trouble exporting just one subtree while using babel and R code blocks

trouble exporting just one subtree while using babel and R code blocks

[Christopher W. Ryan]

I have a long cumulative org file that contains work related to a series
of studies. Each first-level subtree (*) is a new study. I need to be
able to export any given first-level tree on its own, with an output pdf
file name different from the main org filename, and with a title perhaps
different from the * headline. And I need to execute R code as it
exports. I am running org-mode 7.7 on Windows XP

A sample org file to illustrate the problem looks like this:

------------------------------------------

* goodbye

foo foo

* Hello
:PROPERTIES:
:EXPORT_FILE_NAME: TestMyBabelSetup
:EXPORT_TITLE: foobar
:EXPORT_AUTHOR: Christopher W. Ryan, MD MS
:RESULTS: output
:EXPORTS: both
:END:

foo

#+begin_src R
rnorm(3)
#+end_src


--------------------------------------------

When I export the whole file to pdf, everything works fine.

But if I try to export just the * Hello tree, then I get an error:

 Args out of range: "", -1, 0

If I remove anything relating to R and babel from the * Hello tree,
leaving just this:

-----------------------------------------------
* goodbye

foo foo

* Hello
:PROPERTIES:
:EXPORT_FILE_NAME: TestMyBabelSetup
:EXPORT_TITLE: foobar
:EXPORT_AUTHOR: Christopher W. Ryan, MD MS
:END:

foo

-------------------------------------------------

then exporting just the * Hello treee works as expected.

I'm stumped. What am I doing wrong?

Thanks.

--Chris
-- 
Christopher W. Ryan, MD, MS
SUNY Upstate Medical University Clinical Campus at Binghamton
425 Robinson Street, Binghamton, NY  13904
cryanatbinghamtondotedu

"Once we recognize that we do not err out of laziness, stupidity, or
evil intent, we can liberate ourselves from the impossible burden of
trying to be permanently right. We can take seriously the proposition
that we could be in error, without deeming ourselves idiotic or
unworthy." [Karen Schulz, in Being Wrong: Adventures in the Margin of Error]

Re: trouble exporting just one subtree while using babel and R code blocks

[John Hendy]

[-- Attachment #1: Type: text/plain, Size: 2381 bytes --]

On Mon, Feb 18, 2013 at 3:10 PM, Christopher W. Ryan
<cryan@binghamton.edu> wrote:
> I have a long cumulative org file that contains work related to a series
> of studies. Each first-level subtree (*) is a new study. I need to be
> able to export any given first-level tree on its own, with an output pdf
> file name different from the main org filename, and with a title perhaps
> different from the * headline. And I need to execute R code as it
> exports. I am running org-mode 7.7 on Windows XP
>
> A sample org file to illustrate the problem looks like this:
>
> ------------------------------------------
>
> * goodbye
>
> foo foo
>
> * Hello
> :PROPERTIES:
> :EXPORT_FILE_NAME: TestMyBabelSetup
> :EXPORT_TITLE: foobar
> :EXPORT_AUTHOR: Christopher W. Ryan, MD MS
> :RESULTS: output
> :EXPORTS: both
> :END:
>
> foo
>
> #+begin_src R
> rnorm(3)
> #+end_src
>
>
> --------------------------------------------
>
> When I export the whole file to pdf, everything works fine.
>
> But if I try to export just the * Hello tree, then I get an error:
>
>  Args out of range: "", -1, 0

I can't reproduce. =M-x org-version= is Org-mode version 7.9.3e
(7.9.3e-910-g33c4f6)

Can you try updating your orgmode version?

I attached the results of =C-c C-e 1 p= (export subtree) with the
cursor within the * Hello headline contents.


Best regards,
John

>
> If I remove anything relating to R and babel from the * Hello tree,
> leaving just this:
>
> -----------------------------------------------
> * goodbye
>
> foo foo
>
> * Hello
> :PROPERTIES:
> :EXPORT_FILE_NAME: TestMyBabelSetup
> :EXPORT_TITLE: foobar
> :EXPORT_AUTHOR: Christopher W. Ryan, MD MS
> :END:
>
> foo
>
> -------------------------------------------------
>
> then exporting just the * Hello treee works as expected.
>
> I'm stumped. What am I doing wrong?
>
> Thanks.
>
> --Chris
> --
> Christopher W. Ryan, MD, MS
> SUNY Upstate Medical University Clinical Campus at Binghamton
> 425 Robinson Street, Binghamton, NY  13904
> cryanatbinghamtondotedu
>
> "Once we recognize that we do not err out of laziness, stupidity, or
> evil intent, we can liberate ourselves from the impossible burden of
> trying to be permanently right. We can take seriously the proposition
> that we could be in error, without deeming ourselves idiotic or
> unworthy." [Karen Schulz, in Being Wrong: Adventures in the Margin of Error]
>
>

[-- Attachment #2: TestMyBabelSetup.pdf --]
[-- Type: application/pdf, Size: 68302 bytes --]

Re: trouble exporting just one subtree while using babel and R code blocks

[Christopher W. Ryan]

Thanks John. I was a little nervous about upgrading org version. I use
Vince Goulet's version of emacs with ESS built-in, and he removed
org-mode from his latest release (24.2.1)

http://vgoulet.act.ulaval.ca/pub/emacs/NEWS-windows

But I downloaded and installed the newer emacs anyway, and got org-mode
version 7.9.3f from the org website, and that solved my problem. So far,
so good . . . .

