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Install missing packages in a local library #262

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Install missing packages in a local library #262

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a92907b
Install required packages
maurolepore Dec 13, 2024
4bf586d
wip
maurolepore Dec 13, 2024
4390f75
Avoid modifying dependencies at the system level
maurolepore Dec 13, 2024
1779f67
Spellcheck
maurolepore Dec 13, 2024
3a6fd76
Merge branch 'main' into fix_install-missing-packages
maurolepore Dec 13, 2024
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43 changes: 35 additions & 8 deletions posts/2024-12-13_document_yo.../document_your_universe_with_dverse.qmd
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Expand Up @@ -34,13 +34,46 @@ The example here uses the 'admiralverse' -- a toy universe defined as every
package on CRAN today (2024-12-07), with a website, and a name starting with
'admiral'.

```{r admiralverse}
admiralverse <- c(
"admiral",
"admiraldev",
"admiralonco",
"admiralophtha",
"admiralpeds",
"admiralvaccine"
)
```

You need:

* the package {dverse} to <u>d</u>ocument your uni<u>verse</u>,
* each package in the toy 'admiralverse' to access the documentation metadata,
* {dplyr} to manipulate the output of {dverse}, and
* {DT} to create a searchable table.

```{r dependencies}
#| echo: false
#| message: false

# Ensure the packages used here are installed; else install them in a local
# library to avoid forcing new dependencies in the system of the blog
# administrators

local_library <- tempfile()
dir.create(local_library)
# https://adv-r.hadley.nz/functions.html#on-exit
on.exit(unlink(local_library), add = TRUE, after = FALSE)

.libPaths(c(.libPaths(), local_library))

if (!requireNamespace("pak", quietly = TRUE)) {
install.packages("pak", lib = local_library)
}
# The cache is smart. It won't re-install what's already available
pak::pak(c("dverse", admiralverse, "dplyr", "DT"), lib = local_library)
```
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@maurolepore maurolepore Dec 13, 2024 •
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Here I ensure that the packages I need are installed; else I install them in a local library to be polite -- I want to avoid forcing new dependencies in your system.

Let me know if you do prefer me to install them at a more general level, maybe in the Dockerfile?

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We install them as part of a workflow - I have added them now and so can close this PR :) blog is live!


```{r packages}
library(dverse)
library(admiral)
Expand Down Expand Up @@ -74,14 +107,6 @@ dverse::document_universe() takes the names of the packages in the
package.

```{r docs}
admiralverse <- c(
"admiral",
"admiraldev",
"admiralonco",
"admiralophtha",
"admiralpeds",
"admiralvaccine"
)
# For example: https://pharmaverse.github.io/admiral/reference/queries.html
template <- "https://pharmaverse.github.io/{package}/reference/{topic}.html"

Expand Down Expand Up @@ -195,3 +220,5 @@ insert_appendix(
file_name = list.files() %>% stringr::str_subset(".qmd") %>% first()
)
```


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