[BUG] [babel] in :eval never with :session

[BUG] [babel] in :eval never with :session

[Rainer M Krug]

[-- Attachment #1: Type: text/plain, Size: 1509 bytes --]

The error is back:

When one header in a subtree which has the header argument 
:eval never
has the same name as in a following subtree which should be evaluated on
export, the second subtree is not exported. When the name of the header
is changed, the subtree is exported as expected.

--8<---------------cut here---------------start------------->8---
#+PROPERTY: exports both
#+PROPERTY: session *tmp_R*

* Some non-evaluated code
:PROPERTIES:
:eval:      never
:END:
** This is the same header
#+BEGIN_SRC R
cat("\ntwo\n")
#+END_SRC

* Data Assessment Results
** This is the same header
If the name of the header is changed, the subtree is evaluated on export.
#+begin_src R
cat("\nhere it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\n")
#+end_src
--8<---------------cut here---------------end--------------->8---
 
Org-mode version 8.2.6 (release_8.2.6-920-gc6d698 @ /Users/rainerkrug/.emacs.d/org-mode/lisp/)
GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0 AppKit 1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local

Cheers,

Rainer

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

[-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --]

Re: [BUG] [babel] in :eval never with :session

[Eric Schulte]

Rainer M Krug <Rainer@krugs.de> writes:

> The error is back:
>

You say "back", was this error not present recently?  If so could you
isolate the commit at which this error appeared?

Thanks,
Eric

>
> When one header in a subtree which has the header argument
> :eval never
> has the same name as in a following subtree which should be evaluated on
> export, the second subtree is not exported. When the name of the header
> is changed, the subtree is exported as expected.
>
> --8<---------------cut here---------------start------------->8---
> #+PROPERTY: exports both
> #+PROPERTY: session *tmp_R*
>
> * Some non-evaluated code
> :PROPERTIES:
> :eval:      never
> :END:
> ** This is the same header
> #+BEGIN_SRC R
> cat("\ntwo\n")
> #+END_SRC
>
> * Data Assessment Results
> ** This is the same header
> If the name of the header is changed, the subtree is evaluated on export.
> #+begin_src R
> cat("\nhere it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\n")
> #+end_src
> --8<---------------cut here---------------end--------------->8---
>  
> Org-mode version 8.2.6 (release_8.2.6-920-gc6d698 @ /Users/rainerkrug/.emacs.d/org-mode/lisp/)
> GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0 AppKit 1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
>
> Cheers,
>
> Rainer

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D

Re: [BUG] [babel] in :eval never with :session

[Rainer M Krug]

I reported it some time ago but couldn't reproduce it later, so I reported it fixed. Now I realized that the 'reproducible example' did not show the error as the header names were different. So I do not know if it is a new error, but I can check on Friday. 

Cheers,

Rainer

Envoyé de mon iPhone

> Le 7 mai 2014 à 11:19, Eric Schulte <schulte.eric@gmail.com> a écrit :
> 
> Rainer M Krug <Rainer@krugs.de> writes:
> 
>> The error is back:
> 
> You say "back", was this error not present recently?  If so could you
> isolate the commit at which this error appeared?
> 
> Thanks,
> Eric
> 
>> 
>> When one header in a subtree which has the header argument
>> :eval never
>> has the same name as in a following subtree which should be evaluated on
>> export, the second subtree is not exported. When the name of the header
>> is changed, the subtree is exported as expected.
>> 
>> --8<---------------cut here---------------start------------->8---
>> #+PROPERTY: exports both
>> #+PROPERTY: session *tmp_R*
>> 
>> * Some non-evaluated code
>> :PROPERTIES:
>> :eval:      never
>> :END:
>> ** This is the same header
>> #+BEGIN_SRC R
>> cat("\ntwo\n")
>> #+END_SRC
>> 
>> * Data Assessment Results
>> ** This is the same header
>> If the name of the header is changed, the subtree is evaluated on export.
>> #+begin_src R
>> cat("\nhere it is @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@\n")
>> #+end_src
>> --8<---------------cut here---------------end--------------->8---
>> 
>> Org-mode version 8.2.6 (release_8.2.6-920-gc6d698 @ /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>> GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0 AppKit 1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
>> 
>> Cheers,
>> 
>> Rainer
> 
> -- 
> Eric Schulte
> https://cs.unm.edu/~eschulte
> PGP: 0x614CA05D