--Chris

Christopher W. Ryan, MD, MS
SUNY Upstate Medical University Clinical Campus at Binghamton
425 Robinson Street, Binghamton, NY  13904
cryanatbinghamtondotedu

"Once we recognize that we do not err out of laziness, stupidity, or
evil intent, we can liberate ourselves from the impossible burden of
trying to be permanently right. We can take seriously the proposition
that we could be in error, without deeming ourselves idiotic or
unworthy." [Karen Schulz, in Being Wrong: Adventures in the Margin of Error]


John Hendy wrote:
> On Mon, Feb 18, 2013 at 3:10 PM, Christopher W. Ryan
> <cryan@binghamton.edu> wrote:
>> I have a long cumulative org file that contains work related to a series
>> of studies. Each first-level subtree (*) is a new study. I need to be
>> able to export any given first-level tree on its own, with an output pdf
>> file name different from the main org filename, and with a title perhaps
>> different from the * headline. And I need to execute R code as it
>> exports. I am running org-mode 7.7 on Windows XP
>>
>> A sample org file to illustrate the problem looks like this:
>>
>> ------------------------------------------
>>
>> * goodbye
>>
>> foo foo
>>
>> * Hello
>> :PROPERTIES:
>> :EXPORT_FILE_NAME: TestMyBabelSetup
>> :EXPORT_TITLE: foobar
>> :EXPORT_AUTHOR: Christopher W. Ryan, MD MS
>> :RESULTS: output
>> :EXPORTS: both
>> :END:
>>
>> foo
>>
>> #+begin_src R
>> rnorm(3)
>> #+end_src
>>
>>
>> --------------------------------------------
>>
>> When I export the whole file to pdf, everything works fine.
>>
>> But if I try to export just the * Hello tree, then I get an error:
>>
>>  Args out of range: "", -1, 0
> 
> I can't reproduce. =M-x org-version= is Org-mode version 7.9.3e
> (7.9.3e-910-g33c4f6)
> 
> Can you try updating your orgmode version?
> 
> I attached the results of =C-c C-e 1 p= (export subtree) with the
> cursor within the * Hello headline contents.
> 
> 
> Best regards,
> John
> 
>>
>> If I remove anything relating to R and babel from the * Hello tree,
>> leaving just this:
>>
>> -----------------------------------------------
>> * goodbye
>>
>> foo foo
>>
>> * Hello
>> :PROPERTIES:
>> :EXPORT_FILE_NAME: TestMyBabelSetup
>> :EXPORT_TITLE: foobar
>> :EXPORT_AUTHOR: Christopher W. Ryan, MD MS
>> :END:
>>
>> foo
>>
>> -------------------------------------------------
>>
>> then exporting just the * Hello treee works as expected.
>>
>> I'm stumped. What am I doing wrong?
>>
>> Thanks.
>>
>> --Chris
>> --
>> Christopher W. Ryan, MD, MS
>> SUNY Upstate Medical University Clinical Campus at Binghamton
>> 425 Robinson Street, Binghamton, NY  13904
>> cryanatbinghamtondotedu
>>

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Christopher W. Ryan]

Well, with the little test file I initially posted, things worked OK
with org version 7.9.3f.  But things are bit more complicated:

-----------------------------------

* goodbye

foo foo

* Hello
:PROPERTIES:
:EXPORT_FILE_NAME: TestMyBabelSetup
:EXPORT_TITLE: foobar
:EXPORT_AUTHOR: Christopher W. Ryan, MD MS
:RESULTS: output
:EXPORTS: both
:END:

** Big foo

foo

#+begin_src R
rnorm(3)
#+end_src

-----------------------------------

Put cursor on
* Hello
above and then C-c C-e 1 d
The resulting pdf file does not show the results of the R code, only the
verbatim code itself.

Remove the line
** Big foo

Then put cursor on * Hello above and then C-c C-e 1 d
org/babel then asks if I want to execute the R code. Answer yes.
A pdf file will open showing the R code and the results.

I don't understand.

--Chris

Christopher W. Ryan, MD, MS
SUNY Upstate Medical University Clinical Campus at Binghamton
425 Robinson Street, Binghamton, NY  13904
cryanatbinghamtondotedu

"Once we recognize that we do not err out of laziness, stupidity, or
evil intent, we can liberate ourselves from the impossible burden of
trying to be permanently right. We can take seriously the proposition
that we could be in error, without deeming ourselves idiotic or
unworthy." [Karen Schulz, in Being Wrong: Adventures in the Margin of Error]


