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109 changes: 81 additions & 28 deletions README.Rmd
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Expand Up @@ -120,34 +120,87 @@ rix(

The table below illustrates this all the different types of environment you can generate:

|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| **r_ver** | **Intended use** | **State of R** | **State of CRAN** | **State of Bioconductor** | **State of other packages in** |
| | | **version** | **packages** | **packages** | **Nixpkgs** |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"latest-upstream"` | Start of new project where versions | Current or previous | Outdated (up to 6 months) | Outdated (up to 6 months) | Current at time of generation |
| | don’t matter | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"4.4.2"` (or other) | Reproducing old project or starting a new | Same as in `r_ver` | Outdated (up to 2 months | Outdated (up to 2 months | Potentially outdated (up to 12 months) |
| | project where versions don’t matter | | if using latest release) | if using latest release) | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"2024-12-14"` (date) | Reproducing old project or starting a new | Current at that date | Current at that date | Current at that date | Potentially outdated (up to 12 months) |
| | project using the most recent date | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"bleeding-edge"` | To develop against the latest | Always current | Always current | Always current | Always current |
| | release of CRAN | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"frozen-edge"` | To develop against the latest release of | Current at time of | Current at time of | Current at time of | Current at time of generation |
| | CRAN, but manually manage updates | generation | generation | generation | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"r-devel"` | To develop/test against the development | Development version | Always current | Always current | Always current |
| | version of R | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"r-devel-bioc-devel"` | To develop/test against the development | Development version | Always current | Development version | Always current |
| | version of R and Bioconductor | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"bioc-devel"` | To develop/test against the development | Always current | Always current | Development version | Always current |
| | version of Bioconductor | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
```{=html}
<table border="1">
<thead>
<tr>
<th>r_ver</th>
<th>Intended use</th>
<th>State of R version</th>
<th>State of CRAN packages</th>
<th>State of Bioconductor packages</th>
<th>State of other packages in Nixpkgs</th>
</tr>
</thead>
<tbody>
<tr>
<td>"latest-upstream"</td>
<td>Start of new project where versions don’t matter</td>
<td>Current or previous</td>
<td>Outdated (up to 6 months)</td>
<td>Outdated (up to 6 months)</td>
<td>Current at time of generation</td>
</tr>
<tr>
<td>"4.4.2" (or other)</td>
<td>Reproducing old project or starting a new project where versions don’t matter</td>
<td>Same as in `r_ver`</td>
<td>Outdated (up to 2 months if using latest release)</td>
<td>Outdated (up to 2 months if using latest release)</td>
<td>Potentially outdated (up to 12 months)</td>
</tr>
<tr>
<td>"2024-12-14" (date)</td>
<td>Reproducing old project or starting a new project using the most recent date</td>
<td>Current at that date</td>
<td>Current at that date</td>
<td>Current at that date</td>
<td>Potentially outdated (up to 12 months)</td>
</tr>
<tr>
<td>"bleeding-edge"</td>
<td>To develop against the latest release of CRAN</td>
<td>Always current</td>
<td>Always current</td>
<td>Always current</td>
<td>Always current</td>
</tr>
<tr>
<td>"frozen-edge"</td>
<td>To develop against the latest release of CRAN, but manually manage updates</td>
<td>Current at time of generation</td>
<td>Current at time of generation</td>
<td>Current at time of generation</td>
<td>Current at time of generation</td>
</tr>
<tr>
<td>"r-devel"</td>
<td>To develop/test against the development version of R</td>
<td>Development version</td>
<td>Always current</td>
<td>Always current</td>
<td>Always current</td>
</tr>
<tr>
<td>"r-devel-bioc-devel"</td>
<td>To develop/test against the development version of R and Bioconductor</td>
<td>Development version</td>
<td>Always current</td>
<td>Development version</td>
<td>Always current</td>
</tr>
<tr>
<td>"bioc-devel"</td>
<td>To develop/test against the development version of Bioconductor</td>
<td>Always current</td>
<td>Always current</td>
<td>Development version</td>
<td>Always current</td>
</tr>
</tbody>
</table>
```


