Merge pull request #412 from mihem/improve_docs_remote_deps

Improve docs remote deps

vignettes/z-advanced-topic-handling-packages-with-remote-dependencies.Rmd

@@ -198,8 +198,18 @@ Remotes:
 
 `{rix}` uses the GitHub API to fetch the commits of these remote packages and
 will attempt to select the commit of the remote packages, whose date is closest
-to (always before, never after) the date of the commit provided by the user. If
-you don't have a Github Personal Acccess Token set up, it will show:
+to (always before, never after) the date of the commit provided by the user.
+Note: `{rix}` will only be able to fetch a maximum of 1000 commits. That means
+if the commit you provided is rather old or if the package has many commits, this
+will fail and fallback to the `HEAD` of the repository. We have not observed this
+in practice yet, but if this happens you should see a message like this:
+
+```
+Failed to get commit date for <<< satijalab/seurat-wrappers >>> No commits found before or on the target date
+Falling back to <<< HEAD >>>
+```
+
+If you don't have a Github Personal Acccess Token set up, it will show:
 
 ```
 When fetching the commit date from GitHub from <<< ropensci/rix >>>, no GitHub Personal Access Token found.
@@ -211,7 +221,7 @@ This should still work until you hit the API limit, in which case you will see
 messages, such as this one:
 
 ```
-Failed to get commit date from <<< satijalab/seurat-wrappers >>> API request failed with status code 403.
+Failed to get commit date for <<< satijalab/seurat-wrappers >>> API request failed with status code 403.
 Falling back to <<< HEAD >>>
 ```
 
@@ -230,9 +240,19 @@ Of course, you need to create a [GitHub PAT
 first](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-personal-access-token-classic).
 If don't want to always have to set the `GITHUB_PAT` environment variable, you
 can also use a more [long term solution](https://gitcreds.r-lib.org/index.html).
+For more information on GitHub Tokens, please also refer to [Happy Git and GitHub for the useR](https://happygitwithr.com/https-pat). For permanent storage, also refer
+to [this stackoverflow question](https://stackoverflow.com/a/5343146/21417317).
+
+Note: If you use `{gitcreds}`, you still need to set the `GITHUB_PAT` variable explicitly for each session before calling `{rix}`.
+To avoid exposing your PAT in your code, you could use:
+
+```
+my_token <- gitcreds::gitcreds_get()$password
+Sys.setenv(GITHUB_PAT = my_token)
+```
 
 However, you might still be getting the following message, even after
-configuring a GitHub PAT:
+correctly configuring a GitHub PAT:
 
 ```
 Failed to get closest commit for gaborcsardi/gh: Failed to download commit data