Invalid function: org-babel-header-args-safe-fn in Melpa

Invalid function: org-babel-header-args-safe-fn in Melpa

[John Kitchin]

Hi all,

I am trying to debug an issue with installing org-mode from Melpa.

After installing org from Melpa, I get this on starting emacs:

byte-code: Invalid function: org-babel-header-args-safe-fn
Org-mode version 8.3.3 (8.3.3-51-g30bcff-elpaplus @
/Users/jkitchin/Desktop/jmax-git/elpa/org-plus-contrib-20160208/)

It is happening when I try to change some default headers.

Debugger entered--Lisp error: (invalid-function org-babel-header-args-safe-fn)
  org-babel-header-args-safe-fn((:cache :colnames :comments :exports :epilogue :hlines :noeval :noweb :noweb-ref :noweb-sep :padline :prologue :rownames :sep :session :tangle :wrap (:eval "never" "query") (:results lambda (str) (not (string-match "file" str))) :width :height :bg :units :pointsize :antialias :quality :compression :res :type :family :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal))
  byte-code("\301\302\303\304\b!#\210\305\306\307\310\311\312\313\314\315\316&	\207" [ob-R-safe-header-args put org-babel-default-header-args:R safe-local-variable org-babel-header-args-safe-fn custom-declare-variable org-babel-R-command "R --slave --no-save" "Name of command to use for executing R code." :group org-babel :version "24.1" :type string] 10)
  require(ob-R)
  #[(pair) "\bA\303\b@!\211\203

Re: Invalid function: org-babel-header-args-safe-fn in Melpa

[Achim Gratz]

John Kitchin writes:
> I am trying to debug an issue with installing org-mode from Melpa.

There's no Org on Melpa or at least there shouldn't be.

> After installing org from Melpa, I get this on starting emacs:
>
> byte-code: Invalid function: org-babel-header-args-safe-fn

You must not install Org while it has already been loaded (i.e. since
your startup files alkmost certainly reference it somewhere you'll have
to do it from emacs -Q) and you must not use anything from Org in your
startup files before package-initialize has been done.


Regards,
Achim.
-- 
+<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+

Samples for the Waldorf Blofeld:
http://Synth.Stromeko.net/Downloads.html#BlofeldSamplesExtra

Re: Invalid function: org-babel-header-args-safe-fn in Melpa

[Aaron Ecay]

Hi John,

2016ko otsailak 14an, John Kitchin-ek idatzi zuen:
> 
> Hi all,
> 
> I am trying to debug an issue with installing org-mode from Melpa.
> 
> After installing org from Melpa, I get this on starting emacs:
> 
> byte-code: Invalid function: org-babel-header-args-safe-fn
> Org-mode version 8.3.3 (8.3.3-51-g30bcff-elpaplus @
> /Users/jkitchin/Desktop/jmax-git/elpa/org-plus-contrib-20160208/)
> 
> It is happening when I try to change some default headers.
> 
> Debugger entered--Lisp error: (invalid-function org-babel-header-args-safe-fn)
>   org-babel-header-args-safe-fn((:cache :colnames :comments :exports :epilogue :hlines :noeval :noweb :noweb-ref :noweb-sep :padline :prologue :rownames :sep :session :tangle :wrap (:eval "never" "query") (:results lambda (str) (not (string-match "file" str))) :width :height :bg :units :pointsize :antialias :quality :compression :res :type :family :title :fonts :version :paper :encoding :pagecentre :colormodel :useDingbats :horizontal))
>   byte-code("\301\302\303\304\b!#\210\305\306\307\310\311\312\313\314\315\316&	\207" [ob-R-safe-header-args put org-babel-default-header-args:R safe-local-variable org-babel-header-args-safe-fn custom-declare-variable org-babel-R-command "R --slave --no-save" "Name of command to use for executing R code." :group org-babel :version "24.1" :type string] 10)
>   require(ob-R)
>   #[(pair) "\bA\303\b@!\211\203.\304\305\306	P!!\202%\307\305\310	P!!\210\307\305\311	P!!*\207" [pair lang active symbol-name require intern "ob-" fmakunbound "org-babel-execute:" "org-babel-expand-body:"] 5]((R . t))
>   mapc(#[(pair) "\bA\303\b@!\211\203.\304\305\306	P!!\202%\307\305\310	P!!\210\307\305\311	P!!*\207" [pair lang active symbol-name require intern "ob-" fmakunbound "org-babel-execute:" "org-babel-expand-body:"] 5] ((emacs-lisp . t) (python . t) (sh . t) (matlab . t) (sqlite . t) (ruby . t) (perl . t) (org . t) (dot . t) (plantuml . t) (R . t)))
>   org-babel-do-load-languages(org-babel-load-languages ((emacs-lisp . t) (python . t) (sh . t) (matlab . t) (sqlite . t) (ruby . t) (perl . t) (org . t) (dot . t) (plantuml . t) (R . t)))
>   eval-buffer(#<buffer  *load*> nil "/Users/jkitchin/Desktop/jmax-git/jmax-org.el" nil t)  ; Reading at buffer position 7097
> 
> If I run this:
> (byte-recompile-file
>      (expand-file-name "ob-R.el"
>                       (file-name-directory (locate-library "org")))
>      t)
>