John Hendy wrote:
> On Mon, Feb 18, 2013 at 3:10 PM, Christopher W. Ryan
> <cryan@binghamton.edu> wrote:
>> I have a long cumulative org file that contains work related to a series
>> of studies. Each first-level subtree (*) is a new study. I need to be
>> able to export any given first-level tree on its own, with an output pdf
>> file name different from the main org filename, and with a title perhaps
>> different from the * headline. And I need to execute R code as it
>> exports. I am running org-mode 7.7 on Windows XP
>>
>> A sample org file to illustrate the problem looks like this:
>>
>> ------------------------------------------
>>
>> * goodbye
>>
>> foo foo
>>
>> * Hello
>> :PROPERTIES:
>> :EXPORT_FILE_NAME: TestMyBabelSetup
>> :EXPORT_TITLE: foobar
>> :EXPORT_AUTHOR: Christopher W. Ryan, MD MS
>> :RESULTS: output
>> :EXPORTS: both
>> :END:
>>
>> foo
>>
>> #+begin_src R
>> rnorm(3)
>> #+end_src
>>
>>
>> --------------------------------------------
>>
>> When I export the whole file to pdf, everything works fine.
>>
>> But if I try to export just the * Hello tree, then I get an error:
>>
>>  Args out of range: "", -1, 0
> 
> I can't reproduce. =M-x org-version= is Org-mode version 7.9.3e
> (7.9.3e-910-g33c4f6)
> 
> Can you try updating your orgmode version?
> 
> I attached the results of =C-c C-e 1 p= (export subtree) with the
> cursor within the * Hello headline contents.
> 
> 
> Best regards,
> John
> 
>>
>> If I remove anything relating to R and babel from the * Hello tree,
>> leaving just this:
>>
>> -----------------------------------------------
>> * goodbye
>>
>> foo foo
>>
>> * Hello
>> :PROPERTIES:
>> :EXPORT_FILE_NAME: TestMyBabelSetup
>> :EXPORT_TITLE: foobar
>> :EXPORT_AUTHOR: Christopher W. Ryan, MD MS
>> :END:
>>
>> foo
>>
>> -------------------------------------------------
>>
>> then exporting just the * Hello treee works as expected.
>>
>> I'm stumped. What am I doing wrong?
>>
>> Thanks.
>>
>> --Chris
>> --
>> Christopher W. Ryan, MD, MS
>> SUNY Upstate Medical University Clinical Campus at Binghamton
>> 425 Robinson Street, Binghamton, NY  13904
>> cryanatbinghamtondotedu
>>
>> "Once we recognize that we do not err out of laziness, stupidity, or
>> evil intent, we can liberate ourselves from the impossible burden of
>> trying to be permanently right. We can take seriously the proposition
>> that we could be in error, without deeming ourselves idiotic or
>> unworthy." [Karen Schulz, in Being Wrong: Adventures in the Margin of Error]
>>
>>

Re: trouble exporting just one subtree while using babel and R code blocks

[John Hendy]

On Wed, Mar 6, 2013 at 1:33 PM, Christopher W. Ryan
<cryan@binghamton.edu> wrote:
> Thanks John. I was a little nervous about upgrading org version. I use
> Vince Goulet's version of emacs with ESS built-in, and he removed
> org-mode from his latest release (24.2.1)
>
> http://vgoulet.act.ulaval.ca/pub/emacs/NEWS-windows
>
> But I downloaded and installed the newer emacs anyway, and got org-mode
> version 7.9.3f from the org website, and that solved my problem. So far,
> so good . . . .

Yay! Glad things worked for you.

John

>
> --Chris
>
> Christopher W. Ryan, MD, MS
> SUNY Upstate Medical University Clinical Campus at Binghamton
> 425 Robinson Street, Binghamton, NY  13904
> cryanatbinghamtondotedu
>
> "Once we recognize that we do not err out of laziness, stupidity, or
> evil intent, we can liberate ourselves from the impossible burden of
> trying to be permanently right. We can take seriously the proposition
> that we could be in error, without deeming ourselves idiotic or
> unworthy." [Karen Schulz, in Being Wrong: Adventures in the Margin of Error]
>
>
> John Hendy wrote:
>> On Mon, Feb 18, 2013 at 3:10 PM, Christopher W. Ryan
>> <cryan@binghamton.edu> wrote:
>>> I have a long cumulative org file that contains work related to a series
>>> of studies. Each first-level subtree (*) is a new study. I need to be
>>> able to export any given first-level tree on its own, with an output pdf
>>> file name different from the main org filename, and with a title perhaps
>>> different from the * headline. And I need to execute R code as it
>>> exports. I am running org-mode 7.7 on Windows XP
>>>
>>> A sample org file to illustrate the problem looks like this:
>>>
>>> ------------------------------------------
>>>
>>> * goodbye
>>>
>>> foo foo
>>>
>>> * Hello
>>> :PROPERTIES:
>>> :EXPORT_FILE_NAME: TestMyBabelSetup
>>> :EXPORT_TITLE: foobar
>>> :EXPORT_AUTHOR: Christopher W. Ryan, MD MS
>>> :RESULTS: output
>>> :EXPORTS: both
>>> :END:
>>>
>>> foo
>>>
>>> #+begin_src R
>>> rnorm(3)
>>> #+end_src
>>>
>>>
>>> --------------------------------------------
>>>
>>> When I export the whole file to pdf, everything works fine.
>>>
>>> But if I try to export just the * Hello tree, then I get an error:
>>>
>>>  Args out of range: "", -1, 0
>>
>> I can't reproduce. =M-x org-version= is Org-mode version 7.9.3e
>> (7.9.3e-910-g33c4f6)
>>
>> Can you try updating your orgmode version?
>>
>> I attached the results of =C-c C-e 1 p= (export subtree) with the
>> cursor within the * Hello headline contents.
>>
>>
>> Best regards,
>> John
>>
>>>
>>> If I remove anything relating to R and babel from the * Hello tree,
>>> leaving just this:
>>>
>>> -----------------------------------------------
>>> * goodbye
>>>
>>> foo foo
>>>
>>> * Hello
>>> :PROPERTIES:
>>> :EXPORT_FILE_NAME: TestMyBabelSetup
>>> :EXPORT_TITLE: foobar
>>> :EXPORT_AUTHOR: Christopher W. Ryan, MD MS
>>> :END:
>>>
>>> foo
>>>
>>> -------------------------------------------------
>>>
>>> then exporting just the * Hello treee works as expected.
>>>
>>> I'm stumped. What am I doing wrong?
>>>
>>> Thanks.
>>>
>>> --Chris
>>> --
>>> Christopher W. Ryan, MD, MS
>>> SUNY Upstate Medical University Clinical Campus at Binghamton
>>> 425 Robinson Street, Binghamton, NY  13904
>>> cryanatbinghamtondotedu
>>>

