Update PPM package mapping database for R 4.4 #2002

nickybell · 2024-10-01T19:55:32Z

Description

When trying to install historical binaries using PPM on macOS using R 4.4, packages are installed from source rather than binaries. I believe this is because the database mapping package versions to snapshot dates has not been updated for R 4.4.

database <- renv:::renv_p3m_database_load()
key <- renv:::renv_p3m_database_key("macosx/big-sur-arm64", "4.4")
is.null(database[[key]])
#> [1] TRUE
key <- renv:::renv_p3m_database_key("macosx/big-sur-arm64", "4.3")
is.null(database[[key]])
#> [1] FALSE

Reprex

Based on #1699, using duckplyr as an example and attempting to install version 0.2.0 as a binary from the 2023-09-13 snapshot on PPM. (h/t @rszymanski)

Using R 4.4.1

withr::local_options(list(renv.settings.use.cache = FALSE)) # don't use cache to show how package is installed
    project_directory <- withr::local_tempdir()
    
    withr::with_dir(
        new = project_directory,
        code = {
            renv::init(restart = FALSE)
            
            message("Installing [email protected] from https://packagemanager.posit.co/cran/latest")
            # installs from source
            renv::install(
                "[email protected]", 
                prompt = FALSE
            ) 
            
            message("Installing [email protected] from P3M snapshot")
            # installs binary
            renv::install(
                "[email protected]", 
                prompt = FALSE,
                repos = c(
                    "CRAN" = "https://packagemanager.posit.co/cran/2023-09-13"
                )
            )
        }
    )

Output

#> The following package(s) will be updated in the lockfile:
#> 
#> # CRAN -----------------------------------------------------------------------
#> - renv   [* -> 1.0.7]
#> 
#> The version of R recorded in the lockfile will be updated:
#> - R      [* -> 4.4.1]
#> 
#> - Lockfile written to "/private/var/folders/xh/crvwt7596l3b9p1s66q3fr1r0000gp/T/RtmpWDsToA/fileb365693320c5/renv.lock".
#> Installing [email protected] from https://packagemanager.posit.co/cran/latest
#> # Downloading packages -------------------------------------------------------
#> - Downloading duckplyr from Repository ...      OK [216.8 Kb in 0.28s]
#> - Downloading cli from CRAN ...                 OK [file is up to date]
#> - Downloading collections from CRAN ...         OK [64.5 Kb in 0.23s]
#> - Downloading DBI from CRAN ...                 OK [905.4 Kb in 0.43s]
#> - Downloading dplyr from CRAN ...               OK [1.4 Mb in 0.56s]
#> - Downloading generics from CRAN ...            OK [81.7 Kb in 0.23s]
#> - Downloading glue from CRAN ...                OK [file is up to date]
#> - Downloading lifecycle from CRAN ...           OK [file is up to date]
#> - Downloading rlang from CRAN ...               OK [file is up to date]
#> - Downloading magrittr from CRAN ...            OK [219.9 Kb in 0.27s]
#> - Downloading pillar from CRAN ...              OK [643.7 Kb in 0.38s]
#> - Downloading fansi from CRAN ...               OK [306.3 Kb in 0.29s]
#> - Downloading utf8 from CRAN ...                OK [143.2 Kb in 0.24s]
#> - Downloading vctrs from CRAN ...               OK [1.3 Mb in 0.53s]
#> - Downloading R6 from CRAN ...                  OK [file is up to date]
#> - Downloading tibble from CRAN ...              OK [665.8 Kb in 0.37s]
#> - Downloading pkgconfig from CRAN ...           OK [18.3 Kb in 0.21s]
#> - Downloading tidyselect from CRAN ...          OK [221.5 Kb in 0.26s]
#> - Downloading withr from CRAN ...               OK [file is up to date]
#> - Downloading duckdb from CRAN ...              OK [10.4 Mb in 2.8s]
#> - Downloading purrr from CRAN ...               OK [490.2 Kb in 0.34s]
#> Successfully downloaded 21 packages in 13 seconds.
#> 
#> The following package(s) will be installed:
#> - cli         [3.6.3]
#> - collections [0.3.7]
#> - DBI         [1.2.3]
#> - dplyr       [1.1.4]
#> - duckdb      [1.1.0]
#> - duckplyr    [0.2.0]
#> - fansi       [1.0.6]
#> - generics    [0.1.3]
#> - glue        [1.8.0]
#> - lifecycle   [1.0.4]
#> - magrittr    [2.0.3]
#> - pillar      [1.9.0]
#> - pkgconfig   [2.0.3]
#> - purrr       [1.0.2]
#> - R6          [2.5.1]
#> - rlang       [1.1.4]
#> - tibble      [3.2.1]
#> - tidyselect  [1.2.1]
#> - utf8        [1.2.4]
#> - vctrs       [0.6.5]
#> - withr       [3.0.1]
#> These packages will be installed into "/private/var/folders/xh/crvwt7596l3b9p1s66q3fr1r0000gp/T/RtmpWDsToA/fileb365693320c5/renv/library/macos/R-4.4/aarch64-apple-darwin20".
#> 
#> # Installing packages --------------------------------------------------------
#> - Installing cli ...                            OK [installed binary in 0.42s]
#> - Installing collections ...                    OK [installed binary in 0.34s]
#> - Installing DBI ...                            OK [installed binary in 0.37s]
#> - Installing generics ...                       OK [installed binary in 0.33s]
#> - Installing glue ...                           OK [installed binary in 0.35s]
#> - Installing rlang ...                          OK [installed binary in 0.63s]
#> - Installing lifecycle ...                      OK [installed binary in 0.39s]
#> - Installing magrittr ...                       OK [installed binary in 0.75s]
#> - Installing fansi ...                          OK [installed binary in 0.33s]
#> - Installing utf8 ...                           OK [installed binary in 0.33s]
#> - Installing vctrs ...                          OK [installed binary in 0.48s]
#> - Installing pillar ...                         OK [installed binary in 0.69s]
#> - Installing R6 ...                             OK [installed binary in 0.94s]
#> - Installing pkgconfig ...                      OK [installed binary in 0.33s]
#> - Installing tibble ...                         OK [installed binary in 0.94s]
#> - Installing withr ...                          OK [installed binary in 0.8s]
#> - Installing tidyselect ...                     OK [installed binary in 0.91s]
#> - Installing dplyr ...                          OK [installed binary in 0.39s]
#> - Installing duckdb ...                         OK [installed binary in 1.2s]
#> - Installing purrr ...                          OK [installed binary in 0.85s]
#> - Installing duckplyr ...                       OK [built from source in 8.6s]
#> Successfully installed 21 packages in 21 seconds.
#> Installing [email protected] from P3M snapshot
#> # Downloading packages -------------------------------------------------------
#> - Downloading duckplyr from Repository ...      OK [372.9 Kb in 1.2s]
#> Successfully downloaded 1 package in 1.4 seconds.
#> 
#> The following package(s) will be installed:
#> - duckplyr [0.2.0]
#> These packages will be installed into "/private/var/folders/xh/crvwt7596l3b9p1s66q3fr1r0000gp/T/RtmpWDsToA/fileb365693320c5/renv/library/macos/R-4.4/aarch64-apple-darwin20".
#> 
#> # Installing packages --------------------------------------------------------
#> - Installing duckplyr ...                       OK [installed binary in 0.36s]
#> Successfully installed 1 package in 0.38 seconds.

