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@amyheather
amyheather committed Jul 15, 2024
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16 changes: 6 additions & 10 deletions _sources/r/environments.md.txt
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Expand Up @@ -45,13 +45,9 @@ Created using instructions from [here](https://ajstewartlang.github.io/23_introd
2. Create install.R file with package installations
3. Navigate to https://mybinder.org/, paste in GitHub repository, set to "URL to open (optional)" and type in "rstudio", then launch

## Rough notes

R -
\begin{itemize}
\item Renv
\item Posit Public Package Manager - can use Snapshot (earliest is Oct 2017, and 5 most recent versions of R), for Linux can install binary packages (which is much quicker, as usually R installs from source rather than binary unlike for Windows and Mac which makes it really slow) - \href{https://packagemanager.posit.co/client/#/repos/cran/setup}{source 1}, \href{https://docs.posit.co/faq/p3m-faq/#frequently-asked-questions}{source 2}
\item Groundhog - can go back to R 3.2 and April 2015 (and apparently can patch to go earlier) - \href{https://www.brodrigues.co/blog/2023-01-12-repro_r/}{source 1}
\item miniCRAN - \href{https://learn.microsoft.com/en-us/sql/machine-learning/package-management/create-a-local-package-repository-using-minicran?view=sql-server-ver16}{source 1}
\item Docker - requires license for non-academic (e.g. NHS) use - but Podman can drop in as replacement. To do development inside a container isn't natively supported by RStudio but can use RStudioServer via Rocker. By default, it runs in ephemeral mode - any code created or saved is lost when close - but you can use volume argument to mount local folders - \href{https://towardsdatascience.com/running-rstudio-inside-a-container-e9db5e809ff8}{source 1}
\end{itemize}
## A few other options...

* **Posit Public Package Manager**- can use Snapshot (earliest is Oct 2017, and 5 most recent versions of R), for Linux can install binary packages (which is much quicker, as usually R installs from source rather than binary unlike for Windows and Mac which makes it really slow) - [source 1](https://packagemanager.posit.co/client/#/repos/cran/setup), [source 2](https://docs.posit.co/faq/p3m-faq/#frequently-asked-questions)
* **Groundhog** - can go back to R 3.2 and April 2015 (and apparently can patch to go earlier) - [source 1](https://www.brodrigues.co/blog/2023-01-12-repro_r/)
* **miniCRAN** - [source 1](https://learn.microsoft.com/en-us/sql/machine-learning/package-management/create-a-local-package-repository-using-minicran?view=sql-server-ver16)
* - requires license for non-academic (e.g. NHS) use - but Podman can drop in as replacement. To do development inside a container isn't natively supported by RStudio but can use RStudioServer via Rocker. By default, it runs in ephemeral mode - any code created or saved is lost when close - but you can use volume argument to mount local folders [source 1](https://towardsdatascience.com/running-rstudio-inside-a-container-e9db5e809ff8)
26 changes: 15 additions & 11 deletions r/environments.html
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Expand Up @@ -514,16 +514,20 @@ <h2>Binder<a class="headerlink" href="#binder" title="Permalink to this heading"
<li><p>Navigate to https://mybinder.org/, paste in GitHub repository, set to “URL to open (optional)” and type in “rstudio”, then launch</p></li>
</ol>
</div>
<div class="section" id="rough-notes">
<h2>Rough notes<a class="headerlink" href="#rough-notes" title="Permalink to this heading">#</a></h2>
<p>R -
\begin{itemize}
\item Renv
\item Posit Public Package Manager - can use Snapshot (earliest is Oct 2017, and 5 most recent versions of R), for Linux can install binary packages (which is much quicker, as usually R installs from source rather than binary unlike for Windows and Mac which makes it really slow) - \href{https://packagemanager.posit.co/client/#/repos/cran/setup}{source 1}, \href{https://docs.posit.co/faq/p3m-faq/#frequently-asked-questions}{source 2}
\item Groundhog - can go back to R 3.2 and April 2015 (and apparently can patch to go earlier) - \href{https://www.brodrigues.co/blog/2023-01-12-repro_r/}{source 1}
\item miniCRAN - \href{https://learn.microsoft.com/en-us/sql/machine-learning/package-management/create-a-local-package-repository-using-minicran?view=sql-server-ver16}{source 1}
\item Docker - requires license for non-academic (e.g. NHS) use - but Podman can drop in as replacement. To do development inside a container isn’t natively supported by RStudio but can use RStudioServer via Rocker. By default, it runs in ephemeral mode - any code created or saved is lost when close - but you can use volume argument to mount local folders - \href{https://towardsdatascience.com/running-rstudio-inside-a-container-e9db5e809ff8}{source 1}
\end{itemize}</p>
<div class="section" id="a-few-other-options">
<h2>A few other options…<a class="headerlink" href="#a-few-other-options" title="Permalink to this heading">#</a></h2>
<ul class="simple">
<li><p><strong>Posit Public Package Manager</strong>- can use Snapshot (earliest is Oct 2017, and 5 most recent versions of R), for Linux can install binary packages (which is much quicker, as usually R installs from source rather than binary unlike for Windows and Mac which makes it really slow) - <a class="reference external" href="https://packagemanager.posit.co/client/#/repos/cran/setup">source 1</a>, <a class="reference external" href="https://docs.posit.co/faq/p3m-faq/#frequently-asked-questions">source 2</a></p></li>
<li><p><strong>Groundhog</strong> - can go back to R 3.2 and April 2015 (and apparently can patch to go earlier) - <a class="reference external" href="https://www.brodrigues.co/blog/2023-01-12-repro_r/">source 1</a></p></li>
<li><p><strong>miniCRAN</strong> - <a class="reference external" href="https://learn.microsoft.com/en-us/sql/machine-learning/package-management/create-a-local-package-repository-using-minicran?view=sql-server-ver16">source 1</a></p>
<ul>
<li><ul>
<li><p>requires license for non-academic (e.g. NHS) use - but Podman can drop in as replacement. To do development inside a container isn’t natively supported by RStudio but can use RStudioServer via Rocker. By default, it runs in ephemeral mode - any code created or saved is lost when close - but you can use volume argument to mount local folders <a class="reference external" href="https://towardsdatascience.com/running-rstudio-inside-a-container-e9db5e809ff8">source 1</a></p></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>

Expand Down Expand Up @@ -574,7 +578,7 @@ <h2>Rough notes<a class="headerlink" href="#rough-notes" title="Permalink to thi
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#how-to-set-up-renv-for-reproducible-research">How to set-up renv for reproducible research</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#basic-renv-commands">Basic renv commands</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#binder">Binder</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#rough-notes">Rough notes</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#a-few-other-options">A few other options…</a></li>
</ul>
</nav></div>

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