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Eric S Fraga]

"Christopher W. Ryan" <cryan@binghamton.edu> writes:

> Well, with the little test file I initially posted, things worked OK
> with org version 7.9.3f.  But things are bit more complicated:

[...]

> Put cursor on
> * Hello
> above and then C-c C-e 1 d

Are you sure you are using the new exporter?  This binding doesn't work
for me but did work for the old exporter.  The equivalent in the new
exporter would be C-c C-e C-s l o, I believe.  Your configuration must
be mixing up old and new exporters and, believe me, you're not the only
one in this situation.


-- 
: Eric S Fraga, GnuPG: 0xC89193D8FFFCF67D
: in Emacs 24.3.50.1 and Org release_7.9.3f-1199-g3a0e55

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Christopher W Ryan]

I have to admit I'm not yet experienced enough with org mode to know
about the new exporter versus the old. I've been trying to ignore the
conversations on the list about the new exporter, since, at least
until now, whatever org mode was doing was what I needed it to do.

I have org mode 7.9.3f. Does that mean I am using any particular
exporter?  How do I tell which exporter I am using with C-c C-e d ?

I will try  C-c C-e C-s l o with my little test file next time I am on
the Windows system where I am having the problem.

Thanks.

--Chris

On Thu, Mar 7, 2013 at 3:42 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
> "Christopher W. Ryan" <cryan@binghamton.edu> writes:
>
>> Well, with the little test file I initially posted, things worked OK
>> with org version 7.9.3f.  But things are bit more complicated:
>
> [...]
>
>> Put cursor on
>> * Hello
>> above and then C-c C-e 1 d
>
> Are you sure you are using the new exporter?  This binding doesn't work
> for me but did work for the old exporter.  The equivalent in the new
> exporter would be C-c C-e C-s l o, I believe.  Your configuration must
> be mixing up old and new exporters and, believe me, you're not the only
> one in this situation.
>
>
> --
> : Eric S Fraga, GnuPG: 0xC89193D8FFFCF67D
> : in Emacs 24.3.50.1 and Org release_7.9.3f-1199-g3a0e55
>

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Eric S Fraga]

Christopher W Ryan <cryan@binghamton.edu> writes:

> I have to admit I'm not yet experienced enough with org mode to know
> about the new exporter versus the old. I've been trying to ignore the
> conversations on the list about the new exporter, since, at least
> until now, whatever org mode was doing was what I needed it to do.
>
> I have org mode 7.9.3f. Does that mean I am using any particular
> exporter?  How do I tell which exporter I am using with C-c C-e d ?

I believe that, if you are using 7.9.3f, you should be using the new
exporter.  However, the key bindings you mentioned in the previous
posting indicated that you were accessing the old exporter.  This may
mean that you have a confused configuration (easy to do at the moment
due to the transition taking place between old and new exporters).

One way to find out what you are using is to check what C-c C-e is bound
to: C-h c C-c C-e.  If this says org-export-dispatch, it is the new
one.  The old one, I believe, was bound to org-export alone.  The former
gives a two level selection mechanism (e.g. you choose l for LaTeX first
and then another letter for actual target for the export, e.g. tex vs
pdf).  The latter uses only one letter to accomplish both selections.

