPython profile.
INFO: Running build script for package Nettle
WARNING: An exception occured while building binary dependencies.
You may have to take manual steps to complete the installation, see the error me
ssage below.
To reattempt the installation, run Pkg.fixup("Nettle").

 in build at pkg.jl:412
WARNING: backtraces on your platform are often misleading or partially incorrect



ERROR: RPMmd package not installed, please run Pkg.add("RPMmd")
 in error at error.jl:21
 in include at boot.jl:238
 in include_from_node1 at loading.jl:96

at C:\Users\achesterberg\AppData\Roaming\Julia\packages\Nettle\deps\build.jl:9

julia> Pkg.fixup("Nettle")
INFO: Running build script for package IJulia
Found IPython version 1.1.0 ... ok.
Creating julia profile in IPython...
(Existing KernelManager.kernel_cmd setting in ipython_config.py is untouched.)
(Existing IPythonWidget.execute_on_complete_input setting in ipython_qtconsole_c
onfig.py is untouched.)
(Existing NotebookApp.port setting in ipython_notebook_config.py is untouched.)
(Existing Julia IPython png logo file untouched.)
(Existing Julia IPython svg logo file untouched.)
(Existing tooltip.js file untouched.)
(Existing custom.js file untouched.)
INFO: Running build script for package Nettle
WARNING: An exception occured while building binary dependencies.
You may have to take manual steps to complete the installation, see the error me
ssage below.
To reattempt the installation, run Pkg.fixup("Nettle").

 in build at pkg.jl:412

ERROR: RPMmd package not installed, please run Pkg.add("RPMmd")
 in error at error.jl:21
 in include at boot.jl:238
 in include_from_node1 at loading.jl:96

at C:\Users\achesterberg\AppData\Roaming\Julia\packages\Nettle\deps\build.jl:9

julia> Pkg.add("PyPlot")
INFO: Cloning cache of PyPlot from git://github.com/stevengj/PyPlot.jl.git
INFO: Cloning cache of Color from git://github.com/JuliaLang/Color.jl.git
INFO: Cloning cache of PyCall from git://github.com/stevengj/PyCall.jl.git
INFO: Installing PyPlot v1.0.10
INFO: Installing Color v0.2.6
INFO: Installing PyCall v0.0.0
INFO: Removing REPLCompletions v0.0.0
INFO: Removing BinDeps v0.2.6
INFO: Removing IJulia v0.0.0
INFO: Removing ZMQ v0.1.2
INFO: Removing JSON v0.2.2
INFO: Removing Nettle v0.0.0
INFO: Removing URIParser v0.0.0
INFO: REQUIRE updated.

julia> Sys.CPU_CORES
8

julia> nprocs()
1

julia> addprocs(2)
2-element Array{Any,1}:
 2
 3

julia> nprocs()
3

julia> @everywhere begin
         coinflip() = int(randbool())
       end

julia> coinflip()
1

julia> n = 10000000
10000000

julia> nheads = @parallel (+) for i=1:n; coinflip(); end
4997477

julia> using PyPlot
exception on exception on 23: : ERROR: ERROR: PyErrorPyError (PyImport_ImportMod
ule) (PyImport_ImportModule)  <type 'exceptions.ImportError'><type 'exceptions.I
mportError'>

ImportError('No module named matplotlib',)ImportError('No module named matplotli
b',)



 in  in pyerr_checkpyerr_check at  at C:\Users\achesterberg\AppData\Roaming\Juli
a\packages\PyCall\src\exception.jlC:\Users\achesterberg\AppData\Roaming\Julia\pa
ckages\PyCall\src\exception.jl::5858    From worker 2:
        From worker 3:
WARNING: backtraces on your platform are often misleading or partially incorrect
WARNING: backtraces on your platform are often misleading or partially incorrect
        From worker 2:


at C:\Users\achesterberg\AppData\Roaming\Julia\packages\PyPlot\src\PyPlot.jl:32
        From worker 3:


at C:\Users\achesterberg\AppData\Roaming\Julia\packages\PyPlot\src\PyPlot.jl:32
ERROR: PyError (PyImport_ImportModule) <type 'exceptions.ImportError'>
ImportError('No module named matplotlib',)

 in pyerr_check at C:\Users\achesterberg\AppData\Roaming\Julia\packages\PyCall\s
rc\exception.jl:58

at C:\Users\achesterberg\AppData\Roaming\Julia\packages\PyPlot\src\PyPlot.jl:32

Isaiah Norton

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Sep 18, 2013, 6:38:01 PM9/18/13
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profile_julia will be in %HOME%/.ipython ... Please delete that first.

The two steps you need are:

Pkg.add("RPMmd")
Pkg.add("IJulia")

Preferably in that order (sorry about this, the RPMmd dependency is not resolved automatically yet).

