problem with drat package libraries

[tjmahr]

The Stan teams puts some packages in an R package repository https://mc-stan.org/r-packages/ and it appears to created using drat. renv::install() seems to search for a file on this repository, fails and throws an error. Regular install.packages() just throws a warning in this case.

options(
  repos = c(
    stan = "https://mc-stan.org/r-packages/",
    getOption("repos")
  )
)
renv::install("cmdstanr")
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> Error: error downloading 'https://mc-stan.org/r-packages/bin/windows/contrib/4.3/PACKAGES.rds' [curl: (22) The requested URL returned error: 404]

install.packages("cmdstanr")
#> Installing package into 'C:/Users/Tristan/Documents/.renv/library/2021-10-hl-vss-1f875583/R-4.3/x86_64-w64-mingw32'
#> (as 'lib' is unspecified)
#> also installing the dependencies 'gtable', 'isoband', 'numDeriv', 'ggplot2', 'abind', 'tensorA', 'distributional', 'matrixStats', 'checkmate', 'posterior'
#> Warning: unable to access index for repository https://mc-stan.org/r-packages/bin/windows/contrib/4.3:
#>   cannot open URL 'https://mc-stan.org/r-packages/bin/windows/contrib/4.3/PACKAGES'
#> package 'gtable' successfully unpacked and MD5 sums checked
#> package 'isoband' successfully unpacked and MD5 sums checked
#> package 'numDeriv' successfully unpacked and MD5 sums checked
#> package 'ggplot2' successfully unpacked and MD5 sums checked
#> package 'abind' successfully unpacked and MD5 sums checked
#> package 'tensorA' successfully unpacked and MD5 sums checked
#> package 'distributional' successfully unpacked and MD5 sums checked
#> package 'matrixStats' successfully unpacked and MD5 sums checked
#> package 'checkmate' successfully unpacked and MD5 sums checked
#> package 'posterior' successfully unpacked and MD5 sums checked
#> 
#> The downloaded binary packages are in
#>  C:\Users\Tristan\AppData\Local\Temp\Rtmp0cWazJ\downloaded_packages
#> #> installing the source package 'cmdstanr'

^{Created on 2023-05-12 with reprex v2.0.2}

[tjmahr]

Here is the same reprex but with the shim blocked to remove ambiguity.

options(
  repos = c(
    stan = "https://mc-stan.org/r-packages/",
    getOption("repos")
  )
)
renv::install("cmdstanr")
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation

#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> Error: error downloading 'https://mc-stan.org/r-packages/bin/windows/contrib/4.3/PACKAGES.rds' [curl: (22) The requested URL returned error: 404]

utils::install.packages("cmdstanr")
#> Installing package into 'C:/Users/Tristan/Documents/.renv/library/2021-10-hl-vss-1f875583/R-4.3/x86_64-w64-mingw32'
#> (as 'lib' is unspecified)
#> Warning: unable to access index for repository https://mc-stan.org/r-packages/bin/windows/contrib/4.3:
#>   cannot open URL 'https://mc-stan.org/r-packages/bin/windows/contrib/4.3/PACKAGES'
#> installing the source package 'cmdstanr'

^{Created on 2023-05-12 with reprex v2.0.2}

[hadley]

I think a minimal reprex should be this:

renv::install("cmdstanr", repos = "https://mc-stan.org/r-packages/")

(But that works for me, presumably because I'm on 4.2 which has binaries). I'm guessing that this is because stan hasn't built windows binaries for 4.3 yet.

[tjmahr]

Ahh thanks! I've let stan-dev know. stan-dev/r-packages#10

[hadley]

Looks like it's been fixed at their end:

tmp <- tempfile()
dir.create(tmp)
setwd(tmp)

options(
  repos = c(
    stan = "https://mc-stan.org/r-packages/",
    getOption("repos")
  )
)
renv::install("cmdstanr")
#> # Downloading packages -------------------------------------------------------
#> Retrieving 'https://mc-stan.org/r-packages/bin/macosx/big-sur-arm64/contrib/4.2/cmdstanr_0.5.3.tgz' ...
#>  OK [downloaded 1.1 Mb in 0.46 seconds]
#> 
#> # Installing packages into "~/Library/R/arm64/4.2/library" -------------------
#> The following package(s) will be installed:
#> 
#> - cmdstanr [0.5.3]
#> 
#> Installing cmdstanr ... OK [installed binary]
#> Caching    cmdstanr ... OK [copied]
#> Installed 1 package in 2.2 seconds.

^{Created on 2023-06-08 with reprex v2.0.2}

It's possible that there's some renv bug here too, but that's going to be hard to run down now that we don't have a reprex.