From b8db2e1fc67c3edf35f18c665418e0f38c566974 Mon Sep 17 00:00:00 2001 From: Arnaud Legrand Date: Thu, 19 Jul 2018 22:46:16 +0200 Subject: [PATCH] Completed the Rstudio resource webpage. Replacing the lengthy Rstudio/github by an Rstudio/GitLab video would be nice. --- module2/ressources/rstudio.html | 212 +++++++++++++++++++++----------- module2/ressources/rstudio.org | 91 +++++++++----- 2 files changed, 199 insertions(+), 104 deletions(-) diff --git a/module2/ressources/rstudio.html b/module2/ressources/rstudio.html index cf1a13d..5dc3d80 100644 --- a/module2/ressources/rstudio.html +++ b/module2/ressources/rstudio.html @@ -4,40 +4,88 @@

Table of Contents

+

+If you have never used git with Rstudio, we strongly advise that you +follow the step-by-step explanations from Software Carpentry. It comes +with many screenshots and is quite progressive. Alternatively, you +may want to watch this video: +

+ + +

+The next sections provide information on how to install Rstudio, Git +(to interact with GitLab), and SSH (to avoid typing your password +every time you synchronize with GitLab). +

+ +

+Finally, you need to know that the Rstudio team has created a lot of +very good material and tutorials. You should definitively look at the +Cheat sheets webpage. In particular you want to have look at the ones +on: +

+ + +

+In case it helps, here are some (sometimes outdated) French versions +of these documents: +

+ -
-

Installing Rstudio

-
+
+

Installing Rstudio

+
-
-

Linux (debian, ubuntu)

-
+
+

Linux (debian, ubuntu)

+

We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information -for other distributions (e.g.n redhat, fedora). +for other distributions (e.g., redhat, fedora).

@@ -55,9 +103,9 @@ for upgrading…

-
-

Installing R

-
+
+

Installing R

+

Beforehand, you need to install the R language and convenient packages by running (as root): @@ -90,9 +138,9 @@ to run (as root):

-
-

Installing rstudio

-
+
+

Installing rstudio

+

Rstudio is unfortunately not packaged within debian so the easiest is to download the corresponding debian package on the Rstudio webpage @@ -110,9 +158,9 @@ sudo apt-get update ; sudo apt-get -f install -

Mac OSX and Windows

-
+
+

Mac OSX and Windows

+

Some instructions on installing R and knitr must be missing. This @@ -136,17 +184,17 @@ install.packages("ggplot2")

-
-

Installing Git

-
+
+

Installing Git

+
-
-

Linux (debian, ubuntu)

-
+
+

Linux (debian, ubuntu)

+

We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information -for other distributions (e.g.n redhat, fedora). +for other distributions (e.g., redhat, fedora).

@@ -158,9 +206,9 @@ Run (as root):

-
-

Mac OSX and Windows

-
+
+

Mac OSX and Windows

+
  • Download and install Git from the Git website.
  • Optional Git clients (should not be needed if you work within @@ -172,7 +220,7 @@ Rstudio):

    -Apparently, this works with gitlab and https. +Apparently, this works with GitLab and https.

@@ -180,55 +228,69 @@ Rstudio):
-
-

Rstudio and git/github/gitlab

-
-
+
+

Setting up SSH

+

-We may want to redo a screencast in French for this +There are two ways of synchronizing your local repository with GitLab: +through HTTPS or through SSH. The first one does not require any +particular configuration but you will be regularly prompted for your +GitLab password, which can be quite tedious. To avoid this, the best +solution is to set install SSH, to create a pair or private/public +keys, and to upload your SSH public key on GitLab. This section +provides with information on how to do this. +

+
+
+

Installation

+
+
+
+

Linux (debian, ubuntu)

+
+

+We provide here only instructions for debian-based distributions. Feel +free to contribute to this document to provide up-to-date information +for other distributions (e.g., redhat, fedora).

-
-

-Alternatively, we can point to: -http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/ +Run (as root):

-
    -
  • Part 1/item 2: Setup Git in RStudio
    • -
  • Part 2 (to adapt to gitlab)
    • -
  • Part 3
    • -
+
+
apt-get update ; apt-get install openssh-client
+
+
-
-

Cheat Sheets

-
+
+

Mac OSX

+

-The Rstudio team has created a lot of good material and tutorials. You -should definitively look at the Cheat sheets webpage. In particular -you want to have look at the ones on: +You do not have anything to do as it is installed by default.

- - +
+
+
+

Windows

+

-In case it helps, here are some (sometimes outdated) French versions -of these documents: +You should install the Putty client. Once it is installed, look for +the section on generating an SSH key.

