When taking notes, it may be difficult to remember which version of the code or of a file was used. This is what version control is useful for. Here are a few useful commands that we typically insert at the top of our notebooks in shell cells

git log -1

commit 741b0088af5b40588493c23c46d6bab5d0adeb33
Author: Arnaud Legrand <arnaud.legrand@imag.fr>
Date:   Tue Sep 4 12:45:43 2018 +0200

    Fix a few typos and provide information on jupyter-git plugins.

git status -u

On branch master
Your branch is ahead of 'origin/master' by 4 commits.
  (use "git push" to publish your local commits)

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   resources.org

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	../../module2/ressources/replicable_article/IEEEtran.bst
	../../module2/ressources/replicable_article/IEEEtran.cls
	../../module2/ressources/replicable_article/article.bbl
	../../module2/ressources/replicable_article/article.tex
	../../module2/ressources/replicable_article/data.csv
	../../module2/ressources/replicable_article/figure.pdf
	../../module2/ressources/replicable_article/logo.png
	.#resources.org

no changes added to commit (use "git add" and/or "git commit -a")

Note: the -u indicates that git should also display the contents of new directories it did not previously know about.

Then, I often include commands at the end of my notebook indicating how to commit the results (adding the new files, committing with a clear message and pushing). E.g.,

git add resources.org;
git commit -m "Completing the section on getting Git information"
git push

[master 514fe2c1 ] Completing the section on getting Git information
 1 file changed, 61 insertions(+)
Counting objects: 25, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (20/20), done.
Writing objects: 100% (25/25), 7.31 KiB | 499.00 KiB/s, done.
Total 25 (delta 11), reused 0 (delta 0)
To ssh://app-learninglab.inria.fr:9418/learning-lab/mooc-rr-ressources.git
   6359f8c..1f8a567  master -> master

Obviously, in this case you need to save the notebook before running this cell, hence the output of this final command (with the new git hash) will not be stored in the cell. This is not really a problem and is the price to pay for running git from within the notebook itself.

The best way seems to be to rely on the devtools package.

sessionInfo()
devtools::session_info()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.1
Session info ------------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  fr_FR.UTF-8                 
 tz       Europe/Paris                
 date     2018-08-01                  

Packages ----------------------------------------------------------------------
 package   * version date       source        
 base      * 3.5.1   2018-07-02 local         
 compiler    3.5.1   2018-07-02 local         
 datasets  * 3.5.1   2018-07-02 local         
 devtools    1.13.6  2018-06-27 CRAN (R 3.5.1)
 digest      0.6.15  2018-01-28 CRAN (R 3.5.0)
 graphics  * 3.5.1   2018-07-02 local         
 grDevices * 3.5.1   2018-07-02 local         
 memoise     1.1.0   2017-04-21 CRAN (R 3.5.1)
 methods   * 3.5.1   2018-07-02 local         
 stats     * 3.5.1   2018-07-02 local         
 utils     * 3.5.1   2018-07-02 local         
 withr       2.1.2   2018-03-15 CRAN (R 3.5.0)

Some actually advocate that writing a reproducible research compendium can be done by writing an R package. Those of you willing to have a clean R dependency management should thus have a look at Packrat.

Finally, it is good to know that there is a built-in R command (installed.packages) allowing to retrieve and list the details of all packages installed.

head(installed.packages())