[ESS] knitr and ESS

Ottorino ottor|no-|uc@@p@nt@n| @end|ng |rom un|||@|t
Wed Oct 14 14:49:02 CEST 2015 

Here you are the purged history from the terminal.
I cannot document precisely what i did yesterday night from emacs.
I refreshed some obsolete packages (auctex ??)

But I agree with you on the strangeness of the matter.
I'm far from being a lisp literate, but on repeating the procedure on my 
desktop, I ended with a weirdly working emacs.

The message I get this time on opening emacs-24.4 from terminal  is
Warning: Cannot convert string 
"-*-courier-medium-r-*-*-*-120-*-*-*-*-iso8859-*" to type FontStruct
I also found a possible solution here
http://ubuntuforums.org/showthread.php?t=1896584

but unfortunately the solution do not work on my system.
Still struggling


############### HISTORY
Attempts with emacs 24.1, ess 13.09 R 3.0.2

   382  sudo apt-get install markdown
   383  sudo apt-get install emacs-goodies-el
   384  sudo apt-get install pandoc
   ...
   390  pandoc --version
The system was complaining about a too old version of pandoc.
I then installed pandoc 1.15.0.6 from
https://github.com/jgm/pandoc/releases/download/1.15.0.6/pandoc-1.15.0.6-1-amd64.deb

Download of polymode, and modification of my .emacs
   427  cd Documenti/
   428  cd BitBucket/
   429  git clone https://github.com/vitoshka/polymode.git


Installation of packages to compile emacs 24.4.
   439      sudo apt-get install build-essential texinfo libx11-dev 
libxpm-dev libjpeg-dev libpng-dev libgif-dev libtiff-dev libgtk2.0-dev 
libncurses-dev

Installation of emacs 24.4
   451  ./configure
   ...
   453  make
   454  makefile
   455  emacs-24.4

Refresh of the GPG key and change the repository to
deb https://cran.r-project.org/bin/linux/ubuntu trusty/
Yesterday it was not possible to reach the italian repository on unipd

   456  sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 
E084DAB9

Installation of ess 15.09 and R 3.2.2

   460  sudo apt-get install r-base-core r-base-dev
   461  apt-get autoremove
   ...
   464  sudo apt-get update
   465  sudo apt-get upgrade
     ...
   470  sudo apt-get install ess