Steven G. Johnson

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Sep 18, 2013, 11:43:22 PM9/18/13
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If you do a Pkg.update(), the latest version of IJulia's build script should overwrite the Julia-path setting in your .ipython/profile_julia as needed, so you'll no longer have to delete this directory manually.

Adam Hesterberg

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Sep 22, 2013, 11:03:21 AM9/22/13
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Not working, but with different error messages.

First, I uninstalled everything from the last attempt.

Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\achesterberg>conda update conda
# All packages already at latest version, nothing to do.
# packages in environment at C:\Anaconda:
#
conda                     1.9.1                    py27_0

C:\Users\achesterberg>conda update ipython
Updating conda environment at C:\Anaconda

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ipython-1.1.0              |           py27_0         2.9 MB

The following packages will be UN-linked:

    package                    |            build
    ---------------------------|-----------------
    ipython-1.0.0              |           py27_0

The following packages will be linked:

    package                    |            build
    ---------------------------|-----------------
    ipython-1.1.0              |           py27_0

Proceed ([y]/n)? y

Fetching packages ...
ipython-1.1.0-py27_0.tar.bz2 100% |#################| Time: 0:00:02   1.09 MB/s
Extracting packages ...
[      COMPLETE      ] |#################################################| 100%
Unlinking packages ...
[      COMPLETE      ] |#################################################| 100%
Linking packages ...
menuinst Exception:  ] |#################################################| 100%
Traceback (most recent call last):
  File "C:\Anaconda\lib\site-packages\conda\install.py", line 176, in mk_menus
    menuinst.install(join(prefix, f), remove, prefix)
  File "C:\Anaconda\lib\site-packages\menuinst\__init__.py", line 41, in install

    ShortCut(m, sc, prefix=prefix).create()
  File "C:\Anaconda\lib\site-packages\menuinst\win32.py", line 128, in create
    icon,
OSError: Failed to create shortcut 'C:\ProgramData\Microsoft\Windows\Start Menu\
Programs\Anaconda (64-bit)\IPython (Py 2.7).lnk' - error 0x80070005
[      COMPLETE      ] |#################################################| 100%



               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "help()" to list help topics
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.2.0-prerelease+3742
 _/ |\__'_|_|_|\__'_|  |  Commit ce3a772 2013-09-16 04:04:18 UTC
|__/                   |  x86_64-w64-mingw32

julia> Pkg.add("IJulia")
ERROR: could not start process `git rev-parse --git-dir`: no such file or direct
ory (ENOENT)
 in test_success at process.jl:431
 in success at process.jl:439
 in readbytes at process.jl:400
WARNING: backtraces on your platform are often misleading or partially incorrect




At this point, I can run IJulia (from the folder C:\Users\achesterberg\Desktop\julia-ce3a772728\bin), and it opens but gives kernel-restarting errors.


Then I deleted the profile_julia folder manually.



               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "help()" to list help topics
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.2.0-prerelease+3742
 _/ |\__'_|_|_|\__'_|  |  Commit ce3a772 2013-09-16 04:04:18 UTC
|__/                   |  x86_64-w64-mingw32

julia> Pkg.update()
INFO: Updating METADATA...
ERROR: could not start process `git rev-parse --symbolic-full-name --abbrev-ref
HEAD`: no such file or directory (ENOENT)
 in test_success at process.jl:431
 in success at process.jl:439
 in readbytes at process.jl:400
WARNING: backtraces on your platform are often misleading or partially incorrect




julia> Pkg.add("RPMmd")
ERROR: could not start process `git rev-parse --git-dir`: no such file or direct
ory (ENOENT)
 in test_success at process.jl:431
 in success at process.jl:439
 in readbytes at process.jl:400


julia> Pkg.add("IJulia")
ERROR: could not start process `git rev-parse --git-dir`: no such file or direct
ory (ENOENT)
 in test_success at process.jl:431
 in success at process.jl:439
 in readbytes at process.jl:400


julia>



Isaiah Norton

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Sep 22, 2013, 11:08:48 AM9/22/13
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Please update to the latest Julia binary download. The git path issue was resolved in 1200dd0d (after ce3a77 was cut).

