Can't use R in babel

[maxigit]

I'm trying to use R and babel and I get the following error message :

Error in dotspacemacs/user-config: Invalid function: org-babel-header-args-safe-fn

I only get this error message when I add (R . t) in the orb-babel-do-load-languages section. If I use python or ruby it works fine.

[tboby]

Try deleting the Org and org-plus-contrib packages from spacemacs/elpa/.

It's possible this is due to a conflict with the different versions of org, although I'm not quite sure how it happens in the first place.

[Andre0991]

Have a look at "Important Note" in the org layer docs, it might have to do with that too.

Basically, you have to wrap everything that is related to org in (with-eval-after-load 'org ...)

[maxigit]

I suppose so. Everything but R works. Also I get spacemacs updates and
everything. But I can double check, how can I do that ?

On 14 January 2016 at 22:18, tboby notifications@github.com wrote:

Are you sure you have git on your path?

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[maxigit]

It is in the right section. I can get other language work (sql, python,
ruby etc ...). Only R causes this error ...

On 15 January 2016 at 09:23, bmx007 bmx007@gmail.com wrote:

I suppose so. Everything but R works. Also I get spacemacs updates and
everything. But I can double check, how can I do that ?

On 14 January 2016 at 22:18, tboby notifications@github.com wrote:

Are you sure you have git on your path?

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Reply to this email directly or view it on GitHub
#4618 (comment)
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[maxigit]

I upgraded to 0.105.8 and updated all the packages and know it's workingi :-)

[maxigit]

I had the problem again (after upgrading to 0.105.9) the solution was to clear the elpa subdirectory.

[izahn]

This is an upstream bug in org-mode, see http://comments.gmane.org/gmane.emacs.orgmode/99644 and https://www.mail-archive.com/emacs-orgmode@gnu.org/msg98762.html. I think this issue should be closed and an upstream bug reported to org-mode.

[cpaulik]

Just had the same issue. Removing ob-R.elc fixed it.

[GregorySchwartz]

I have this issue and no amount of recompiling, restarting, removing org-* folders, or anything of that sort work. The only solution for me is to remove R . t from my configuration, but then I can't use R in babel. Is there some other solution?

[TheBB]

@GregorySchwartz The solution of @cpaulik should work. Remove only the file ob-R.elc.

I don't know for sure but I assume this happens because ob-R.elc is byte-compiled with the old version of org.

[GregorySchwartz]

@TheBB Unfortunately that solution did not work for me. I should mention that these techniques of removal did work a few weeks ago--this just started happening.

[izahn]

It usually happens in spacemacs that you end up with both org and org-plus-contrib package, making it harder to know where the broken ob-R.elc file is. Start package manager with M-x paradox, delete org and org-plus-contrib, then install only prg-plus-contrib. This usually works for me.

[syl20bnr]

@izahn do you think we can automate these steps in Spacemacs to have a clean org installation ?

Also moving org to :step pre would ensure that the above steps are executed prior to other packages configuration.

EDIT: never mind this issue is at installation time, right now packages are all installed in alphabetical order. Maybe taking into account the :step keyword for installation as well could solve the issue.

[izahn]

I think the right thing is to fix this in upstream org-mode. I'm super busy now but I will look into it when I get a free moment.

[GregorySchwartz]

@izahn That solution using paradox worked. It must be because deleteing just org-plus-contrib or both org and that package repeated installs, but with your way it works.

[bmag]

Just adding two links to (slightly) better understand possible problem in compiling packages during installation of new packages:

• http://emacs.stackexchange.com/questions/13574/technical-considerations-for-package-maintainers-to-not-use-the-emacs-package-ma
• `magit-status' doesn't accept alternate directory names magit/magit#2154

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