evaluating all R code blocks (newbie question)

evaluating all R code blocks (newbie question)

[Julian Burgos]

Dear list,

Hopefully this is not too basic, nor has been answered before.

I would like to know if there is away to have alll R code blocks in a
document evaluated automatically (i.e. without query) when exporting
to Latex.  Now I have to answer "yes" multiple times to the question
"Evaluate this R code block in your system" every time I do an export,
which is somewhat annoying.
Many thanks,

Julian

-- 
Julian Mariano Burgos
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian@hafro.is, jmburgos@uw.edu

Re: evaluating all R code blocks (newbie question)

[Lawrence Mitchell]

Julian Burgos wrote:
> Dear list,

> Hopefully this is not too basic, nor has been answered before.

> I would like to know if there is away to have alll R code blocks in a
> document evaluated automatically (i.e. without query) when exporting
> to Latex.  Now I have to answer "yes" multiple times to the question
> "Evaluate this R code block in your system" every time I do an export,
> which is somewhat annoying.

See the variable `org-confirm-babel-evaluate'.  Be careful about
unilaterally setting it to nil in case you receive org files with
code blocks from people you don't trust.

Cheers,
Lawrence
-- 
Lawrence Mitchell <wence@gmx.li>

Re: Re: evaluating all R code blocks (newbie question)

[Julian Burgos]

Many thanks Lawrence.  Yes, I´m aware of the risks, but for now I am
only working with my own files.
Do you know if it is possible to evaluation confirmation as a header
option, so I can left it on but turn it off in my own files?
Thanks again,

Julian

On Thu, Jan 20, 2011 at 3:38 PM, Lawrence Mitchell <wence@gmx.li> wrote:
> Julian Burgos wrote:
>> Dear list,
>
>> Hopefully this is not too basic, nor has been answered before.
>
>> I would like to know if there is away to have alll R code blocks in a
>> document evaluated automatically (i.e. without query) when exporting
>> to Latex.  Now I have to answer "yes" multiple times to the question
>> "Evaluate this R code block in your system" every time I do an export,
>> which is somewhat annoying.
>
> See the variable `org-confirm-babel-evaluate'.  Be careful about
> unilaterally setting it to nil in case you receive org files with
> code blocks from people you don't trust.
>
> Cheers,
> Lawrence
> --
> Lawrence Mitchell <wence@gmx.li>
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>



-- 
Julian Mariano Burgos
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian@hafro.is, jmburgos@uw.edu

Re: evaluating all R code blocks (newbie question)

[Lawrence Mitchell]

Julian Burgos wrote:
> Many thanks Lawrence.  Yes, I'm aware of the risks, but for now I am
> only working with my own files.
> Do you know if it is possible to evaluation confirmation as a header
> option, so I can left it on but turn it off in my own files?

I don't believe it is.  If you think about, this is also a
security hole, since a malicious user could put the relevant
header in, even if you've set org-confirm-babel-evaluate to t.

Cheers,
Lawrence

Re: Re: evaluating all R code blocks (newbie question)

[Julian Burgos]

Yes, you are right.  For now, I´ll turn confirmation off for R code
only, and keep an eye on .org files from unknown origins.
All the best,

Julian

On Thu, Jan 20, 2011 at 4:00 PM, Lawrence Mitchell <wence@gmx.li> wrote:
> Julian Burgos wrote:
>> Many thanks Lawrence.  Yes, I'm aware of the risks, but for now I am
>> only working with my own files.
>> Do you know if it is possible to evaluation confirmation as a header
>> option, so I can left it on but turn it off in my own files?
>
> I don't believe it is.  If you think about, this is also a
> security hole, since a malicious user could put the relevant
> header in, even if you've set org-confirm-babel-evaluate to t.
>
> Cheers,
> Lawrence
>
>
> _______________________________________________
> Emacs-orgmode mailing list
> Please use `Reply All' to send replies to the list.
> Emacs-orgmode@gnu.org
> http://lists.gnu.org/mailman/listinfo/emacs-orgmode
>



-- 
Julian Mariano Burgos
Hafrannsóknastofnunin/Marine Research Institute
Skúlagata 4, 121 Reykjavík, Iceland
Sími/Telephone : +354-5752037
Bréfsími/Telefax:  +354-5752001
Netfang/Email: julian@hafro.is, jmburgos@uw.edu

Re: Re: evaluating all R code blocks (newbie question)

[Eric Schulte]

Lawrence Mitchell <wence@gmx.li> writes:

> Julian Burgos wrote:
>> Many thanks Lawrence.  Yes, I'm aware of the risks, but for now I am
>> only working with my own files.
>> Do you know if it is possible to evaluation confirmation as a header
>> option, so I can left it on but turn it off in my own files?
>
> I don't believe it is.  If you think about, this is also a
> security hole, since a malicious user could put the relevant
> header in, even if you've set org-confirm-babel-evaluate to t.
>

Indeed this is the case, the :eval header argument [1] can be used
inhibit the evaluation of some code blocks, if the user already has

  (setq org-confirm-babel-evaluate nil)

but it can not be used to remove the need for confirmation of code block
evaluation when the user has

  (setq org-confirm-babel-evaluate t)

For security reasons.

Personally I don't require confirmation of evaluation as I find that I
both trust everyone sharing org-mode files with me, and generally I read
code blocks before I evaluate them.

Best -- Eric

Footnotes: 
[1]  http://orgmode.org/manual/eval.html

Re: evaluating all R code blocks (newbie question)

[Leo Alekseyev]

Julian Burgos <jmburgos <at> uw.edu> writes:

> 
> Dear list,
> 
> Hopefully this is not too basic, nor has been answered before.
> 
> I would like to know if there is away to have alll R code blocks in a
> document evaluated automatically (i.e. without query) when exporting
> to Latex.  Now I have to answer "yes" multiple times to the question
> "Evaluate this R code block in your system" every time I do an export,
> which is somewhat annoying.
> Many thanks,

I don't have experience w/ LaTeX export, but try this to turn off the "evaluate
this block?" prompt: (setq org-confirm-babel-evaluate nil)