Re: [BUG] [babel] in :eval never with :session

[Charles Berry]

Eric Schulte <schulte.eric <at> gmail.com> writes:

> 
> Rainer M Krug <Rainer <at> krugs.de> writes:
> 
> > The error is back:
> >
> 
> You say "back", was this error not present recently?  If so could you
> isolate the commit at which this error appeared?
> 

The bug seems to be in the use of

    (org-link-search heading) 

in org-babel-exp-in-export-file which is called in 
org-babel-exp-process-buffer. 

That search will find the first heading that is a match after 
(point-min). So it will mess up other header args, too.

It was there back in 8.0.7 and recent commits did not touch it AFAICS.

HTH,

Chuck

> Thanks,
> Eric
> 
> >
> > When one header in a subtree which has the header argument
> > :eval never
> > has the same name as in a following subtree which should be evaluated on
> > export, the second subtree is not exported. When the name of the header
> > is changed, the subtree is exported as expected.
> >
> > --8<---------------cut here---------------start------------->8---
> > #+PROPERTY: exports both
> > #+PROPERTY: session *tmp_R*
> >
> > * Some non-evaluated code
> > :PROPERTIES:
> > :eval:      never
> > :END:
> > ** This is the same header
> > #+BEGIN_SRC R
> > cat("\ntwo\n")
> > #+END_SRC
> >
> > * Data Assessment Results
> > ** This is the same header
> > If the name of the header is changed, the subtree is evaluated on export.
> > #+begin_src R
> > cat("\nhere it is  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>
 <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at> 
<at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>
 <at>  <at>  <at>  <at>  <at>  <at> \n")
> > #+end_src
> > --8<---------------cut here---------------end--------------->8---
> >  
> > Org-mode version 8.2.6 (release_8.2.6-920-gc6d698  <at> 
/Users/rainerkrug/.emacs.d/org-mode/lisp/)
> > GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0 AppKit
1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
> >
> > Cheers,
> >
> > Rainer
> 

Re: [BUG] [babel] in :eval never with :session

[Rainer M Krug]

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Charles Berry <ccberry@ucsd.edu> writes:

> Eric Schulte <schulte.eric <at> gmail.com> writes:
>
>> 
>> Rainer M Krug <Rainer <at> krugs.de> writes:
>> 
>> > The error is back:
>> >
>> 
>> You say "back", was this error not present recently?  If so could you
>> isolate the commit at which this error appeared?
>> 
>
> The bug seems to be in the use of
>
>     (org-link-search heading) 
>
> in org-babel-exp-in-export-file which is called in 
> org-babel-exp-process-buffer. 
>
> That search will find the first heading that is a match after 
> (point-min). So it will mess up other header args, too.
>
> It was there back in 8.0.7 and recent commits did not touch it AFAICS.

Org-mode version 7.9.3f (release_7.9.3f-17-g7524ef @
/usr/local/Cellar/emacs-mac/emacs-24.3-mac-4.6/share/emacs/24.3/lisp/org/)

as well. I don't think it makes sense to go further back. 

So no regression, but bug.

Cheers,

Rainer

>
> HTH,
>
> Chuck
>
>> Thanks,
>> Eric
>> 
>> >
>> > When one header in a subtree which has the header argument
>> > :eval never
>> > has the same name as in a following subtree which should be evaluated on
>> > export, the second subtree is not exported. When the name of the header
>> > is changed, the subtree is exported as expected.
>> >
>> > --8<---------------cut here---------------start------------->8---
>> > #+PROPERTY: exports both
>> > #+PROPERTY: session *tmp_R*
>> >
>> > * Some non-evaluated code
>> > :PROPERTIES:
>> > :eval:      never
>> > :END:
>> > ** This is the same header
>> > #+BEGIN_SRC R
>> > cat("\ntwo\n")
>> > #+END_SRC
>> >
>> > * Data Assessment Results
>> > ** This is the same header
>> > If the name of the header is changed, the subtree is evaluated on export.
>> > #+begin_src R
>> > cat("\nhere it is  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>
>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at> 
> <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>
>  <at>  <at>  <at>  <at>  <at>  <at> \n")
>> > #+end_src
>> > --8<---------------cut here---------------end--------------->8---
>> >  
>> > Org-mode version 8.2.6 (release_8.2.6-920-gc6d698  <at> 
> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>> > GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0 AppKit
> 1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
>> >
>> > Cheers,
>> >
>> > Rainer
>> 
>
>
>
>
>

