R Notebook does not connect to R kernel after initial install on 64 bit Windows 7

[ActionPace]

I have a fresh install of R 64bit and Anaconda on Windows 7 64bit

I ran the instructions to install Jupyter for R (typed in the R Console)

install.packages(c('rzmq','repr','IRkernel','IRdisplay'),
                 repos = c('http://irkernel.github.io/', getOption('repos')))
IRkernel::installspec()

Now when I try to create an R notebook, I see the R option in the Jupyter dropdown list but I see an error when it tries to connect to the R kernel

Here is the output when I try to connect to qtconsole (same error):

C:\Users\David>jupyter qtconsole --kernel=ir
'jupyter' is not recognized as an internal or external command,
operable program or batch file.

C:\Users\David>ipython qtconsole --kernel=ir
Traceback (most recent call last):
  File "C:\Anaconda\Scripts\ipython-script.py", line 5, in <module>
    sys.exit(start_ipython())
  File "C:\Anaconda\lib\site-packages\IPython\__init__.py", line 120, in start_i
python
    return launch_new_instance(argv=argv, **kwargs)
  File "C:\Anaconda\lib\site-packages\IPython\config\application.py", line 573,
in launch_instance
    app.initialize(argv)
  File "<string>", line 2, in initialize
  File "C:\Anaconda\lib\site-packages\IPython\config\application.py", line 75, i
n catch_config_error
    return method(app, *args, **kwargs)
  File "C:\Anaconda\lib\site-packages\IPython\terminal\ipapp.py", line 321, in i
nitialize
    super(TerminalIPythonApp, self).initialize(argv)
  File "<string>", line 2, in initialize
  File "C:\Anaconda\lib\site-packages\IPython\config\application.py", line 75, i
n catch_config_error
    return method(app, *args, **kwargs)
  File "C:\Anaconda\lib\site-packages\IPython\core\application.py", line 369, in
 initialize
    self.parse_command_line(argv)
  File "C:\Anaconda\lib\site-packages\IPython\terminal\ipapp.py", line 316, in p
arse_command_line
    return super(TerminalIPythonApp, self).parse_command_line(argv)
  File "<string>", line 2, in parse_command_line
  File "C:\Anaconda\lib\site-packages\IPython\config\application.py", line 75, i
n catch_config_error
    return method(app, *args, **kwargs)
  File "C:\Anaconda\lib\site-packages\IPython\config\application.py", line 471,
in parse_command_line
    return self.initialize_subcommand(subc, subargv)
  File "<string>", line 2, in initialize_subcommand
  File "C:\Anaconda\lib\site-packages\IPython\config\application.py", line 75, i
n catch_config_error
    return method(app, *args, **kwargs)
  File "C:\Anaconda\lib\site-packages\IPython\config\application.py", line 409,
in initialize_subcommand
    self.subapp.initialize(argv)
  File "<string>", line 2, in initialize
  File "C:\Anaconda\lib\site-packages\IPython\config\application.py", line 75, i
n catch_config_error
    return method(app, *args, **kwargs)
  File "C:\Anaconda\lib\site-packages\IPython\qt\console\qtconsoleapp.py", line
359, in initialize
    IPythonConsoleApp.initialize(self,argv)
  File "C:\Anaconda\lib\site-packages\IPython\consoleapp.py", line 342, in initi
alize
    self.init_kernel_manager()
  File "C:\Anaconda\lib\site-packages\IPython\consoleapp.py", line 298, in init_
kernel_manager
    self.kernel_manager.start_kernel(**kwargs)
  File "C:\Anaconda\lib\site-packages\IPython\kernel\manager.py", line 240, in s
tart_kernel
    **kw)
  File "C:\Anaconda\lib\site-packages\IPython\kernel\manager.py", line 189, in _
launch_kernel
    return launch_kernel(kernel_cmd, **kw)
  File "C:\Anaconda\lib\site-packages\IPython\kernel\launcher.py", line 202, in
launch_kernel
    proc = Popen(cmd, **kwargs)
  File "C:\Anaconda\lib\subprocess.py", line 710, in __init__
    errread, errwrite)
  File "C:\Anaconda\lib\subprocess.py", line 958, in _execute_child
    startupinfo)
WindowsError: [Error 2] The system cannot find the file specified

If you suspect this is an IPython bug, please report it at:
    https://github.com/ipython/ipython/issues
or send an email to the mailing list at ipython-dev@scipy.org

You can print a more detailed traceback right now with "%tb", or use "%debug"
to interactively debug it.

Extra-detailed tracebacks for bug-reporting purposes can be enabled via:
    c.Application.verbose_crash=True

Please advise, Thanks

[takluyver]

That sounds like R is not on PATH. Can you try with master? Clone this repo, run R CMD INSTALL IRkernel, and then run IRkernel::installspec() inside R again.

[ActionPace]

Thanks.. I added the location of the R executables on the windows PATH variable and it worked.. I didn't understand the other instructions.

[takluyver]

OK, glad that worked. We've made a change to IRkernel so you shouldn't need that, and we need someone to test it on Windows - I was hoping you could lend a hand with that.

[ActionPace]

OK, so what do I do? Remove R from the PATH, reinstall R and start from scratch?

[takluyver]

No need to reinstall R. If you have, or can install, the R package 'devtools', grab that and do:

library(devtools)
install_github('IRkernel/IRkernel')

If not, download this and unzip it, then use a command prompt to run R CMD INSTALL IRkernel (IRkernel being the folder from the zip file).

Either way, then run IRkernel::installspec() again. This should put the new kernelspec on your system. Then try creating an R notebook and see if it works.

Thanks!

[takluyver]

@flying-sheep @JanSchulz I'd like to get a new release out with this fix in. Is there anything else you want to land soon, or should we go for 0.5?

[flying-sheep]

not really, but #153 would be a low-hanging fruit bugfix.

[takluyver]

Fancy doing a PR? ;-)

[EarlGlynn]

FWIW, the fix above helped me tonight, so it is needed.

[flying-sheep]

i directly commited 13ed0d7, it was trivial enough.

quit() is seemingly a bigger undertaking, so let’s not wait for that one and go with 0.5 instead

[takluyver]

Thanks @flying-sheep

I've bumped the version number and tagged 0.5. @JanSchulz @asmeurer, please work your packaging magic whenever it's convenient. :-)

[jankatins]

I submitted a PR in irkernel.github.io for both the source and the windows binaries

[asmeurer]

@groutr and @ilanschnell are the people to bug about this now.

[flying-sheep]

this is fixed right?

[takluyver]

I believe so, yes.