I hope this makes sense.
-- 
: Eric S Fraga, GnuPG: 0xC89193D8FFFCF67D
: in Emacs 24.3.50.1 and Org release_7.9.3f-1199-g3a0e55

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[John Hendy]

[-- Attachment #1: Type: text/plain, Size: 1632 bytes --]

On Thu, Mar 7, 2013 at 7:13 AM, Christopher W Ryan <cryan@binghamton.edu> wrote:
> I have to admit I'm not yet experienced enough with org mode to know
> about the new exporter versus the old. I've been trying to ignore the
> conversations on the list about the new exporter, since, at least
> until now, whatever org mode was doing was what I needed it to do.
>
> I have org mode 7.9.3f. Does that mean I am using any particular
> exporter?  How do I tell which exporter I am using with C-c C-e d ?
>
> I will try  C-c C-e C-s l o with my little test file next time I am on
> the Windows system where I am having the problem.
>

Cursor on * Hello, C-c C-e p and I get the attached (seems to work).
Have not removed ** Big foo. I'm using the old exporter.

Can you post your babel-related .emacs section?

John

> Thanks.
>
> --Chris
>
> On Thu, Mar 7, 2013 at 3:42 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
>> "Christopher W. Ryan" <cryan@binghamton.edu> writes:
>>
>>> Well, with the little test file I initially posted, things worked OK
>>> with org version 7.9.3f.  But things are bit more complicated:
>>
>> [...]
>>
>>> Put cursor on
>>> * Hello
>>> above and then C-c C-e 1 d
>>
>> Are you sure you are using the new exporter?  This binding doesn't work
>> for me but did work for the old exporter.  The equivalent in the new
>> exporter would be C-c C-e C-s l o, I believe.  Your configuration must
>> be mixing up old and new exporters and, believe me, you're not the only
>> one in this situation.
>>
>>
>> --
>> : Eric S Fraga, GnuPG: 0xC89193D8FFFCF67D
>> : in Emacs 24.3.50.1 and Org release_7.9.3f-1199-g3a0e55
>>
>

[-- Attachment #2: test.pdf --]
[-- Type: application/pdf, Size: 95727 bytes --]

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Christopher W Ryan]

Thanks John.  I will post the babel-related part of my .emacs when I
am back at the office, on the computer in question.

Could you try exporting just the * Hello subtree with C-c C-e 1 p ?
That's where I am experiencing the trouble, rather than with exporting
the whole document with C-c C-e p.

--Chris

On Thu, Mar 7, 2013 at 10:00 AM, John Hendy <jw.hendy@gmail.com> wrote:
> On Thu, Mar 7, 2013 at 7:13 AM, Christopher W Ryan <cryan@binghamton.edu> wrote:
>> I have to admit I'm not yet experienced enough with org mode to know
>> about the new exporter versus the old. I've been trying to ignore the
>> conversations on the list about the new exporter, since, at least
>> until now, whatever org mode was doing was what I needed it to do.
>>
>> I have org mode 7.9.3f. Does that mean I am using any particular
>> exporter?  How do I tell which exporter I am using with C-c C-e d ?
>>
>> I will try  C-c C-e C-s l o with my little test file next time I am on
>> the Windows system where I am having the problem.
>>
>
> Cursor on * Hello, C-c C-e p and I get the attached (seems to work).
> Have not removed ** Big foo. I'm using the old exporter.
>
> Can you post your babel-related .emacs section?
>
> John
>
>> Thanks.
>>
>> --Chris
>>
>> On Thu, Mar 7, 2013 at 3:42 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
>>> "Christopher W. Ryan" <cryan@binghamton.edu> writes:
>>>
>>>> Well, with the little test file I initially posted, things worked OK
>>>> with org version 7.9.3f.  But things are bit more complicated:
>>>
>>> [...]
>>>
>>>> Put cursor on
>>>> * Hello
>>>> above and then C-c C-e 1 d
>>>
>>> Are you sure you are using the new exporter?  This binding doesn't work
>>> for me but did work for the old exporter.  The equivalent in the new
>>> exporter would be C-c C-e C-s l o, I believe.  Your configuration must
>>> be mixing up old and new exporters and, believe me, you're not the only
>>> one in this situation.
>>>
>>>
>>> --
>>> : Eric S Fraga, GnuPG: 0xC89193D8FFFCF67D
>>> : in Emacs 24.3.50.1 and Org release_7.9.3f-1199-g3a0e55
>>>
>>

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[John Hendy]

On Thu, Mar 7, 2013 at 9:54 AM, Christopher W Ryan <cryan@binghamton.edu> wrote:
> Thanks John.  I will post the babel-related part of my .emacs when I
> am back at the office, on the computer in question.
>
> Could you try exporting just the * Hello subtree with C-c C-e 1 p ?
> That's where I am experiencing the trouble, rather than with exporting
> the whole document with C-c C-e p.

Yikes, and duh. I completely forgot the whole point. I do *not* get
the right behavior! Odd, as I thought I had been with your original
post. I'm on 7.9.3e.

C-c C-e is bound to =org-export= for me (old exporter).