Il 14/10/2015 09:53, Vitalie Spinu ha scritto:
> That's very strange because the error that you reported is an elisp error. But,
> it's great that you could fix it.
>
> The problem is the same as reported in this issue:
>
>   https://github.com/vspinu/polymode/issues/25
>
>
> Would you please add a comment there on how you managed to fix it?
>
>
> Thanks,
>
>
>     Vitalie
>
>>> On Tue, Oct 13 2015 22:38, ottorino wrote:
>> GOT IT !!
>> The responsible was R 3.0.2 !!
>> I've updated to 3.2.2 and I'm back in business.
>> THANKS A LOT, Vitalie, for the support.
>> Here, in my university, in a non-unix world I sometime feel desperate.
>> Thanks again
>> Mint 17.2 Rafaela -- MATE
>> GNU Emacs 24.4.1 (x86-64-pc-linux-gnu, GTK+ Version 2.24.23)
>> ESS version 15.09-1 -- R 3.2.2
>> Il 13/10/2015 21:48, ottorino ha scritto:
>>> I've installed emacs 24.4, polymode still in git version, and unfortunately
>>> the very same result on the laptop.
>>> At first with ESS 13.09, then, after installing from melpa, also with ESS
>>> version 15.09-1.
>>>
>>> I suspect there's something related with my system. Tomorrow I'll try on the
>>> desktop
>>>
>>> Wrong number of arguments: (lambda (proc name) (let ((wfile (pm--ESS-callback
>>> proc name))) (pm--display-file wfile) wfile)), 1
>>> byte-code: End of buffer
>>>
>>> Il 13/10/2015 18:18, Vitalie Spinu ha scritto:
>>>> I guess your problem is some local immutability between ESS, polymode ,emacs and
>>>> eieio.
>>>>
>>>> I am developing on 25, and testing on 24.4 and occasionally on 24.3. Polymode on
>>>> 24.3 has some issues but it's usable and just yesterday a user reported that
>>>> everything was working fine. There have been too many changes on eieio in the
>>>> past year or so that I am even considering removing 24.3 from the supported
>>>> list.
>>>>
>>>> I am back on developing polymode, (slowly but surely) and I will eventually fix
>>>> all the issues. For now, if you can upgrade emacs to the most recent version you
>>>> can please do that.
>>>>
>>>>
>>>>     Vitalie
>>>>
>>>>>> On Tue, Oct 13 2015 12:58, Ottorino wrote:
>>>>> Hi  all.
>>>>> this morning I tried to install polymode (git version, no elpa packages around)
>>>>> on the desktop in my office, but only to get this message:
>>>>> Warning (initialization): An error occurred while loading
>>>>> `/home/ottorino/.emacs':
>>>>> error: Unknown class type pm-chunkmode in method parameters
>>>>> The two systems are slightly different;
>>>>> Desktop
>>>>> Mint 17.2 Rafaela -- Cinnamon
>>>>> GNU Emacs 24.3.1 (x86-64-pc-linux-gnu, GTK+ Version 3.10.7)
>>>>> ESS version 15.09-1 -- R 3.2.2
>>>>> Laptop (I wrongly assumed it was a 17.1 Qiana: it's not)
>>>>> Mint 17.2 Rafaela -- MATE
>>>>> GNU Emacs 24.3.1 (x86-64-pc-linux-gnu, GTK+ Version 3.10.7)
>>>>> ESS version 13.09-1 -- R 3.0.2
>>>>> I think there are signals that I can't use ESS + polymode !!
>>>>> Il 11/10/2015 01:14, ottorino ha scritto:
>>>>>> Dear ESS users,
>>>>>> after many years of use, I'm eventually moving from sweave to knitr and
>>>>>> therefore setting up my system
>>>>>>
>>>>>> Mint 17.1 Qiana -- MATE
>>>>>> GNU Emacs 24.3.1 (x86-64-pc-linux-gnu, GTK+ Version 3.10.7)
>>>>>> ESS version 13.09-1 -- R 3.0.2
>>>>>>
>>>>>> with all the necessary packages.
>>>>>>
>>>>>> I wrote my first simple "AnalisiReport.Rmd" file and tried to knit it to an
>>>>>> html one
>>>>>>
>>>>>>   From the terminal everything went well with:
>>>>>>
>>>>>> library(knitr)
>>>>>> library(rmarkdown)
>>>>>> render('AnalisiReport.Rmd', "html_document")
>>>>>>
>>>>>>   From emacs,  (polymode installed and apparently working), after pressing M-n w
>>>>>> and selecting knitr-ESS as weaver, I can see the knitr processing the file in
>>>>>> the *R* buffer, but then I get the following message
>>>>>>
>>>>>> Weaving 'AnalisiReport.Rmd' with 'knitR-ESS' weaver ...
>>>>>> Type C-h m for help on ESS version 13.09-1
>>>>>> ess-tracebug mode enabled
>>>>>> using process '*R*'
>>>>>> Wrong number of arguments: (lambda (proc name) (let ((wfile (pm--ESS-callback
>>>>>> proc name))) (pm--display-file wfile) wfile)), 1
>>>>>> byte-code: End of buffer
>>>>>>
>>>>>> In the meanwhile I get a AnalisiReport[woven].md file in the same directory
>>>>>> where the .Rmd file reside.
>>>>>>
>>>>>> All the above is valid also for the minimal example found in the knitr site.
>>>>>>
>>>>>> What am I missing ?
>>>>>>
>>>>> ______________________________________________
>>>>> ESS-help using r-project.org  mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/ess-help>

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