^{Created on 2024-10-01 with reprex v2.1.1}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.1 (2024-06-14)
#>  os       macOS Sonoma 14.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2024-10-01
#>  pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package     * version date (UTC) lib source
#>  P cli           3.6.3   2024-06-21 [?] RSPM
#>  R digest        0.6.37  <NA>       [?] <NA>
#>  R evaluate      1.0.0   <NA>       [?] <NA>
#>  R fastmap       1.2.0   <NA>       [?] <NA>
#>  R fs            1.6.4   <NA>       [?] <NA>
#>  P glue          1.8.0   2024-09-30 [?] RSPM
#>  R htmltools     0.5.8.1 <NA>       [?] <NA>
#>  R knitr         1.48    <NA>       [?] <NA>
#>  P lifecycle     1.0.4   2023-11-07 [?] RSPM
#>  P renv          1.0.7   2024-04-11 [?] CRAN (R 4.4.1)
#>  R reprex        2.1.1   <NA>       [?] <NA>
#>  P rlang         1.1.4   2024-06-04 [?] RSPM
#>  R rmarkdown     2.28    <NA>       [?] <NA>
#>  R rstudioapi    0.16.0  <NA>       [?] <NA>
#>  R sessioninfo   1.2.2   <NA>       [?] <NA>
#>  P withr         3.0.1   2024-07-31 [?] RSPM
#>  R xfun          0.47    <NA>       [?] <NA>
#>  R yaml          2.3.10  <NA>       [?] <NA>
#> 
#>  [1] /private/var/folders/xh/crvwt7596l3b9p1s66q3fr1r0000gp/T/RtmpWDsToA/fileb365693320c5/renv/library/macos/R-4.4/aarch64-apple-darwin20
#>  [2] /Users/nickybell/Library/Caches/org.R-project.R/R/renv/sandbox/macos/R-4.4/aarch64-apple-darwin20/f7156815
#> 
#>  P ── Loaded and on-disk path mismatch.
#>  R ── Package was removed from disk.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Using R 4.3.1

withr::local_options(list(renv.settings.use.cache = FALSE)) # don't use cache to show how package is installed
    project_directory <- withr::local_tempdir()
    
    withr::with_dir(
        new = project_directory,
        code = {
            renv::init(restart = FALSE)
            
            message("Installing [email protected] from https://packagemanager.posit.co/cran/latest")
            # installs from source
            renv::install(
                "[email protected]", 
                prompt = FALSE
            )
        }
    )