John

>
> --Chris
>
> On Thu, Mar 7, 2013 at 10:00 AM, John Hendy <jw.hendy@gmail.com> wrote:
>> On Thu, Mar 7, 2013 at 7:13 AM, Christopher W Ryan <cryan@binghamton.edu> wrote:
>>> I have to admit I'm not yet experienced enough with org mode to know
>>> about the new exporter versus the old. I've been trying to ignore the
>>> conversations on the list about the new exporter, since, at least
>>> until now, whatever org mode was doing was what I needed it to do.
>>>
>>> I have org mode 7.9.3f. Does that mean I am using any particular
>>> exporter?  How do I tell which exporter I am using with C-c C-e d ?
>>>
>>> I will try  C-c C-e C-s l o with my little test file next time I am on
>>> the Windows system where I am having the problem.
>>>
>>
>> Cursor on * Hello, C-c C-e p and I get the attached (seems to work).
>> Have not removed ** Big foo. I'm using the old exporter.
>>
>> Can you post your babel-related .emacs section?
>>
>> John
>>
>>> Thanks.
>>>
>>> --Chris
>>>
>>> On Thu, Mar 7, 2013 at 3:42 AM, Eric S Fraga <e.fraga@ucl.ac.uk> wrote:
>>>> "Christopher W. Ryan" <cryan@binghamton.edu> writes:
>>>>
>>>>> Well, with the little test file I initially posted, things worked OK
>>>>> with org version 7.9.3f.  But things are bit more complicated:
>>>>
>>>> [...]
>>>>
>>>>> Put cursor on
>>>>> * Hello
>>>>> above and then C-c C-e 1 d
>>>>
>>>> Are you sure you are using the new exporter?  This binding doesn't work
>>>> for me but did work for the old exporter.  The equivalent in the new
>>>> exporter would be C-c C-e C-s l o, I believe.  Your configuration must
>>>> be mixing up old and new exporters and, believe me, you're not the only
>>>> one in this situation.
>>>>
>>>>
>>>> --
>>>> : Eric S Fraga, GnuPG: 0xC89193D8FFFCF67D
>>>> : in Emacs 24.3.50.1 and Org release_7.9.3f-1199-g3a0e55
>>>>
>>>

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Achim Gratz]

Eric S Fraga writes:
> I believe that, if you are using 7.9.3f, you should be using the new
> exporter.

The question to answer is whether he's using the maint or the master
branch.  I'd think the Op is using the 7.9.3f release, i.e. maint.

Bastien, I think it would make sense to clear up this confusion by
tagging 8dd2bfc291 with version 7.9.9 or 8.0-pre or something like that
(must be an annotated tag, of course).  That'll help to easier determine
who's using the new and the old exporter.


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

Factory and User Sound Singles for Waldorf Blofeld:
http://Synth.Stromeko.net/Downloads.html#WaldorfSounds

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Bastien]

Achim Gratz <Stromeko@nexgo.de> writes:

> Bastien, I think it would make sense to clear up this confusion by
> tagging 8dd2bfc291 with version 7.9.9 or 8.0-pre or something like that
> (must be an annotated tag, of course).  That'll help to easier determine
> who's using the new and the old exporter.

I used 8.0-pre -- thanks for the suggestion!

-- 
 Bastien

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Achim Gratz]

Bastien writes:
>> Bastien, I think it would make sense to clear up this confusion by
>> tagging 8dd2bfc291 with version 7.9.9 or 8.0-pre or something like that
>> (must be an annotated tag, of course).  That'll help to easier determine
>> who's using the new and the old exporter.
>
> I used 8.0-pre -- thanks for the suggestion!

Thanks, but you tagged a different commit.  The commit I named is the
one that moved the new exporter into core which I consider an important
milestone.  I suggest to add two extra annotated tags to account
correctly (in the way version-to-list numbers things) for the history
leading up to the 8.0 release:

8dd2bfc291 release_8.0-alpha (move the new exporter into core)
ee3b3eb421 release_8.0-beta  (remove /contrib/oldexp/)


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: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Bastien]

Hi Achim,

Achim Gratz <Stromeko@nexgo.de> writes:

> Thanks, but you tagged a different commit.  The commit I named is the
> one that moved the new exporter into core which I consider an important
> milestone.  I suggest to add two extra annotated tags to account
> correctly (in the way version-to-list numbers things) for the history
> leading up to the 8.0 release:
>
> 8dd2bfc291 release_8.0-alpha (move the new exporter into core)
> ee3b3eb421 release_8.0-beta  (remove /contrib/oldexp/)

Okay, please go ahead.

Thanks,

-- 
 Bastien

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Achim Gratz]

Bastien writes:
>> 8dd2bfc291 release_8.0-alpha (move the new exporter into core)
>> ee3b3eb421 release_8.0-beta  (remove /contrib/oldexp/)
>
> Okay, please go ahead.

Done.


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

SD adaptations for KORG EX-800 and Poly-800MkII V0.9:
http://Synth.Stromeko.net/Downloads.html#KorgSDada

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Bastien]

Achim Gratz <Stromeko@nexgo.de> writes:

> Bastien writes:
>>> 8dd2bfc291 release_8.0-alpha (move the new exporter into core)
>>> ee3b3eb421 release_8.0-beta  (remove /contrib/oldexp/)
>>
>> Okay, please go ahead.
>
> Done.

Thanks!

-- 
 Bastien

Re: trouble exporting just one subtree while using babel and R code blocks--spoke too soon

[Christopher W. Ryan]

OK< back at the office computer . . .

In org version 7.9.3f on Windows XP, my C-c C-e is bound to org-export.
I guess that's the old exporter.