This looks like the kind of problem that results when org is byte-compiled
in an emacs with a different version of org loaded.  This used to be a
problem when installing via package.el (and not just for org), but I think
there has been some work put into making sure it doesn’t happen any more.
(I know emacs developers were discussing them and then they seemed to go
away so I assumed they were fixed...it’s possible I was mistaken though.)

If I had to guess, I’d say that line 63 of packages.el in your jmax
setup defeats these fixes.  Try commenting it out.  It should not be
necessary to manually byte-compile packages: package.el should do that
for you.  And in this case, I hypothesize that it is actually harmful.

Hope this helps,

-- 
Aaron Ecay

Re: Invalid function: org-babel-header-args-safe-fn in Melpa

[Achim Gratz]

Aaron Ecay writes:
> This looks like the kind of problem that results when org is byte-compiled
> in an emacs with a different version of org loaded.  This used to be a
> problem when installing via package.el (and not just for org), but I think
> there has been some work put into making sure it doesn’t happen any more.
> (I know emacs developers were discussing them and then they seemed to go
> away so I assumed they were fixed...it’s possible I was mistaken though.)

No, this is bug #10125 and the others that it was merged with (most
recently #21267, with the exact same error message as John got).

> If I had to guess, I’d say that line 63 of packages.el in your jmax
> setup defeats these fixes.  Try commenting it out.  It should not be
> necessary to manually byte-compile packages: package.el should do that
> for you.  And in this case, I hypothesize that it is actually harmful.

Yes it is.  Although I'd venture to guess that it would have happened
anyway.


Regards,
Achim.
-- 
+<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+

Wavetables for the Waldorf Blofeld:
http://Synth.Stromeko.net/Downloads.html#BlofeldUserWavetables

Re: Invalid function: org-babel-header-args-safe-fn in Melpa

[John Kitchin]

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It does happen anyway. I had that in to get around this issue a while ago
(long story, but it is why we still run 8.2.10), and I still get the issue
without it.

I think I have figured it out. The order the packages are installed is
important. The code below illustrates the issue for me. If I install
org-plus-contrib first, the issue goes away. Note the first thing the pydoc
package does is:

(require 'org), which I guess interferes with subsequent building of org.
(I am using GNU Emacs 25.1.50.1).

Also, you need to have (R . t) in there. that specifically triggers the
error.


(setq user-emacs-directory "./sandbox/")

(require 'package)

(setq package-archives
      '(("org" . "http://orgmode.org/elpa/")
("gnu" . "http://elpa.gnu.org/packages/")
("melpa" . "http://melpa.org/packages/")))

(package-initialize)
(package-refresh-contents)


(package-install 'pydoc)
(package-install 'org-plus-contrib)


(org-babel-do-load-languages
 'org-babel-load-languages
 '((emacs-lisp . t)
   (R . t)
   ))


(message "done")


John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Sun, Feb 14, 2016 at 11:36 AM, Achim Gratz <Stromeko@nexgo.de> wrote:

> Aaron Ecay writes:
> > This looks like the kind of problem that results when org is
> byte-compiled
> > in an emacs with a different version of org loaded.  This used to be a
> > problem when installing via package.el (and not just for org), but I
> think
> > there has been some work put into making sure it doesn’t happen any more.
> > (I know emacs developers were discussing them and then they seemed to go
> > away so I assumed they were fixed...it’s possible I was mistaken though.)
>
> No, this is bug #10125 and the others that it was merged with (most
> recently #21267, with the exact same error message as John got).
>
> > If I had to guess, I’d say that line 63 of packages.el in your jmax
> > setup defeats these fixes.  Try commenting it out.  It should not be
> > necessary to manually byte-compile packages: package.el should do that
> > for you.  And in this case, I hypothesize that it is actually harmful.
>
> Yes it is.  Although I'd venture to guess that it would have happened
> anyway.
>
>
> Regards,
> Achim.
> --
> +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+
>
> Wavetables for the Waldorf Blofeld:
> http://Synth.Stromeko.net/Downloads.html#BlofeldUserWavetables
>
>
>

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