Output

#> The following package(s) will be updated in the lockfile:
#> 
#> # RSPM -----------------------------------------------------------------------
#> - renv   [* -> 1.0.7]
#> 
#> The version of R recorded in the lockfile will be updated:
#> - R      [* -> 4.3.1]
#> 
#> - Lockfile written to "/private/var/folders/xh/crvwt7596l3b9p1s66q3fr1r0000gp/T/RtmpSXShFq/filed7ba529bb07c/renv.lock".
#> Installing [email protected] from https://packagemanager.posit.co/cran/latest
#> # Downloading packages -------------------------------------------------------
#> - Downloading duckplyr from P3M ...             OK [377.3 Kb in 1.3s]
#> - Downloading cli from CRAN ...                 OK [file is up to date]
#> - Downloading collections from CRAN ...         OK [63.3 Kb in 0.38s]
#> - Downloading DBI from CRAN ...                 OK [878.6 Kb in 0.43s]
#> - Downloading dplyr from CRAN ...               OK [1.4 Mb in 0.57s]
#> - Downloading generics from CRAN ...            OK [74.5 Kb in 0.22s]
#> - Downloading glue from CRAN ...                OK [file is up to date]
#> - Downloading lifecycle from CRAN ...           OK [file is up to date]
#> - Downloading rlang from CRAN ...               OK [file is up to date]
#> - Downloading magrittr from CRAN ...            OK [212.9 Kb in 0.25s]
#> - Downloading pillar from CRAN ...              OK [634.5 Kb in 0.37s]
#> - Downloading fansi from CRAN ...               OK [296 Kb in 0.28s]
#> - Downloading utf8 from CRAN ...                OK [140.5 Kb in 0.24s]
#> - Downloading vctrs from CRAN ...               OK [1.2 Mb in 0.54s]
#> - Downloading R6 from CRAN ...                  OK [file is up to date]
#> - Downloading tibble from CRAN ...              OK [658 Kb in 0.38s]
#> - Downloading pkgconfig from CRAN ...           OK [17.7 Kb in 0.21s]
#> - Downloading tidyselect from CRAN ...          OK [217 Kb in 0.27s]
#> - Downloading withr from CRAN ...               OK [file is up to date]
#> - Downloading duckdb from CRAN ...              OK [10.4 Mb in 3.0s]
#> - Downloading purrr from CRAN ...               OK [477.1 Kb in 0.33s]
#> Successfully downloaded 21 packages in 14 seconds.
#> 
#> The following package(s) will be installed:
#> - cli         [3.6.3]
#> - collections [0.3.7]
#> - DBI         [1.2.3]
#> - dplyr       [1.1.4]
#> - duckdb      [1.1.0]
#> - duckplyr    [0.2.0]
#> - fansi       [1.0.6]
#> - generics    [0.1.3]
#> - glue        [1.8.0]
#> - lifecycle   [1.0.4]
#> - magrittr    [2.0.3]
#> - pillar      [1.9.0]
#> - pkgconfig   [2.0.3]
#> - purrr       [1.0.2]
#> - R6          [2.5.1]
#> - rlang       [1.1.4]
#> - tibble      [3.2.1]
#> - tidyselect  [1.2.1]
#> - utf8        [1.2.4]
#> - vctrs       [0.6.5]
#> - withr       [3.0.1]
#> These packages will be installed into "/private/var/folders/xh/crvwt7596l3b9p1s66q3fr1r0000gp/T/RtmpSXShFq/filed7ba529bb07c/renv/library/R-4.3/aarch64-apple-darwin20".
#> 
#> # Installing packages --------------------------------------------------------
#> - Installing cli ...                            OK [installed binary in 0.44s]
#> - Installing collections ...                    OK [installed binary in 0.33s]
#> - Installing DBI ...                            OK [installed binary in 0.86s]
#> - Installing generics ...                       OK [installed binary in 0.34s]
#> - Installing glue ...                           OK [installed binary in 0.34s]
#> - Installing rlang ...                          OK [installed binary in 0.38s]
#> - Installing lifecycle ...                      OK [installed binary in 0.35s]
#> - Installing magrittr ...                       OK [installed binary in 0.35s]
#> - Installing fansi ...                          OK [installed binary in 0.35s]
#> - Installing utf8 ...                           OK [installed binary in 0.33s]
#> - Installing vctrs ...                          OK [installed binary in 0.38s]
#> - Installing pillar ...                         OK [installed binary in 0.38s]
#> - Installing R6 ...                             OK [installed binary in 0.34s]
#> - Installing pkgconfig ...                      OK [installed binary in 0.36s]
#> - Installing tibble ...                         OK [installed binary in 0.92s]
#> - Installing withr ...                          OK [installed binary in 0.35s]
#> - Installing tidyselect ...                     OK [installed binary in 0.53s]
#> - Installing dplyr ...                          OK [installed binary in 0.39s]
#> - Installing duckdb ...                         OK [installed binary in 0.93s]
#> - Installing purrr ...                          OK [installed binary in 0.59s]
#> - Installing duckplyr ...                       OK [installed binary in 0.77s]
#> Successfully installed 21 packages in 10 seconds.

