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jkitchin / scimax

An emacs starterkit for scientists and engineers
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Any R-users successfully creating Jupyter notebooks with Scimax? #500

Open mbujosab opened 1 week ago

mbujosab commented 1 week ago

Hello,

I am wondering if there are any users who have successfully created Jupyter notebooks with R code using Scimax. I have attempted to do so, but I have not been able to get it to work.

Any guidance or suggestions would be greatly appreciated.

Thank you!

Best regards,

Marcos Bujosa

jkitchin commented 1 week ago

Good news for me, I was able to get it working again by running M-x jupyter-refresh-kernelspecs. The reason it was failing for me is there was an out of date kernelspec that was trying to load an older version of R that no longer existed.

mbujosab commented 1 week ago

Maybe it is because I have an old version of Scimax, but I can't find the function M-x jupyter-refresh-kernelspecs.

mbujosab commented 1 week ago

When I try to run an R code block, I get the following message:

ess-mode: Customise alist is not specified, nor ess-local-customize-alist is set

jkitchin commented 1 week ago

jupyter-refresh-kernelspecs is an autoloaded interactive byte-compiled Lisp function in ‘jupyter-kernelspec.el’.

I have jupyter-20231204.529 installed. It also seems to exist in the most recent package.

mbujosab commented 1 week ago

Dear Professor Kitchin,

I have installed a new version of Scimax (I did a manual installation by cloning the GitHub repository). During the process, I encountered several warning errors and another error when I tried to load 'ox-ipynb'. (Error (use-package): Cannot load ox-ipynb)

I am not sure what I did wrong.

Error (use-package): Failed to install aggressive-indent: Assertion failed: (or (= (buffer-size tar-data-buffer) (buffer-size)) (eq tar-data-swapped (> (buffer-size tar-data-buffer) (buffer-size)))) Error (use-package): Cannot load aggressive-indent Error (use-package): Failed to install citeproc: https://elpa.gnu.org/packages/queue-0.2.el: Not found Error (use-package): Cannot load citeproc Error (use-package): Failed to install org-ref: https://elpa.gnu.org/packages/queue-0.2.el: Not found Error (use-package): Cannot load org-ref Error (use-package): Failed to parse package org-ref-ivy: Wrong type argument: stringp, nil Error (use-package): Failed to install rainbow-mode: Failed to verify signature: "rainbow-mode-1.0.6.tar.sig" Error (use-package): Cannot load rainbow-mode Error (use-package): Failed to install undo-tree: https://elpa.gnu.org/packages/queue-0.2.el: Not found Error (use-package): Cannot load undo-tree Error (use-package): scimax-email/:catch: Cannot open load file: No existe el fichero o el directorio, org-ref-export Error (use-package): Failed to install org-ql: Failed to verify signature: "peg-1.0.1.tar.sig" Error (use-package): Cannot load org-ql

When I try to run the code in

work misspelled. Type C-; to fix it. Executing Jupyter-R unknown at position 1313... Launching ir kernel... Starting ir kernel process...done Launching ir kernel...done Requesting kernel info... Loading /home/marcos/.emacs.d/elpa/zmq-20230608.1856/emacs-zmq (module)... zmq-load: Module could not be opened: "/home/marcos/.emacs.d/elpa/zmq-20230608.1856/emacs-zmq.so", "/lib/x86_64-linux-gnu/libc.so.6: version GLIBC_2.33' not found (required by /home/marcos/.emacs.d/elpa/zmq-20230608.1856/emacs-zmq.so)" Executing Emacs-Lisp unknown at position 694... Code block produced no output. Executing Jupyter-R unknown at position 1313... Launching ir kernel... Starting ir kernel process...done Launching ir kernel...done Requesting kernel info... Loading /home/marcos/.emacs.d/elpa/zmq-20230608.1856/emacs-zmq (module)... zmq-load: Module could not be opened: "/home/marcos/.emacs.d/elpa/zmq-20230608.1856/emacs-zmq.so", "/lib/x86_64-linux-gnu/libc.so.6: versionGLIBC_2.33' not found (required by /home/marcos/.emacs.d/elpa/zmq-20230608.1856/emacs-zmq.so)" Mark set [5 times]

With the new version of scimax It seems that the R-kernel runs (but I have to solve a problem with de 'emacs-zmq.so' module in my PC)

Thank you for all your help and also for your recent series of videos.

Regards,

Marcos Bujosa

mbujosab commented 1 week ago

Sorry I missed the file I run:

https://github.com/jkitchin/scimax/blob/master/scimax-jupyter-r.org

jkitchin commented 6 days ago

You probably have to get ox-ipynb from https://github.com/jkitchin/ox-ipynb. I don't think it auto installs from anywhere. The rest of those look like use-package failed to download packages from elpa/melpa. The last error about zmq might mean you have to build that library, eg cd to /home/marcos/.emacs.d/elpa/zmq-20230608.1856, and check the makefile to see if you can build it manually.