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

[-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --]

Re: [BUG] [babel] in :eval never with :session

[Eric Schulte]

Rainer M Krug <Rainer@krugs.de> writes:

> Charles Berry <ccberry@ucsd.edu> writes:
>
>> Eric Schulte <schulte.eric <at> gmail.com> writes:
>>
>>> 
>>> Rainer M Krug <Rainer <at> krugs.de> writes:
>>> 
>>> > The error is back:
>>> >
>>> 
>>> You say "back", was this error not present recently?  If so could you
>>> isolate the commit at which this error appeared?
>>> 
>>
>> The bug seems to be in the use of
>>
>>     (org-link-search heading) 
>>
>> in org-babel-exp-in-export-file which is called in 
>> org-babel-exp-process-buffer. 
>>
>> That search will find the first heading that is a match after 
>> (point-min). So it will mess up other header args, too.
>>
>> It was there back in 8.0.7 and recent commits did not touch it AFAICS.
>
> Org-mode version 7.9.3f (release_7.9.3f-17-g7524ef @
> /usr/local/Cellar/emacs-mac/emacs-24.3-mac-4.6/share/emacs/24.3/lisp/org/)
>
> as well. I don't think it makes sense to go further back. 
>
> So no regression, but bug.
>

Thanks Charles for pointing out the use of `org-link-search' in
`org-babel-exp-in-export-file' as the source of the problem.  I'm not
sure there's a clear solution here.  Given that there may be a different
outline structure between the original and exported file (e.g., some
headlines may be present in the former and absent from the later), in
the presence of multiple headings with the same name there is no obvious
(to me) way to find a given heading from the exported file in the
original file.

I've just pushed up a change, so that when headings have IDs these will
be used instead of the heading text to find related heading in the
original buffer.  This should provide a workaround when multiple
headings with the same text are desired---just add IDs to all such
headings.

Best,

>
> Cheers,
>
> Rainer
>
>>
>> HTH,
>>
>> Chuck
>>
>>> Thanks,
>>> Eric
>>> 
>>> >
>>> > When one header in a subtree which has the header argument
>>> > :eval never
>>> > has the same name as in a following subtree which should be evaluated on
>>> > export, the second subtree is not exported. When the name of the header
>>> > is changed, the subtree is exported as expected.
>>> >
>>> > --8<---------------cut here---------------start------------->8---
>>> > #+PROPERTY: exports both
>>> > #+PROPERTY: session *tmp_R*
>>> >
>>> > * Some non-evaluated code
>>> > :PROPERTIES:
>>> > :eval:      never
>>> > :END:
>>> > ** This is the same header
>>> > #+BEGIN_SRC R
>>> > cat("\ntwo\n")
>>> > #+END_SRC
>>> >
>>> > * Data Assessment Results
>>> > ** This is the same header
>>> > If the name of the header is changed, the subtree is evaluated on export.
>>> > #+begin_src R
>>> > cat("\nhere it is  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>
>>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at> 
>> <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>
>>  <at>  <at>  <at>  <at>  <at>  <at> \n")
>>> > #+end_src
>>> > --8<---------------cut here---------------end--------------->8---
>>> >  
>>> > Org-mode version 8.2.6 (release_8.2.6-920-gc6d698  <at> 
>> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>>> > GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0 AppKit
>> 1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
>>> >
>>> > Cheers,
>>> >
>>> > Rainer
>>> 
>>
>>
>>
>>
>>

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D (see https://u.fsf.org/yw)

Re: [BUG] [babel] in :eval never with :session

[Rainer M Krug]

[-- Attachment #1: Type: text/plain, Size: 4165 bytes --]