Adam Hesterberg

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Sep 23, 2013, 2:28:59 PM9/23/13
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Downloaded the latest Julia binary (d6f7c7c7...). Ran the installer. Typed Pkg.add("IJulia"). The result:

               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "help()" to list help topics
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.2.0-prerelease+3768
 _/ |\__'_|_|_|\__'_|  |  Commit d6f7c7c 2013-09-18 04:01:51 UTC
|__/                   |  x86_64-w64-mingw32

julia> Pkg.add("IJulia")
INFO: Installing BinDeps v0.2.6
INFO: Installing IJulia v0.0.0
INFO: Installing JSON v0.2.2
INFO: Installing Nettle v0.0.0
INFO: Installing REPLCompletions v0.0.0
INFO: Installing URIParser v0.0.0
INFO: Installing ZMQ v0.1.2
INFO: Running build script for package IJulia
Found IPython version 1.1.0 ... ok.
Creating julia profile in IPython...
[ProfileCreate] Generating default config file: u'C:\\Users\\achesterberg\\.ipyt
hon\\profile_julia\\ipython_config.py'
[ProfileCreate] Generating default config file: u'C:\\Users\\achesterberg\\.ipyt
hon\\profile_julia\\ipython_qtconsole_config.py'
[ProfileCreate] Generating default config file: u'C:\\Users\\achesterberg\\.ipyt
hon\\profile_julia\\ipython_notebook_config.py'
[ProfileCreate] Generating default config file: u'C:\\Users\\achesterberg\\.ipyt
hon\\profile_julia\\ipython_nbconvert_config.py'
Adding KernelManager.kernel_cmd = ["C:\\Users\\achesterberg\\Desktop\\julia-d6f7
c7c781\\bin\\julia.bat", "C:\\Users\\achesterberg\\AppData\\Roaming\\Julia\\pack
ages\\IJulia\\src\\kernel.jl", "{connection_file}"] to ipython_config.py...
Adding IPythonWidget.execute_on_complete_input = False to ipython_qtconsole_conf
ig.py...
Adding NotebookApp.port = 8998 to ipython_notebook_config.py...
Copying IJulia png logo to Julia IPython profile.
Copying IJulia svg logo to Julia IPython profile.
Copying tooltip.js to Julia IPython profile.
Copying custom.js to Julia IPython profile.
INFO: Running build script for package Nettle
WARNING: An exception occured while building binary dependencies.
You may have to take manual steps to complete the installation, see the error me
ssage below.
To reattempt the installation, run Pkg.fixup("Nettle").

 in build at pkg.jl:412
WARNING: backtraces on your platform are often misleading or partially incorrect



Adam Hesterberg

unread,
Sep 23, 2013, 2:29:29 PM9/23/13
to julia...@googlegroups.com
For good measure, I tried again with Pkg.add("RPMmd") first. The result:


               _
   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: http://docs.julialang.org
   _ _   _| |_  __ _   |  Type "help()" to list help topics
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.2.0-prerelease+3768
 _/ |\__'_|_|_|\__'_|  |  Commit d6f7c7c 2013-09-18 04:01:51 UTC
|__/                   |  x86_64-w64-mingw32

julia> Pkg.add("RPMmd")
INFO: Cloning cache of HTTPClient from git://github.com/amitmurthy/HTTPClient.jl
.git
INFO: Cloning cache of LibCURL from git://github.com/amitmurthy/LibCURL.jl.git
INFO: Cloning cache of RPMmd from https://github.com/JuliaLang/RPMmd.jl.git
INFO: Cloning cache of LibExpat from git://github.com/amitmurthy/LibExpat.jl.git

INFO: Cloning cache of URLParse from git://github.com/tanmaykm/URLParse.jl.git
INFO: Cloning cache of Zlib from git://github.com/dcjones/Zlib.jl.git
INFO: Installing HTTPClient v0.0.0
INFO: Installing LibCURL v0.0.0
INFO: Installing RPMmd v0.0.5
INFO: Installing LibExpat v0.0.0
INFO: Installing URLParse v0.0.0
INFO: Installing Zlib v0.1.2
INFO: Removing REPLCompletions v0.0.0
INFO: Removing BinDeps v0.2.6
INFO: Removing IJulia v0.0.0
INFO: Removing ZMQ v0.1.2
INFO: Removing JSON v0.2.2
INFO: Removing Nettle v0.0.0
INFO: Removing URIParser v0.0.0
INFO: REQUIRE updated.

julia> Pkg.add("IJulia")
INFO: Installing IJulia v0.0.0
INFO: Installing JSON v0.2.2
INFO: Installing Nettle v0.0.0
INFO: Installing REPLCompletions v0.0.0
INFO: Installing URIParser v0.0.0
INFO: Installing ZMQ v0.1.2
INFO: Installing BinDeps v0.2.6
INFO: Running build script for package IJulia
Found IPython version 1.1.0 ... ok.
Creating julia profile in IPython...
(Existing KernelManager.kernel_cmd setting in ipython_config.py is untouched.)
(Existing IPythonWidget.execute_on_complete_input setting in ipython_qtconsole_c
onfig.py is untouched.)
(Existing NotebookApp.port setting in ipython_notebook_config.py is untouched.)
(Existing Julia IPython png logo file untouched.)
(Existing Julia IPython svg logo file untouched.)
(Existing tooltip.js file untouched.)
(Existing custom.js file untouched.)
INFO: Running build script for package Nettle
WARNING: skipping repodata/repomd.xml, not in cache
 in cacheget at C:\Users\achesterberg\AppData\Roaming\Julia\packages\RPMmd\src\R
PMmd.jl:86
WARNING: backtraces on your platform are often misleading or partially incorrect