The org-related parts of my  .eamcs are below. Clearly not the most
elegant .emacs file--I'm still pretty new at this!

----------------------------------------------

;; Load org-mode
(add-to-list 'load-path "c:/Org/org-7.9.3f/lisp")
(add-to-list 'load-path "c:/Org/org-7.9.3f/contrib/lisp")
(require 'org)

;; The following lines are always needed.  Choose your own keys.
(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
(add-hook 'org-mode-hook 'turn-on-font-lock) ; not needed when
global-font-lock-mode is on
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-ca" 'org-agenda)
(global-set-key "\C-cb" 'org-iswitchb)


;; Capture
(global-set-key (kbd "C-c r") 'org-capture)
 (setq org-default-notes-file (concat org-directory "/junknotes.org"))
 (setq org-capture-templates
      '(("t" "Agenda Todo" entry
	 (file+headline "c:/Org/junk1.org" "Agenda")
	 "\n\n** TODO %?\n%T\n\n%i\n%a\n\n\n"
	 :empty-lines 1)

	("n" "Agenda Notes" entry
	 (file "c:/Org/junk1.org")
	 "\n\n** %?\n%T\n%i\n%a\n\n\n"
	 :empty-lines 1)

       ("a" "admission" entry
        (file "c:/DATA/MedicalShelterAdmissions.org")
        "\n\n* IN  %^{LAST NAME, first name}
         %^{IDnumber}p %^{Birthdate}p %^{Age}p %^{Doctor1}p
         %^{Adress1}p %^{Address2}p %^{City}p
         %U"
         :empty-lines 1)
))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; set-up for use as a medical shelter record
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; I've attempted to remove redundancies with capture settings that
appear above this point

'(org-agenda-files (quote ("~/Shelter/ShelterAdmissions.org"
"~/DATA/BookIdeas.org" "~/orgjunk.org")))

(setq org-default-notes-file (concat  "~/notes.org"))

(defun prompt-for-lastname-and-upcase ()
 (upcase (read-string "Last name: ")))

(defun prompt-and-upcase (prompt-str)
  (upcase (read-string prompt-str)))

 (setq org-capture-templates
      '(("a" "Admit" entry
        (file "~/Shelter/ShelterAdmissions.org")
         "* admit  %(prompt-for-lastname-and-upcase),  %^{firstname}      %U
          :PROPERTIES:
          %^{IDnumber}p
          %^{Birthdate}p
          %^{Age}p
          %^{Sex}p
          %^{Address1}p
          %^{Address2}p
          %^{City}p
          %^{State}p
          %^{Zipcode}p
          %^{Doctor1}p
          %^{Doctor2}p
          %^{Pharmacy1}p
          %^{Pharmacy2}p"
          :empty-lines: 1)
          )
)


;; Insert immediate timestamp
(setq org-agenda-skip-additional-timestamps nil)
(define-key global-map (kbd "<f8>")
  '(lambda () (interactive)
              (when (eq major-mode 'org-mode)
                    (org-insert-time-stamp nil t t)
                    (insert "\n"))))



;;; This was installed by package-install.el.
;;; This provides support for the package system and
;;; interfacing with ELPA, the package archive.
;;; Move this code earlier if you want to reference
;;; packages in your .emacs.
(when
    (load
     (expand-file-name "~/.emacs.d/elpa/package.el"))
  (package-initialize))



(custom-set-variables
  ;; custom-set-variables was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 '(load-home-init-file t t)
 '(org-agenda-files (quote ("c:/DATA/MedicalShelterAdmissions.org"
"c:/DATA/SCHOLAR/HeatWaves/HeatWaves1.org")))
 '(org-inlinetask-export nil)
 '(sentence-end-double-space nil)
 '(show-paren-mode t)
 '(text-mode-hook (quote (text-mode-hook-identify)))
 '(transient-mark-mode t))
(custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 )


;;;;; bunch of cosmetic stuff in here: font, background color, etc


;; make ESS use the correct version of R
;; (setq inferior-R-program-name "c:/progra~1/R/R-2.14.1/bin/Rterm.exe")

;; active Babel languages
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)
   (python . t)
   (perl . t)
   ))

;; turn off auto-fill-mode
(auto-fill-mode 0)
(global-visual-line-mode -1)

(cd "C:/DATA/")

;; activate RefTex mode with org-mode
;; insert a citation with "C-c )"
(defun org-mode-reftex-setup ()
  (load-library "reftex")
  (and (buffer-file-name)
       (file-exists-p (buffer-file-name))
       (reftex-parse-all))
  (define-key org-mode-map (kbd "C-c )") 'reftex-citation))
(add-hook 'org-mode-hook 'org-mode-reftex-setup)

;; in org-mode, by default, long lines disappear into the right window
edge. If you prefer them wrapped, you can add this to your init file:

(add-hook 'org-mode-hook 'soft-wrap-lines)

(defun soft-wrap-lines ()
"Make lines wrap at window edge and on word boundary,
in current buffer."
(interactive)
(setq truncate-lines nil)
(setq word-wrap t)
)

;; show all todos in the current buffer with one key press
(global-set-key (kbd "<f9>") (lambda ()
			       (interactive)
			       (org-agenda nil "t" 'file)))