If you want to benefit from relatively fresh packages and have a stable environment
that for production purposes, using a date for `r_ver` is your best option.
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108 changes: 80 additions & 28 deletions vignettes/c-using-rix-to-build-project-specific-environments.Rmd
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Expand Up @@ -131,34 +131,86 @@ packages. We will explore this in greater detail in the vignette
There are several options for `r_ver` and each have a specific purpose. The
table below explains this:

|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| **r_ver** | **Intended use** | **State of R** | **State of CRAN** | **State of Bioconductor** | **State of other packages in** |
| | | **version** | **packages** | **packages** | **Nixpkgs** |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"latest-upstream"` | Start new project and versions | Current or previous | Outdated (up to 6 months) | Outdated (up to 6 months) | Current at time of generation |
| | don’t matter | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"4.4.2"` (or other) | Reproducing old project or starting a new | Same as in `r_ver` | Outdated (up to 2 months | Outdated (up to 2 months | Potentially outdated (up to 12 months) |
| | project where versions don’t matter | | if using latest release) | if using latest release) | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"2024-12-14"` (date) | Reproducing old project or starting a new | Current at that date | Current at that date | Current at that date | Potentially outdated (up to 12 months) |
| | project using the most recent date | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"bleeding-edge"` | To develop against the latest | Always current | Always current | Always current | Always current |
| | release of CRAN | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"frozen-edge"` | To develop against the latest release of | Current at time of | Current at time of | Current at time of | Current at time of generation |
| | CRAN, but manually manage updates | generation | generation | generation | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"r-devel"` | To develop/test against the development | Development version | Always current | Always current | Always current |
| | version of R | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"r-devel-bioc-devel"` | To develop/test against the development | Development version | Always current | Development version | Always current |
| | version of R and Bioconductor | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
| `"bioc-devel"` | To develop/test against the development | Always current | Always current | Development version | Always current |
| | version of Bioconductor | | | | |
|------------------------|--------------------------------------------|-------------------------|----------------------------|------------------------------------|-----------------------------------------|
```{=html}
<table border="1">
<thead>
<tr>
<th>r_ver</th>
<th>Intended use</th>
<th>State of R version</th>
<th>State of CRAN packages</th>
<th>State of Bioconductor packages</th>
<th>State of other packages in Nixpkgs</th>
</tr>
</thead>
<tbody>
<tr>
<td>"latest-upstream"</td>
<td>Start of new project where versions don’t matter</td>
<td>Current or previous</td>
<td>Outdated (up to 6 months)</td>
<td>Outdated (up to 6 months)</td>
<td>Current at time of generation</td>
</tr>
<tr>
<td>"4.4.2" (or other)</td>
<td>Reproducing old project or starting a new project where versions don’t matter</td>
<td>Same as in `r_ver`</td>
<td>Outdated (up to 2 months if using latest release)</td>
<td>Outdated (up to 2 months if using latest release)</td>
<td>Potentially outdated (up to 12 months)</td>
</tr>
<tr>
<td>"2024-12-14" (date)</td>
<td>Reproducing old project or starting a new project using the most recent date</td>
<td>Current at that date</td>
<td>Current at that date</td>
<td>Current at that date</td>
<td>Potentially outdated (up to 12 months)</td>
</tr>
<tr>
<td>"bleeding-edge"</td>
<td>To develop against the latest release of CRAN</td>
<td>Always current</td>
<td>Always current</td>
<td>Always current</td>
<td>Always current</td>
</tr>
<tr>
<td>"frozen-edge"</td>
<td>To develop against the latest release of CRAN, but manually manage updates</td>
<td>Current at time of generation</td>
<td>Current at time of generation</td>
<td>Current at time of generation</td>
<td>Current at time of generation</td>
</tr>
<tr>
<td>"r-devel"</td>
<td>To develop/test against the development version of R</td>
<td>Development version</td>
<td>Always current</td>
<td>Always current</td>
<td>Always current</td>
</tr>
<tr>
<td>"r-devel-bioc-devel"</td>
<td>To develop/test against the development version of R and Bioconductor</td>
<td>Development version</td>
<td>Always current</td>
<td>Development version</td>
<td>Always current</td>
</tr>
<tr>
<td>"bioc-devel"</td>
<td>To develop/test against the development version of Bioconductor</td>
<td>Always current</td>
<td>Always current</td>
<td>Development version</td>
<td>Always current</td>
</tr>
</tbody>
</table>
```

If you want to benefit from relatively fresh packages and have a stable
environment for production purposes, using `"latest-upstream"` or the most
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