[Babel] R, multiple lines #+results, LaTeX-export

[Babel] R, multiple lines #+results, LaTeX-export

[Bernd Weiss]

Dear all,

While working on my presentation I came across the following two issues:

(1) If I execute the following code block (see "Before codeblock 
execution") which is followed by a headline or another codeblock, the 
results-block (see "After codeblock execution") interferes with the 
headline/codeblock/whatever.

(2) The results-block is complex insofar as it has multiple lines. If I 
choose "export as LaTeX and process to PDF" (I corrected the wrong 
#+end_example line manually), the resulting PDF file only shows the code 
but not the results. However, this behaviour is only related to my 
meta-analysis example. If I use, for example, summary(lm(rnorm(100)~1)), 
the resulting PDF file shows code + results.

I am using Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)

Thanks for your help,

Bernd


------- Before codeblock execution ---------

#+BEGIN_SRC R  :results output :exports both
library(meta)
data(Fleiss93)
meta1 <- metabin(event.e, n.e, event.c, n.c, data=Fleiss93, sm="RR", 
meth="I")
summary(meta1)
#+END_SRC



* new headline

------- Before codeblock execution ---------



------- After codeblock execution ---------

#+BEGIN_SRC R  :results output :exports both
library(meta)
data(Fleiss93)
meta1 <- metabin(event.e, n.e, event.c, n.c, data=Fleiss93, sm="RR", 
meth="I")
summary(meta1)
#+END_SRC

#+results:
#+begin_example
load meta:  d:/programme/R/library ...
Number of trials combined: 7

                          RR            95%-CI       z  p.value
Fixed effect model   0.9137  [0.8658; 0.9643] -3.2822   0.001
Random effects model 0.8929  [0.8006; 0.9959] -2.0347   0.0419

Quantifying heterogeneity:
tau^2 = 0.0074; H = 1.29 [1; 1.98]; I^2 = 39.6% [0%; 74.6%]

Test of heterogeneity:
     Q d.f.  p.value
  9.93    6   0.1277

Method: Inverse variance method



* new headlin#+end_example
e

------- After codeblock execution ---------

Re: [Babel] R, multiple lines #+results, LaTeX-export

[Sébastien Vauban]

Hi Bernd,

Bernd Weiss wrote:
> (1) If I execute the following code block (see "Before codeblock 
> execution") which is followed by a headline or another codeblock, the
> results-block (see "After codeblock execution") interferes with the
> headline/codeblock/whatever.

Same thing just reported by Eric (12 min before you), and experienced by me as
well.


> (2) The results-block is complex insofar as it has multiple lines. If I 
> choose "export as LaTeX and process to PDF" (I corrected the wrong 
> #+end_example line manually), the resulting PDF file only shows the code
> but not the results. However, this behaviour is only related to my 
> meta-analysis example. If I use, for example, summary(lm(rnorm(100)~1)), 
> the resulting PDF file shows code + results.
>
> I am using Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)

That sounds weird to me: version 7.3 and a 7.01 tag!?

Best regards,
  Seb

-- 
Sébastien Vauban


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Re: Re: [Babel] R, multiple lines #+results, LaTeX-export

[Bernd Weiss]

Am 03.12.2010 03:41, schrieb Sébastien Vauban:

[...]

>> I am using Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)
>
> That sounds weird to me: version 7.3 and a 7.01 tag!?

Hi Sébastien,

That's what I get when I run "Show Version":

release_7.01h-1081-gcfd7
Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)


Bernd

Re: [Babel] R, multiple lines #+results, LaTeX-export

[Eric Schulte]

Hi Bernd,

Bernd Weiss <bernd.weiss@uni-koeln.de> writes:

> Dear all,
>
> While working on my presentation I came across the following two issues:
>
> (1) If I execute the following code block (see "Before codeblock 
> execution") which is followed by a headline or another codeblock, the 
> results-block (see "After codeblock execution") interferes with the 
> headline/codeblock/whatever.
>

I've just pushed up a fix for this issue.

>
> (2) The results-block is complex insofar as it has multiple lines. If I 
> choose "export as LaTeX and process to PDF" (I corrected the wrong 
> #+end_example line manually), the resulting PDF file only shows the code 
> but not the results. However, this behaviour is only related to my 
> meta-analysis example. If I use, for example, summary(lm(rnorm(100)~1)), 
> the resulting PDF file shows code + results.
>
> I am using Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)
>
> Thanks for your help,
>

This is odd, could you send a self-contained org-mode file which
reproduces this error?