Eric Schulte <schulte.eric@gmail.com> writes:

> Rainer M Krug <Rainer@krugs.de> writes:
>
>> Charles Berry <ccberry@ucsd.edu> writes:
>>
>>> Eric Schulte <schulte.eric <at> gmail.com> writes:
>>>
>>>> 
>>>> Rainer M Krug <Rainer <at> krugs.de> writes:
>>>> 
>>>> > The error is back:
>>>> >
>>>> 
>>>> You say "back", was this error not present recently?  If so could you
>>>> isolate the commit at which this error appeared?
>>>> 
>>>
>>> The bug seems to be in the use of
>>>
>>>     (org-link-search heading) 
>>>
>>> in org-babel-exp-in-export-file which is called in 
>>> org-babel-exp-process-buffer. 
>>>
>>> That search will find the first heading that is a match after 
>>> (point-min). So it will mess up other header args, too.
>>>
>>> It was there back in 8.0.7 and recent commits did not touch it AFAICS.
>>
>> Org-mode version 7.9.3f (release_7.9.3f-17-g7524ef @
>> /usr/local/Cellar/emacs-mac/emacs-24.3-mac-4.6/share/emacs/24.3/lisp/org/)
>>
>> as well. I don't think it makes sense to go further back. 
>>
>> So no regression, but bug.
>>
>
> Thanks Charles for pointing out the use of `org-link-search' in
> `org-babel-exp-in-export-file' as the source of the problem.  I'm not
> sure there's a clear solution here.  Given that there may be a different
> outline structure between the original and exported file (e.g., some
> headlines may be present in the former and absent from the later), in
> the presence of multiple headings with the same name there is no obvious
> (to me) way to find a given heading from the exported file in the
> original file.
>
> I've just pushed up a change, so that when headings have IDs these will
> be used instead of the heading text to find related heading in the
> original buffer.  This should provide a workaround when multiple
> headings with the same text are desired---just add IDs to all such
> headings.

Sounds great - thanks. This leaves just one question: is there a way of
automatically creating IDs for new headers?

Thanks,

Rainer


>
> Best,
>
>>
>> Cheers,
>>
>> Rainer
>>
>>>
>>> HTH,
>>>
>>> Chuck
>>>
>>>> Thanks,
>>>> Eric
>>>> 
>>>> >
>>>> > When one header in a subtree which has the header argument
>>>> > :eval never
>>>> > has the same name as in a following subtree which should be evaluated on
>>>> > export, the second subtree is not exported. When the name of the header
>>>> > is changed, the subtree is exported as expected.
>>>> >
>>>> > --8<---------------cut here---------------start------------->8---
>>>> > #+PROPERTY: exports both
>>>> > #+PROPERTY: session *tmp_R*
>>>> >
>>>> > * Some non-evaluated code
>>>> > :PROPERTIES:
>>>> > :eval:      never
>>>> > :END:
>>>> > ** This is the same header
>>>> > #+BEGIN_SRC R
>>>> > cat("\ntwo\n")
>>>> > #+END_SRC
>>>> >
>>>> > * Data Assessment Results
>>>> > ** This is the same header
>>>> > If the name of the header is changed, the subtree is evaluated on export.
>>>> > #+begin_src R
>>>> > cat("\nhere it is  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>
>>>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at> 
>>> <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>  <at>
>>>  <at>  <at>  <at>  <at>  <at>  <at> \n")
>>>> > #+end_src
>>>> > --8<---------------cut here---------------end--------------->8---
>>>> >  
>>>> > Org-mode version 8.2.6 (release_8.2.6-920-gc6d698  <at> 
>>> /Users/rainerkrug/.emacs.d/org-mode/lisp/)
>>>> > GNU Emacs 24.3.1 (x86_64-apple-darwin13.0.0, Carbon Version 1.6.0 AppKit
>>> 1265) of 2014-02-13 on Rainers-MacBook-Pro-2.local
>>>> >
>>>> > Cheers,
>>>> >
>>>> > Rainer
>>>> 
>>>
>>>
>>>
>>>
>>>

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer@krugs.de

Skype:      RMkrug

PGP: 0x0F52F982

[-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --]