Add FAQ #26 (#51) [no CI]

* Add FAQ #26

* Fix FAQ as per review [no CI]

DESCRIPTION

@@ -12,6 +12,8 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Imports: 
@@ -25,3 +27,4 @@ Imports:
     gh
 Depends: 
     R (>= 3.5.0)
+VignetteBuilder: knitr

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R

vignettes/faq.Rmd

@@ -0,0 +1,221 @@
+---
+title: "FAQ"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{FAQ}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+# General questions
+
+**GQ1: Tell me in 10 lines how to use this package.**
+
+**GA1:** Get the dependency graph of several R packages on CRAN or Github at a specific snapshot date(time)
+
+```r
+graph <- resolve(c("crsh/papaja", "rio"), snapshot_date = "2019-07-21")
+```
+
+Dockerize the dependency graph to a directory
+
+```r
+dockerize(graph, output_dir = "rangtest")
+```
+
+You can build the Docker image either by the R package `stevedore` or Docker CLI client. We use the CLI client.
+
+```sh
+cd rangtest
+docker build -t rangtest . ## might need sudo
+```
+
+Launch the container with the built image
+
+```sh
+docker run --rm --name "rangcontainer" -ti rangtest
+```
+
+And the tenth line is not needed.
+
+**GQ2: For running `resolve()`, how do I know which packages are used in a project?**
+
+**GA2:** We recommend `renv::dependencies()`.
+
+Suppose in a directory called "project" there are two R files:
+
+```r
+here::here()
+```
+
+```r
+library(rio)
+x <- import("hello.csv")
+```
+
+Running this reveals
+
+```{r include = FALSE}
+## x <- tempfile()
+## dir.create(x)
+## writeLines(c("library(rio)", "here::here()"), file.path(x, "fake.R"))
+## y <- renv::dependencies(x)
+## y$Source <- c("myproject/1.R", "myproject/2.R")
+## y
+```
+
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true"></a>renv<span class="op">::</span><span class="kw">dependencies</span>(<span class="st">&quot;project&quot;</span>)</span></code></pre></div>
+<pre><code>#&gt; Finding R package dependencies ... Done!
+#&gt;          Source Package Require Version   Dev
+#&gt; 1 myproject/1.R    here                 FALSE
+#&gt; 2 myproject/2.R     rio                 FALSE</code></pre>
+
+You may still need to manually review which packages are from Github.
+
+**GQ3: Why is the R script generated by `dockerize()` and `export_rang()` so strange/unidiomatic/inefficient/did you guys read `fortunes::fortune("answer is parse")`?**
+
+**GA3:** It is because we optimize the R code in `rang.R` for backward compatibility. We need to make sure that the code runs well in vanilla R environments since 2.1.0.
+
+**GQ4: Why doesn't `rang` support reconstructing computational environments with R < 2.1.0 yet?**
+
+**GA4:** It is because installing source packages from within R was introduced in R 2.1.0. Before that one needed to install source packages with `R CMD INSTALL`. But we are working on supporting R in the 1.x series.
+
+**GQ5: Does `rang.R` (generated by `export_rang()` or `dockerize()`) run on non-Linux OSes?**
+
+**GA5:** Theoretically speaking, yes. But strongly not recommended. If the system requirements are fulfilled, `rang.R` should probably run fine on OS X if the R packages do not contain compiled code. C and Fortran compilers are needed if it is the case. See [this entry](https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#Installation-of-source-packages) in R Mac OS X FAQ. On Windows, installing Github packages requires properly set up PATH and `tar`. Similarly, R packages with compiled code require C / Fortran compilers. See [this entry](https://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f) in R for Windows FAQ.
+
+**GQ6: What are the caveats of using rang?**
+
+**GA6:** Many
+
+* `rang` does not support reconstructing computational environments with R < 2.1.0 (i.e. `snapshot_date` < "2005-04-19 09:01") yet
+* `dockerize()` can only generate Debian/Ubuntu-based Docker images
+* `dockerize(cache = TRUE)` does not cache [R source code](https://cran.r-project.org/src/base/) (yet) and System Requirements (in `deb` packages)
+* `query_sysreqs()` (as well as `resolve(query_sysreqs = TRUE)`) queries for System Requirements based on the latest version of the packages on CRAN / Github. Therefore:
+    * Removed CRAN packages are assumed to have no System Requirements
+	* R Packages with changed System Requirements between `snapshot_date` and the date of running `resolve()` might produce incorrect System Requirements
+* A result from `resolve()` with R version < 3.1 and has at least one Github package must be dockerized with caching (i.e. `dockerize(cache = TRUE)`). It is because the outdated version of Debian cannot communicate with the Github API
+* R packages on Github or CRAN might not be available in the near future (Github: likely; CRAN: very unlikely). But one can cache the packages (`dockerize(cache = TRUE)`).
+* The Rocker project and its host Docker Hub might not be available in the near future (unlikely)
+* Ubuntu / Debian archives (for System Requirements) might not be available in the future (super unlikely)
+
+**GQ7: `rang` depends on R >= 3.5.0. Several of the dependencies depend on many modern R packages. How dare you claiming your package supports R >= 2.1.0?**
+
+**GA7:** To clarify, it is true that `resolve()` and `dockerize()` depend on many factors, including a modern version of R. But the reconstruction process (if with caching of R packages) depends only on the availability of Docker images from Docker Hub, availability of R source code on CRAN (R < 3.1.0), and `deb` packages from Ubuntu and Debian in the future. If you don't believe in all of these, see also: DQ4.
+
+**GQ8: What are the data sources of `resolve()`?**
+
+**GA8:** Several
+
+* Dependencies / R version / System Requirements: r-hub APIs [pkgsearch](https://r-hub.github.io/pkgsearch/) [r-versions](https://api.r-hub.io/rversions) [sysreqs](https://sysreqs.r-hub.io/)
+* Github: [Github API](https://docs.github.com/en/rest)
+* Dependencies of Github packages: [Package manager from Posit](https://github.com/rstudio/r-system-requirements#operating-systems)
+
+**GQ9: I am not convinced by this package. What are the alternatives?**
+
+**GA9:** If you don't consider the Dockerization part of `rang`, the date-based pinning of R packages can be done by:
+
+* Using [Package Manager](https://packagemanager.rstudio.com/)
+
+```r
+library(pak)
+options(repos = c(REPO_NAME = "https://packagemanager.rstudio.com/cran/2019-07-21"))
+pkg_install("rio")
+pkg_install("crsh/papaja")
+```
+
+* Using [groundhog](https://groundhogr.com/)
+
+```r
+library(groundhog)
+pkgs <- c("rio","crsh/papaja")
+groundhog.library(pkgs, "2019-07-21")
+```
+
+If you don't consider the date-based pinning of R packages, the Dockerization can be done by:
+
+* Using [containerit](https://github.com/o2r-project/containerit) [not on CRAN]
+
+```r
+library(containerit)
+## combine with Package Manager to pin packages by date
+install.packages("rio")
+remotes::install_github("crsh/papaja")
+library(rio)
+library(papaja)
+print(containerit::dockerfile(from = utils::sessionInfo()))
+```
+
+* Using [dockerfiler](https://cran.r-project.org/web/packages/dockerfiler/index.html)
+
+```r
+library(dockerfiler)
+my_dock <- Dockerfile$new()
+## combine with Package Manager to pin packages by date
+my_dock$RUN(r(install.packages(c("remotes", "rio"))))
+my_dock$RUN(r(remotes::install_github("crsh/papaja")))
+my_dock
+```
+
+# Docker questions
+
+**DQ1: Is Docker an overkill to simply ensure that a few lines of R code are reproducible?**
+
+**DA1:** It might be the case for recent R code, e.g. R >= 3.0 (or `snapshot_date` > "2013-04-03 09:10"). But we position `rang` as an archaeological tool to run really old R code (`snapshot_date` >= "2005-04-19 09:01", but see GQ4). For this, Docker is essential because R in the 2.x (or even 1.x in future) series might not be installable anymore in a non-virtualized environment.
+
+According to [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/compendia.html), a research compendium that aids computational reproducibility should contain a complete description of the computational environment. The directory exported by `dockerize()`, especially when `materials_dir` and `cache` were used, can be directly shared as a research compendium.
+
+**DQ2: How do I access bash instead of R?**
+
+**DA2:** By default, containers launched with the images generated by `rang` goes to R. One can override this by launching the container with an alternative entry point.
+
+Suppose an image was built as per GA1.
+
+```sh
+docker run --rm --name "rangcontainer" --entrypoint bash -ti rangtest
+```
+
+**DQ3: How do I copy files from and to a launched container?**
+
+**DA3:** Again an image was built as per GA1 and launched as below
+
+```sh
+docker run --rm --name "rangcontainer" -ti rangtest
+```
+
+```sh
+# probably you need to run this from another terminal
+docker cp rangcontainer:/rang.R rang2.R
+docker cp rang2.R rangcontainer:/rang2.R
+```
+
+We want to emphasize here that launching a container with `--name` is useful because the name of the container is randomly generated when `--name` was not used to launch it. It is also important to remind you that a relaunched container goes back to the initial state. Any file generated inside the container previously will be removed. So use `docker cp` to copy any artifact if one wants to preserve any artifact.
+
+**DQ4: How do I back up an image?**
+
+**DA4:** If you don't believe Docker Hub / Debian archives / Ubuntu archives would be available forever, you may back up the generated image.
+
+```sh
+docker save rangtest | gzip > rangtest.tar.gz
+```
+
+You can also share the back up gzipped tarball file (usually < 1G, depending on the size of `materials_dir`, thus sharable on Zenodo).
+
+To restore the backup image:
+
+```sh
+docker load < rangtest.tar.gz
+```
+
+And launch a container the same way
+
+```sh
+docker run --rm --name "rangcontainer" -ti rangtest
+```