- +
+
+
+
+

Setting up SSH on Framagit

+
+

+Here are all the official explanations on how to set up your SSH key +on GitLab. Alternatively, you may also want to have a look at this +video: +

+ +
diff --git a/module2/ressources/rstudio.org b/module2/ressources/rstudio.org index 71786c2..e9587e9 100644 --- a/module2/ressources/rstudio.org +++ b/module2/ressources/rstudio.org @@ -5,11 +5,41 @@ #+STARTUP: overview indent #+OPTIONS: num:nil toc:t + +If you have never used git with Rstudio, *we strongly advise that you +follow the [[https://swcarpentry.github.io/git-novice/14-supplemental-rstudio/index.html][step-by-step explanations from Software Carpentry]]*. It comes +with many screenshots and is quite progressive. Alternatively, you +may want to watch this video: +#+BEGIN_EXPORT html + +#+END_EXPORT + +The next sections provide information on how to install Rstudio, Git +(to interact with GitLab), and SSH (to avoid typing your password +every time you synchronize with GitLab). + +Finally, you need to know that the Rstudio team has created a lot of +very good material and tutorials. You should definitively look at the +[[https://www.rstudio.com/resources/cheatsheets/][Cheat sheets webpage]]. In particular you want to have look at the ones +on: +- [[https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf][The Rstudio IDE]], +- [[https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf][R Markdown]], +- The [[https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf][R Markdown Reference guide]], +- [[https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf][Data visualization with ggplot2]], +- [[https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf][Data transformation with dplyr]] + +In case it helps, here are some (sometimes outdated) French versions +of these documents: +- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf][L'IDE Rstudio]] +- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf][Visualisation de données avec ggplot2]] +- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf][Transformation de données avec dplyr]] +- [[https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf][Un court document sur R Markdown]] + * Installing Rstudio ** Linux (debian, ubuntu) We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information -for other distributions (e.g.n redhat, fedora). +for other distributions (e.g., redhat, fedora). Today, the stable versions of the most common distributions provide recent enough versions of emacs and org-mode: @@ -71,7 +101,7 @@ install.packages("ggplot2") ** Linux (debian, ubuntu) We provide here only instructions for debian-based distributions. Feel free to contribute to this document to provide up-to-date information -for other distributions (e.g.n redhat, fedora). +for other distributions (e.g., redhat, fedora). Run (as root): #+begin_src sh :results output :exports both @@ -84,32 +114,35 @@ apt-get update ; apt-get install git - [[https://www.sourcetreeapp.com/][SourceTree]] - [[https://desktop.github.com/][GitHub Desktop]] #+BEGIN_QUOTE - [[https://github.com/desktop/desktop/issues/852][Apparently]], this works with gitlab and https. + [[https://github.com/desktop/desktop/issues/852][Apparently]], this works with GitLab and https. #+END_QUOTE -* Rstudio and git/github/gitlab -#+BEGIN_QUOTE -We may want to redo a screencast in French for this -#+END_QUOTE -- [[https://www.rstudio.com/resources/webinars/rstudio-essentials-webinar-series-managing-part-2/][This video on using git/githugb/gitlab from Rstudio]] (starting at time 9:09) - -Alternatively, we can point to: -http://www.geo.uzh.ch/microsite/reproducible_research/post/rr-rstudio-git/ -- Part 1/item 2: Setup Git in RStudio -- Part 2 (to adapt to gitlab) -- Part 3 -* Cheat Sheets -The Rstudio team has created a lot of good material and tutorials. You -should definitively look at the [[https://www.rstudio.com/resources/cheatsheets/][Cheat sheets webpage]]. In particular -you want to have look at the ones on: -- [[https://github.com/rstudio/cheatsheets/raw/master/rstudio-ide.pdf][the Rstudio IDE]], -- [[https://github.com/rstudio/cheatsheets/raw/master/rmarkdown-2.0.pdf][R Markdown]], -- the [[https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf][R Markdown Reference guide]], -- [[https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf][data visualization with ggplot2]], -- [[https://github.com/rstudio/cheatsheets/raw/master/data-transformation.pdf][data transformation with dplyr]] +* Setting up SSH +There are two ways of synchronizing your local repository with GitLab: +through HTTPS or through SSH. The first one does not require any +particular configuration but you will be regularly prompted for your +GitLab password, which can be quite tedious. To avoid this, the best +solution is to set install SSH, to create a pair or private/public +keys, and to upload your SSH public key on GitLab. This section +provides with information on how to do this. +** Installation +*** Linux (debian, ubuntu) +We provide here only instructions for debian-based distributions. Feel +free to contribute to this document to provide up-to-date information +for other distributions (e.g., redhat, fedora). -In case it helps, here are some (sometimes outdated) French versions -of these documents: -- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/rstudio-IDE-cheatsheet.pdf][L'IDE Rstudio]] -- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/ggplot2-french-cheatsheet.pdf][Visualisation de données avec ggplot2]] -- [[https://github.com/rstudio/cheatsheets/raw/master/translations/french/data-wrangling-french.pdf][Transformation de données avec dplyr]] -- [[https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.pdf][Un court document sur R Markdown]] +Run (as root): +#+begin_src sh :results output :exports both +apt-get update ; apt-get install openssh-client +#+end_src +*** Mac OSX +You do not have anything to do as it is installed by default. +*** Windows +You should install the [[https://www.ssh.com/ssh/putty/windows/][Putty]] client. Once it is installed, look for +the section on [[https://www.ssh.com/ssh/putty/windows/puttygen][generating an SSH key]]. +** Setting up SSH on Framagit +Here are [[https://docs.gitlab.com/ee/ssh/][all the official explanations on how to set up your SSH key +on GitLab]]. Alternatively, you may also want to have a look at this +video: +#+BEGIN_EXPORT html + +#+END_EXPORT -- 2.18.1