;; activate inline tasks
(require 'org-inlinetask)

;; override out-of-the-box ESS setting that makes
;; texi2pdf the default latex command
(setq ess-swv-pdflatex-commands '("pdflatex" "make"))
(put 'narrow-to-region 'disabled nil)

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; vvvvvv  custom code to make workflow for meeting minutes, agendas,
and action items vvvvvvvv
;; as in
;; http://orgmode.org/worg/org-tutorials/org-meeting-tasks.html
;;

(defcustom org-mactions-numbered-action-format "TODO Action #%d "
  "Default structure of the headling of a new action.
    %d will become the number of the action."
  :group 'org-edit-structure
  :type 'string)

(defcustom org-mactions-change-id-on-copy t
  "Non-nil means make new IDs in copied actions.
If an action copied with the command `org-mactions-collect-todos-in-subtree'
contains an ID, that ID will be replaced with a new one."
  :group 'org-edit-structure
  :type 'string)

(defun org-mactions-new-numbered-action (&optional inline)
  "Insert a new numbered action, using
`org-mactions-numbered-action-format'.
    With prefix argument, insert an inline task."
  (interactive "P")
  (let* ((num (let ((re "\\`#\\([0-9]+\\)\\'"))
                (1+ (apply 'max 0
                           (mapcar
                            (lambda (e)
                              (if (string-match re (car e))
                                  (string-to-number (match-string 1 (car
e)))
                                0))
                            (org-get-buffer-tags))))))
         (tag (concat "#" (number-to-string num))))
    (if inline
        (org-inlinetask-insert-task)
      (org-insert-heading 'force))
    (unless (eql (char-before) ?\ ) (insert " "))
    (insert (format org-mactions-numbered-action-format num))
    (org-toggle-tag tag 'on)
    (if (= (point-max) (point-at-bol))
        (save-excursion (goto-char (point-at-eol)) (insert "\n")))
    (unless (eql (char-before) ?\ ) (insert " "))))

(defun org-mactions-collect-todos-in-subtree ()
  "Collect all TODO items in the current subtree into a flat list."
  (interactive)
  (let ((buf (get-buffer-create "Org TODO Collect"))
        (cnt 0) beg end string s)
    (with-current-buffer buf (erase-buffer) (org-mode))
    (org-map-entries
     (lambda ()
       (setq beg (point) end (org-end-of-subtree t t) cnt (1+ cnt)
             string (buffer-substring beg end)
             s 0)
       (when org-mactions-change-id-on-copy
         (while (string-match "^\\([ \t]*:ID:\\)[ \t\n]+\\([^ \t\n]+\\)[
\t]*$"
                              string s)
           (setq s (match-end 1)
                 string (replace-match (concat "\\1 "
                                               (save-match-data
(org-id-new)))
                                       t nil string))))
       (with-current-buffer buf (org-paste-subtree 1 string)
                            (goto-char (point-max))))
     (format "TODO={%s}" (regexp-opt org-not-done-keywords))
     'tree)
    (if (= cnt 0)
        (message "No TODO items in subtree")
      (message "%d TODO entries copied to kill ring" cnt)
      (prog1 (with-current-buffer buf
               (kill-new (buffer-string)))
        (kill-buffer buf)))))
;;
;;
;;
;;
;; ^^^ end of custom code for workflow for meeting minutes, etc ^^^^

----------------------------------------------------

Christopher W. Ryan, MD, MS
SUNY Upstate Medical University Clinical Campus at Binghamton
425 Robinson Street, Binghamton, NY  13904
cryanatbinghamtondotedu

"Once we recognize that we do not err out of laziness, stupidity, or
evil intent, we can liberate ourselves from the impossible burden of
trying to be permanently right. We can take seriously the proposition
that we could be in error, without deeming ourselves idiotic or
unworthy." [Karen Schulz, in Being Wrong: Adventures in the Margin of Error]


Eric S Fraga wrote:
> Christopher W Ryan <cryan@binghamton.edu> writes:
> 
>> I have to admit I'm not yet experienced enough with org mode to know
>> about the new exporter versus the old. I've been trying to ignore the
>> conversations on the list about the new exporter, since, at least
>> until now, whatever org mode was doing was what I needed it to do.
>>
>> I have org mode 7.9.3f. Does that mean I am using any particular
>> exporter?  How do I tell which exporter I am using with C-c C-e d ?
> 
> I believe that, if you are using 7.9.3f, you should be using the new
> exporter.  However, the key bindings you mentioned in the previous
> posting indicated that you were accessing the old exporter.  This may
> mean that you have a confused configuration (easy to do at the moment
> due to the transition taking place between old and new exporters).
> 
> One way to find out what you are using is to check what C-c C-e is bound
> to: C-h c C-c C-e.  If this says org-export-dispatch, it is the new
> one.  The old one, I believe, was bound to org-export alone.  The former
> gives a two level selection mechanism (e.g. you choose l for LaTeX first
> and then another letter for actual target for the export, e.g. tex vs
> pdf).  The latter uses only one letter to accomplish both selections.
> 
> I hope this makes sense.