from-source packages reported during deploy when unrelated to project

[aronatkins]

> rsconnect::writeManifest("~/dev/rstudio/standalone/rmarkdown")
ℹ Capturing R dependencies with renv
The following package(s) were installed from sources, but may be available from the following remotes:

- rsconnect  [rstudio/rsconnect]

Would you like to use these remote sources for these packages?
See 'snapshot.inference' in ?renv::config for more details.
Otherwise, these packages will be recorded with an unknown source.

Allow renv to update the remote sources for these packages? [Y/n]: 

The target directory contains an rsconnect folder, which renv sees as needing the rsconnect package.

[aronatkins]

This may be happening any time the GitHub version of rsconnect is in use.

td <- tempfile()
dir.create(td)
fn <- file.path(td, "index.Rmd")
writeLines(c("hello, markdown"), fn)
rsconnect::writeManifest(td)

This is enough to trigger the warning from renv.

[aronatkins]

When running these commands, my working directory was the rsconnect directory, not a content directory.

[hadley]

Possibly a similar case to https://github.com/rstudio/renv/issues/1469, but for snapshot()?

[hadley]

Also worth noting that I see this for every (?) dev package I have installed, so I don't think it's related to rsconnect. And I don't think it's related to package dependencies, since nothing should depend on S7:

The following package(s) were installed from sources, but may be available from the following remotes:

- admiral       [pharmaverse/admiral]
- bigrquery     [r-dbi/bigrquery]
- bookdown      [rstudio/bookdown]
- cmdstanr      [stan-dev/cmdstanr]
- cocktails     [hadley/cocktails]
- codebook      [rubenarslan/codebook]
- downlit       [r-lib/downlit]
- flexsurv      [chjackson/flexsurv-dev]
- freshr        [shawnlinxl/freshr]
- gtreg         [shannonpileggi/gtreg]
- hockeyR       [danmorse314/hockeyR]
- htmlbook      [hadley/htmlbook]
- inti          [flavjack/inti]
- log4r         [johnmyleswhite/log4r]
- multidplyr    [tidyverse/multidplyr]
- partialised   [UchidaMizuki/partialised]
- pryr          [hadley/pryr]
- rATTAINS      [mps9506/rATTAINS]
- rsconnect     [rstudio/rsconnect]
- S7            [rconsortium/OOP-WG]
- tidyjson      [colearendt/tidyjson]
- tidytemplate  [tidyverse/tidytemplate]
- TreeTools     [ms609/TreeTools]
- tsibble       [tidyverts/tsibble]
- urlchecker    [r-lib/urlchecker]
- wakefield     [trinker/wakefield]

And the manifest doesn't end up including any of these packages.

[hadley]

Argh, I've re-installed renv (from CRAN) and rsconnect (from source), and tweaked the reprex to run in a non-interactive environment, and now it seems ok:

td <- tempfile()
dir.create(td)
fn <- file.path(td, "index.Rmd")
writeLines(c("hello, markdown"), fn)

callr::r(\() rsconnect::writeManifest(), wd = td, show = TRUE)
#> ℹ Capturing R dependencies with renv
#> ✔ Found 31 dependencies
#> NULL

^{Created on 2023-07-17 with reprex v2.0.2}

[aronatkins]

Possible workaround:

Sys.setenv(RENV_CONFIG_SNAPSHOT_INFERENCE = "false")
rsconnect::writeManifest(td)

Unfortunately, if a package is missing (rmarkdown, for example), we are prompted to install some unknown set of packages:

> Sys.setenv(RENV_CONFIG_SNAPSHOT_INFERENCE = "false")
> rsconnect::writeManifest(td)
ℹ Capturing R dependencies with renv
What do you want to do? 

1: Snapshot, just using the currently installed packages.
2: Install the packages, then snapshot.
3: Cancel, and resolve the situation on your own.

Selection: 3
- Operation canceled.

[aronatkins]

Workaround: disable renv valiation:

Sys.setenv(RENV_CONFIG_SNAPSHOT_VALIDATE = "false")
rsconnect::writeManifest(td)
#> ℹ Capturing R dependencies with renv
#> ✔ Found 31 dependencies

[aronatkins]

The renv:::renv_snapshot_preflight function is called only when snapshot validation is enabled, and its call to renv:::renv_snapshot_preflight_check_sources only happens when interactive().

[aronatkins]

I am also no longer seeing the What do you want to do? prompt. Could the CRAN mirror propagation to cran.rstudio.com be in play?

[aronatkins]

Filed https://github.com/rstudio/renv/issues/1559 to track the problem with rsconnect-from-source.

[aronatkins]

The formatting of the message has changed with the latest GitHub version of renv:

> rsconnect::writeManifest(td)
ℹ Capturing R dependencies with renv
The following package(s) were installed from sources, but may be available from the following remotes:
- rsconnect  [rstudio/rsconnect]
Would you like to use these remote sources for these packages?
See 'snapshot.inference' in ?renv::config for more details.
Otherwise, these packages will be recorded with an unknown source.

Allow renv to update the remote sources for these packages? [Y/n]: n

✔ Found 31 dependencies

[kevinushey]

@aronatkins: how are you installing the development version of rsconnect?

[aronatkins]

@kevinushey - rsconnect was installed using the IDE "Install" button in the Build pane. Normal package development workflow. The same warning would happen for renv if it was installed using the IDE, as well.

[hadley]

With a local version of rsconnect and latest CRAN renv, I now see:

td <- tempfile()
dir.create(td)
fn <- file.path(td, "index.Rmd")
writeLines(c("hello, markdown"), fn)
rsconnect::writeManifest(td)
#> ℹ Capturing R dependencies with renv
#> ✔ Found 31 dependencies

^{Created on 2023-10-26 with reprex v2.0.2}

So maybe this is fixed now?

[aronatkins]

So maybe this is fixed now?

Seems like it. I've not recently hit this.