WARNING: skipping repodata/repomd.xml, not in cache
 in cacheget at C:\Users\achesterberg\AppData\Roaming\Julia\packages\RPMmd\src\R
PMmd.jl:86

INFO: Updating RPMmd package list
2/openSUSE_Factory//repodata/repomd.xml
2/openSUSE_Factory//repodata/49002282ce79ee000e161927c84cce569913eb6b-primary.xm
l.gz
4/openSUSE_Factory//repodata/repomd.xml
4/openSUSE_Factory//repodata/2fc5c7fc61e450a87444dcfb631937b50ad193bd-primary.xm
l.gz
WARNING: contains(collection, item) is deprecated, use in(item, collection) inst
ead

INFO: Packages to install: libnettle
INFO: Downloading: libnettle
INFO: Extracting: libnettle

7-Zip [64] 9.20  Copyright (c) 1999-2010 Igor Pavlov  2010-11-18

Processing archive: C:\Users\achesterberg\AppData\Roaming\Julia\packages\RPMmd\c
ache\http%3a%2f%2fdownload.opensuse.org%2frepositories%2fwindows%3a%2fmingw%3a%2
fwin64%2fopenSUSE_Factory%2f\noarch%2fmingw64-libnettle-2.7-1.56.noarch.rpm

Extracting  noarch%2fmingw64-libnettle-2.7-1.56.noarch.cpio

Everything is Ok

Size:       205204
Compressed: 88811

7-Zip [64] 9.20  Copyright (c) 1999-2010 Igor Pavlov  2010-11-18

Processing archive: C:\Users\achesterberg\AppData\Roaming\Julia\packages\RPMmd\c
ache\http%3a%2f%2fdownload.opensuse.org%2frepositories%2fwindows%3a%2fmingw%3a%2
fwin64%2fopenSUSE_Factory%2f\noarch%2fmingw64-libnettle-2.7-1.56.noarch.cpio

Extracting  .\usr\x86_64-w64-mingw32\sys-root\mingw\bin\libnettle-4-6.dll

Everything is Ok

Size:       204906
Compressed: 205204
INFO: Success
INFO: Running build script for package ZMQ
WARNING: An exception occured while building binary dependencies.
You may have to take manual steps to complete the installation, see the error me
ssage below.
To reattempt the installation, run Pkg.fixup("ZMQ").

 in build at pkg.jl:412

ERROR: None of the selected providers can install dependency zmq
 in error at error.jl:21
 in satisfy! at C:\Users\achesterberg\AppData\Roaming\Julia\packages\BinDeps\src
\dependencies.jl:439

at C:\Users\achesterberg\AppData\Roaming\Julia\packages\ZMQ\deps\build.jl:17

julia>

Steven G. Johnson

unread,
Sep 23, 2013, 4:21:38 PM9/23/13
to julia...@googlegroups.com

INFO: Success
INFO: Running build script for package ZMQ
WARNING: An exception occured while building binary dependencies.
You may have to take manual steps to complete the installation, see the error me
ssage below.
To reattempt the installation, run Pkg.fixup("ZMQ").

 in build at pkg.jl:412

ERROR: None of the selected providers can install dependency zmq

This may be due to Julia bug 4328 (https://github.com/JuliaLang/julia/issues/4328): you have a broken ZMQ directory from an earlier installation attempt, and for some reason Pkg refuses to upgrade it.

On my machine, this was fixed by deleting the AppData/Roaming/julia/packages directory (the Windows equivalent of .julia) (note that AppData is a "hidden" subdirectory of your home directory, but turning on "View Hidden Files" in the file explorer should make it show up).  Then do:


    Pkg.add("RPMmd")
    Pkg.add("IJulia")

and it should work.   Two notes:

* Make sure you are downloading the 64-bit Windows binary of Julia 0.2.  (I don't know if we have the 32-bit binary dependencies pre-built yet.)

* In order to run IJulia, you need to run
        ipython notebook --profile julia
when the command-line in the "bin" subdirectory of your Julia directory (this was fixed in #4327, but I don't think a new binary has been posted yet).

See also the installation and troubleshooting instructions in:

     https://github.com/stevengj/julia-mit

--SGJ
 

Adam Hesterberg

unread,
Sep 23, 2013, 6:50:04 PM9/23/13
to julia...@googlegroups.com
Jeff Bezanson fixed this in person at about the same time you posted that, by roughly that process.

Thanks!
-Adam
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