org babel R source blocks :results output with :session includes extra blank lines

org babel R source blocks :results output with :session includes extra blank lines

[Dylan Schwilk]

Hello,

I recently have run into a change in output from my R language source code blocks.

I have found that when I include :session to the source block header, I now get
extra blank lines in the #+results. This has broken my lecture slides for my
courses with too much extra blank space.

for example:

#+begin_src R :results output :exports both :session
1 + 2
3 + 4
print("the end")
#+end_src

#+results:
: [1] 3
:
: [1] 7
:
: [1] "the end"


I do not have this issue when I omit the :session header argument, eg:

#+begin_src R :results output :exports both
1 + 2
3 + 4
print("the end")
#+end_src

#+results:
: [1] 3
: [1] 7
: [1] "the end"


I am using org-mode version 9.1.13, emacs 25.2.2 and R version 3.4.4
(2018-03-15) with no .Rprofile.

This does not happen with python source blocks, only with R

Sincerely,

Dylan

Re: org babel R source blocks :results output with :session includes extra blank lines

[Berry, Charles]

Cannot confirm. See inline.

> On Aug 28, 2018, at 7:48 AM, Dylan Schwilk <dylan@schwilk.org> wrote:
> 
> Hello,
> 
> I recently have run into a change in output from my R language source code blocks.
> 
> I have found that when I include :session to the source block header, I now get
> extra blank lines in the #+results. This has broken my lecture slides for my
> courses with too much extra blank space.
> 
> for example:
> 
> #+begin_src R :results output :exports both :session
> 1 + 2
> 3 + 4
> print("the end")
> #+end_src
> 
> #+results:
> : [1] 3
> :
> : [1] 7
> :
> : [1] "the end"
> 

With the :session arg I get the output as you show it below.

This was with master on commit f79545 from last month and on today's master (commit 38a8901).

> 
> I do not have this issue when I omit the :session header argument, eg:
> 
> #+begin_src R :results output :exports both
> 1 + 2
> 3 + 4
> print("the end")
> #+end_src
> 
> #+results:
> : [1] 3
> : [1] 7
> : [1] "the end"
> 
> 


FWIW, my R session looks like this


--8<---------------cut here---------------start------------->8---
[...]
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> setwd('/Users/cberry/')
> 1 + 2
3 + 4
print("the end")
'org_babel_R_eoe'
[1] 3
> [1] 7
> 
[1] "the end"
> [1] "org_babel_R_eoe"
--8<---------------cut here---------------end--------------->8---

If this is what your session looks like, then we need to dig deeper into ob-R.

HTH,

Chuck

Re: org babel R source blocks :results output with :session includes extra blank lines

[Dylan Schwilk]

Thank you and my apologies. Seeing the session output you posted convinced me
the problem was with my ess settings.

Of course I should have known that because I could find no-one else with the
same problem and I could see no change to ob-R.el in the git repo in the past
months that could have affected this.

The problem turned out to be the ess variable ess-eval-visibly. The default, nil
works fine with ob-R (doc: "If nil, ESS doesn’t print input commands and doesn’t
wait for the process.").  I had accidentally set to 'nowait (doc: If ’nowait,
ESS still shows the input commands, but don’t wait for the process.).

My apologies for the spurious post. I had not realized that I was setting that
ess variable.

Sincerely,

Dylan


On 08/28/2018 11:57 AM, Berry, Charles wrote:
> Cannot confirm. See inline.
> 
>> On Aug 28, 2018, at 7:48 AM, Dylan Schwilk <dylan@schwilk.org> wrote:
>>
>> Hello,
>>
>> I recently have run into a change in output from my R language source code blocks.
>>
>> I have found that when I include :session to the source block header, I now get
>> extra blank lines in the #+results. This has broken my lecture slides for my
>> courses with too much extra blank space.
>>
>> for example:
>>
>> #+begin_src R :results output :exports both :session
>> 1 + 2
>> 3 + 4
>> print("the end")
>> #+end_src
>>
>> #+results:
>> : [1] 3
>> :
>> : [1] 7
>> :
>> : [1] "the end"
>>
> 
> With the :session arg I get the output as you show it below.
> 
> This was with master on commit f79545 from last month and on today's master (commit 38a8901).
> 
>>
>> I do not have this issue when I omit the :session header argument, eg:
>>
>> #+begin_src R :results output :exports both
>> 1 + 2
>> 3 + 4
>> print("the end")
>> #+end_src
>>
>> #+results:
>> : [1] 3
>> : [1] 7
>> : [1] "the end"
>>
>>
> 
> 
> FWIW, my R session looks like this
> 
> 
> --8<---------------cut here---------------start------------->8---
> [...]
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
>> setwd('/Users/cberry/')
>> 1 + 2
> 3 + 4
> print("the end")
> 'org_babel_R_eoe'
> [1] 3
>> [1] 7
>>
> [1] "the end"
>> [1] "org_babel_R_eoe"
> --8<---------------cut here---------------end--------------->8---
> 
> If this is what your session looks like, then we need to dig deeper into ob-R.
> 
> HTH,
> 
> Chuck
> 
> 
> 
>