[ESS] A few issues and questions from a newbie in R/ESS

[Vincent Goulet]

Hi Joakim,

Please keep ess-help in the loop since the discussion originated there. I'm cc'ing the list back.

> Le 12 janv. 2020 à 19:31, Joakim Frögren <joakim using frogren.se> a écrit :
> 
> Hi Vincent,
> 
> Thank you so much for your very informative replies to my questions! I am very grateful to you for making this effort. This seems to be a great community, and since I am so new to this field this gives me some comfort and confidence. Now, based on what you write I have some additional questions that I would really appreciate if you could look into when you have time.
> 
>> Do you use CRAN R. I think the general consensus in the R community (at least the "core" community) is that there is no advantage in using homebrew R. Furthermore, you will find it more difficult to get help in the official mailing lists if you don't use CRAN R.
>  
> No, unfortunately I did not install R from https://cran.r-project.org/ but I realize now that I should have done that. Instead I installed it by writing 'brew install r' in the terminal. In addition to  R also installed a few other things this way after reading on some threads that they were necessary for R in order for it to function properly. Now, when I write 'brew deps r', it lists the following: gcc, gettext, gmp, isl, jpeg, libmpc, libpng, mpfr, openblas, pcre, readline, xz. I suppose before installing CRAN R I should uninstall my current version of R, right? From Homebrew this seems possible with the command 'brew uninstall r', but do I also need to uninstall some or all of the dependencies?

Hum, perhaps. I make a very limited use of brew myself.

With CRAN R, the only things you need "for it to function properly" is XCode and the XCode command-line tools *if you want/need to compile packages from source*. You may also find useful to install XQuartz for some graphic devices.

In any case, all the relevant info for R on macOS is at http://mac.r-project.org.

> 
>> If you allow the shameless plug, climb on my back and use my distribution of Emacs for macOS bundled with ESS, AUCTeX and some other goodies. You'll have something that works out of the box (and that I use daily myself) and that fixes some of the problems you have (see below).
>> https://vigou3.gitlab.io/emacs-modified-macos/
>  
> I am considering to climb on your back, since you seem so knowledgeable and your distribution so safe, but I also have some doubts. I will try to explain my concerns here briefly. Now, an important reason I decided to finally try out Emacs as a text editor (and much more!) relates to the following guide by Kieran Healy. With him as a guide Emacs seemed safe enough to try out considering the limited computer skills I have. Please check out Figure 5.1 on page 23 in his guide. This illustrates the workflow that I strive for. It is thus very important for me to be able to continue to write my academic texts in plaintext initially, and not LaTeX. It is also important for me to be able to use BibDesk in combination with the Emacs package helm-bibtex for reference management since I have grown used to handling my references this way. Lastly, my concern is git. I have struggled quite much to gain a conceptual understanding of git (please see Figure 2.1 on page 10 in Kieran Healy's guide). This have resulted in a quite messy git structure, but a structure that at least works when I puch things and pull things through using Magit. My fear is now that if I use your distribution I would have to abort all those versions I have saved using git and Github and start all over again. On the one hand I would like to do that, but on the other I am a bit afraid of it since I have been struggling so much with when and how to pull and push things and from where. I can see that you seem to have a preference for Gitlab rather than Github. If I restructure my git system would it be a good idea also to migrate everything to Gitlab? All this, just to explain why I am doubting. I would be grateful if you could give me a bit of comfort here and tell me that your distribution works well based on my requirements.

As explained in the web page, my distribution is stock Emacs with a few addons. So you need not fear any incompatibility with normal Emacs packages.


>> It's not a bug, it's a feature, and most likely one you'll come to appreciate in the long run. Actually, I'm pretty confident most ESS folks will agree that this is something RStudio got completely wrong: always launching R with the same working directory.
>> 
>> Just imagine you need to work on two different projects simultaneously, each with its own R session. Emacs and ESS allow this and you set separate working directories right from the outset. Good luck doing this with RStudio.
>  
> Thanks for explaining this! You just convinced my why the ESS solution is better than the RStudio one.
>  
>> Yes, Emacs does not import the shell environment on macOS. I take care of this in my distribution.
>  
> So, another good reason to climb on your back then :)

Certainly!

>  
>> Take 5 minutes to setup a personal library for R packages.
>> 
>> 1. Create a directory to host the library. In the sequel I'll use ~/Library/R/library.
>> 
>> 2. Create a ~/.Renviron file with the following contents:
>> 
>> R_LIBS_USER="~/Library/R/library/"
>> R_INTERACTIVE_DEVICE=quartz
>> 
>> 3. Restart R and check with '.libPaths()' that your personal library is now in first position.
>> 
>> 4. Install R packages from R with 'install.packages()'.
>> 
>> 5. Don't look behind.
>  
> I suppose that I should be doing these thing right after I installed CRAN R, right? What do you mean by "in first position" on point number three?

.libPaths() returns a vector of paths (character strings) and your personal library should just be the first item in the vector.

>  Thanks once more for your support! I am truly, truly grateful to you.
>  
> 
> Best regards, 
> Joakim

Cheers,

v.