Thanks -- Eric

>
> Bernd
>
>
> ------- Before codeblock execution ---------
>
> #+BEGIN_SRC R  :results output :exports both
> library(meta)
> data(Fleiss93)
> meta1 <- metabin(event.e, n.e, event.c, n.c, data=Fleiss93, sm="RR", 
> meth="I")
> summary(meta1)
> #+END_SRC
>
>
>
>
> * new headline
>
> ------- Before codeblock execution ---------
>
>
>
> ------- After codeblock execution ---------
>
> #+BEGIN_SRC R  :results output :exports both
> library(meta)
> data(Fleiss93)
> meta1 <- metabin(event.e, n.e, event.c, n.c, data=Fleiss93, sm="RR", 
> meth="I")
> summary(meta1)
> #+END_SRC
>
>
> #+results:
> #+begin_example
> load meta:  d:/programme/R/library ...
> Number of trials combined: 7
>
>                           RR            95%-CI       z  p.value
> Fixed effect model   0.9137  [0.8658; 0.9643] -3.2822   0.001
> Random effects model 0.8929  [0.8006; 0.9959] -2.0347   0.0419
>
> Quantifying heterogeneity:
> tau^2 = 0.0074; H = 1.29 [1; 1.98]; I^2 = 39.6% [0%; 74.6%]
>
> Test of heterogeneity:
>      Q d.f.  p.value
>   9.93    6   0.1277
>
> Method: Inverse variance method
>
>
>
> * new headlin#+end_example
> e
>
> ------- After codeblock execution ---------
>
> _______________________________________________
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> Please use `Reply All' to send replies to the list.
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Re: [Babel] R, multiple lines #+results, LaTeX-export

[Bernd Weiss]

Am 03.12.2010 09:14, schrieb Eric Schulte:
> Hi Bernd,
>
> Bernd Weiss<bernd.weiss@uni-koeln.de>  writes:

[...]

>> (2) The results-block is complex insofar as it has multiple lines. If I
>> choose "export as LaTeX and process to PDF" (I corrected the wrong
>> #+end_example line manually), the resulting PDF file only shows the code
>> but not the results. However, this behaviour is only related to my
>> meta-analysis example. If I use, for example, summary(lm(rnorm(100)~1)),
>> the resulting PDF file shows code + results.

[...]

> This is odd, could you send a self-contained org-mode file which
> reproduces this error?

Hi Eric,

I just updated my org-mode repository and now everything works fine.

Thanks a lot,

Bernd

Re: Re: [Babel] R, multiple lines #+results, LaTeX-export

[Nick Dokos]

Bernd Weiss <bernd.weiss@uni-koeln.de> wrote:

> Am 03.12.2010 03:41, schrieb S=C3=A9bastien Vauban:
> 
> [...]
> 
> >> I am using Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)
> >
> > That sounds weird to me: version 7.3 and a 7.01 tag!?
> 
> Hi S=C3=A9bastien,
> 
> That's what I get when I run "Show Version":
> 
> release_7.01h-1081-gcfd7
> Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)
> 
> 

You are probably missing the 7.3 tag, so it has to go back all the
way to 7.01h to find a starting point: you are 1081 commits past 7.01h.
Mine says 

   Org-mode version 7.3 (release_7.3.148.gc3b7e.dirty)

so I'm 148 commits past 7.3, so I'd expect roughly 930 commits between
7.01h and 7.3 (roughly, because we probably don't have the same HEAD). I
get

   $ git log --oneline release_7.01h..release_7.3 | wc -l
   917

so it checks out.

Do ``git tag'' to make sure the relase_7.3 tag is missing. Then do ``git
fetch --tags'' and check with ``git tag'' again. If the tag shows up,
org-version should then show you 7.3 as the starting point.

Nick

Re: Re: [Babel] R, multiple lines #+results, LaTeX-export

[Bernd Weiss]

Am 03.12.2010 10:05, schrieb Nick Dokos:
> Bernd Weiss<bernd.weiss@uni-koeln.de>  wrote:
>
>> Am 03.12.2010 03:41, schrieb S=C3=A9bastien Vauban:
>>
>> [...]
>>
>>>> I am using Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)
>>>
>>> That sounds weird to me: version 7.3 and a 7.01 tag!?
>>
>> Hi S=C3=A9bastien,
>>
>> That's what I get when I run "Show Version":
>>
>> release_7.01h-1081-gcfd7
>> Org-mode version 7.3 (release_7.01h.1081.gcfd7.dirty)
>>
>>
>
> You are probably missing the 7.3 tag, so it has to go back all the
> way to 7.01h to find a starting point: you are 1081 commits past 7.01h.
> Mine says
>
>     Org-mode version 7.3 (release_7.3.148.gc3b7e.dirty)
>
> so I'm 148 commits past 7.3, so I'd expect roughly 930 commits between
> 7.01h and 7.3 (roughly, because we probably don't have the same HEAD). I
> get
>
>     $ git log --oneline release_7.01h..release_7.3 | wc -l
>     917
>
> so it checks out.
>
> Do ``git tag'' to make sure the relase_7.3 tag is missing. Then do ``git
> fetch --tags'' and check with ``git tag'' again. If the tag shows up,
> org-version should then show you 7.3 as the starting point.
>
> Nick


Hi Nick,

Thanks! "git fetch --tags" was what I was missing. I simply (naively?) 
assumed that "git pull origin master" would be sufficient.

Bernd