^{Created on 2024-10-01 with reprex v2.1.1}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.1 (2023-06-16)
#>  os       macOS Sonoma 14.5
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2024-10-01
#>  pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package     * version date (UTC) lib source
#>  P cli           3.6.3   2024-06-21 [?] RSPM
#>  R digest        0.6.37  <NA>       [?] <NA>
#>  R evaluate      1.0.0   <NA>       [?] <NA>
#>  R fastmap       1.2.0   <NA>       [?] <NA>
#>  R fs            1.6.4   <NA>       [?] <NA>
#>  P glue          1.8.0   2024-09-30 [?] RSPM
#>  R htmltools     0.5.8.1 <NA>       [?] <NA>
#>  R knitr         1.48    <NA>       [?] <NA>
#>  P lifecycle     1.0.4   2023-11-07 [?] RSPM
#>  P renv          1.0.7   2024-04-11 [?] RSPM (R 4.3.1)
#>  R reprex        2.1.1   <NA>       [?] <NA>
#>  P rlang         1.1.4   2024-06-04 [?] RSPM
#>  R rmarkdown     2.28    <NA>       [?] <NA>
#>  R rstudioapi    0.16.0  <NA>       [?] <NA>
#>  R sessioninfo   1.2.2   <NA>       [?] <NA>
#>  P withr         3.0.1   2024-07-31 [?] RSPM
#>  R xfun          0.47    <NA>       [?] <NA>
#>  R yaml          2.3.10  <NA>       [?] <NA>
#> 
#>  [1] /private/var/folders/xh/crvwt7596l3b9p1s66q3fr1r0000gp/T/RtmpSXShFq/filed7ba529bb07c/renv/library/R-4.3/aarch64-apple-darwin20
#>  [2] /Users/nickybell/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/ac5c2659
#> 
#>  P ── Loaded and on-disk path mismatch.
#>  R ── Package was removed from disk.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

The text was updated successfully, but these errors were encountered:

kevinushey · 2024-10-02T01:29:29Z

Thanks -- I've updated the PPM database, but it looks like we didn't get the older versions of duckplyr for R 4.4.x.

> db <- renv:::renv_p3m_database_load()
> pkgs <- ls(envir = db$`/bin/macosx/big-sur-arm64/contrib/4.4`)
> grep("duckplyr", pkgs, value = TRUE)
[1] "duckplyr 0.3.2" "duckplyr 0.4.0" "duckplyr 0.4.1"

renv only synchronizes available packages from the release date of R, so you'd only see package releases from 2024-04-24 for R 4.4.x.

nickybell · 2024-10-02T03:07:16Z

Thanks! I am curious, what's the reason to only make available the package releases from the version release date? To ensure compatibility?

kevinushey · 2024-10-03T18:21:31Z

Mainly because I didn't realize that PPM was actually producing binary packages for snapshot dates that are older than the associated release of R. 😅

We might be able to expand this, but it would take some extra thought.

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Update PPM package mapping database for R 4.4 #2002

Update PPM package mapping database for R 4.4 #2002

nickybell commented Oct 1, 2024

kevinushey commented Oct 2, 2024 •

edited

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nickybell commented Oct 2, 2024

kevinushey commented Oct 3, 2024

Update PPM package mapping database for R 4.4 #2002

Update PPM package mapping database for R 4.4 #2002

Comments

nickybell commented Oct 1, 2024

Description

Reprex

Using R 4.4.1

Using R 4.3.1

kevinushey commented Oct 2, 2024 • edited Loading

nickybell commented Oct 2, 2024

kevinushey commented Oct 3, 2024

kevinushey commented Oct 2, 2024 •

edited

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