diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 04c06df..878e008 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -49,7 +49,7 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::rcmdcheck + extra-packages: any::rcmdcheck, any::yaml needs: check - name: Install reticulate diff --git a/DESCRIPTION b/DESCRIPTION index d5099f2..c3e8042 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: bundle Title: Serialize Model Objects with a Consistent Interface -Version: 0.1.2.9000 +Version: 0.1.3 Authors@R: c( person("Julia", "Silge", , "julia.silge@posit.co", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3671-836X")), @@ -30,7 +30,7 @@ Imports: withr Suggests: bonsai, - butcher (>= 0.3.6.9000), + butcher (>= 0.4.0), callr, caret, covr, @@ -58,8 +58,6 @@ Suggests: xgboost (>= 1.6.0.1) VignetteBuilder: knitr -Remotes: - tidymodels/butcher Config/Needs/website: tidyverse/tidytemplate Config/testthat/edition: 3 Config/usethis/last-upkeep: 2025-12-08 diff --git a/NEWS.md b/NEWS.md index 1940359..4ade83f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ -# bundle (development version) +# bundle 0.1.3 -* Make to work with new versions of xgboost models (#75). +* Updated to support new versions of xgboost models (#75). # bundle 0.1.2 diff --git a/README.Rmd b/README.Rmd index 73e5463..e1675af 100644 --- a/README.Rmd +++ b/README.Rmd @@ -24,8 +24,7 @@ knitr::opts_chunk$set( [![R-CMD-check](https://github.com/rstudio/bundle/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rstudio/bundle/actions/workflows/R-CMD-check.yaml) [![CRAN status](https://www.r-pkg.org/badges/version/bundle)](https://CRAN.R-project.org/package=bundle) -[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -[![Codecov test coverage](https://codecov.io/gh/rstudio/bundle/branch/main/graph/badge.svg)](https://app.codecov.io/gh/rstudio/bundle?branch=main) +[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![Codecov test coverage](https://codecov.io/gh/rstudio/bundle/graph/badge.svg)](https://app.codecov.io/gh/rstudio/bundle) @@ -78,10 +77,10 @@ Fit the boosted tree model: ```{r} # fit an boosted tree with xgboost via parsnip mod <- - boost_tree(trees = 5, mtry = 3) |> - set_mode("regression") |> - set_engine("xgboost") |> - fit(mpg ~ ., data = mtcars[1:25,]) + boost_tree(trees = 5, mtry = 3) |> + set_mode("regression") |> + set_engine("xgboost") |> + fit(mpg ~ ., data = mtcars[1:25, ]) mod ``` @@ -120,7 +119,7 @@ r( unbundled_mod <- unbundle(bundled_mod) - predict(unbundled_mod, new_data = mtcars[26:32,]) + predict(unbundled_mod, new_data = mtcars[26:32, ]) }, args = list( bundled_mod = bundled_mod diff --git a/README.md b/README.md index 28fddfb..dbc9419 100644 --- a/README.md +++ b/README.md @@ -9,11 +9,9 @@ [![CRAN status](https://www.r-pkg.org/badges/version/bundle)](https://CRAN.R-project.org/package=bundle) [![Lifecycle: -experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) +stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable) [![Codecov test coverage](https://codecov.io/gh/rstudio/bundle/branch/main/graph/badge.svg)](https://app.codecov.io/gh/rstudio/bundle?branch=main) -[![Codecov test -coverage](https://codecov.io/gh/rstudio/bundle/graph/badge.svg)](https://app.codecov.io/gh/rstudio/bundle) Typically, models in R exist in memory and can be saved as `.rds` files. @@ -89,10 +87,10 @@ Fit the boosted tree model: ``` r # fit an boosted tree with xgboost via parsnip mod <- - boost_tree(trees = 5, mtry = 3) |> - set_mode("regression") |> - set_engine("xgboost") |> - fit(mpg ~ ., data = mtcars[1:25,]) + boost_tree(trees = 5, mtry = 3) |> + set_mode("regression") |> + set_engine("xgboost") |> + fit(mpg ~ ., data = mtcars[1:25, ]) mod #> parsnip model object @@ -110,11 +108,11 @@ mod #> evaluation_log: #> iter training_rmse #> -#> 1 4.618358 -#> 2 3.627921 -#> 3 2.891176 -#> 4 2.300624 -#> 5 1.852596 +#> 1 4.655552 +#> 2 3.648086 +#> 3 2.877980 +#> 4 2.302021 +#> 5 1.850090 ``` Note that simply saving and loading the model results in changes to the @@ -126,8 +124,8 @@ saveRDS(mod, temp_file) mod2 <- readRDS(temp_file) compare(mod, mod2, ignore_formula_env = TRUE) -#> `old$fit$ptr` is -#> `new$fit$ptr` is +#> `old$fit$ptr` is +#> `new$fit$ptr` is ``` Saving and reloading `mod2` didn’t preserve XGBoost’s reference to its @@ -158,7 +156,7 @@ r( unbundled_mod <- unbundle(bundled_mod) - predict(unbundled_mod, new_data = mtcars[26:32,]) + predict(unbundled_mod, new_data = mtcars[26:32, ]) }, args = list( bundled_mod = bundled_mod @@ -167,13 +165,13 @@ r( #> # A tibble: 7 × 1 #> .pred #> -#> 1 28.7 -#> 2 25.0 -#> 3 23.7 -#> 4 18.0 -#> 5 20.3 -#> 6 14.9 -#> 7 22.2 +#> 1 28.6 +#> 2 25.8 +#> 3 25.8 +#> 4 16.7 +#> 5 20.2 +#> 6 15.3 +#> 7 21.2 ``` For a more in-depth demonstration of the package, see the [main diff --git a/cran-comments.md b/cran-comments.md index c320579..d6e9166 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,12 @@ ## revdepcheck results -We checked 1 reverse dependency, comparing R CMD check results across CRAN and dev versions of this package. +We checked 3 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems - * We failed to check 0 packages + * We failed to check 1 packages + +Issues with CRAN packages are summarised below. + +### Failed to check + +* ldmppr (NA) diff --git a/revdep/README.md b/revdep/README.md index 14a53d8..f1c1fe5 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,23 +1,30 @@ # Platform -|field |value | -|:--------|:------------------------------| -|version |R version 4.4.0 (2024-04-24) | -|os |macOS 15.0.1 | -|system |aarch64, darwin20 | -|ui |X11 | -|language |(EN) | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |America/Denver | -|date |2024-11-11 | -|pandoc |3.5 @ /opt/homebrew/bin/pandoc | +|field |value | +|:--------|:------------------------------------------| +|version |R version 4.5.2 (2025-10-31) | +|os |macOS Tahoe 26.1 | +|system |aarch64, darwin20 | +|ui |X11 | +|language |(EN) | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/Denver | +|date |2025-12-09 | +|pandoc |3.8.3 @ /opt/homebrew/bin/ (via rmarkdown) | +|quarto |1.9.3 @ /usr/local/bin/quarto | # Dependencies |package |old |new |Δ | |:-------|:-----|:----------|:--| -|bundle |0.1.1 |0.1.1.9000 |* | +|bundle |0.1.2 |0.1.2.9000 |* | # Revdeps +## Failed to check (1) + +|package |version |error |warning |note | +|:-------|:-------|:-----|:-------|:----| +|ldmppr |1.0.4 |1 | | | + diff --git a/revdep/cran.md b/revdep/cran.md index 782ef68..d6e9166 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,7 +1,12 @@ ## revdepcheck results -We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 3 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems - * We failed to check 0 packages + * We failed to check 1 packages +Issues with CRAN packages are summarised below. + +### Failed to check + +* ldmppr (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 9a20736..7194a0d 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1 +1,72 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# ldmppr + +
+ +* Version: 1.0.4 +* GitHub: https://github.com/lanedrew/ldmppr +* Source code: https://github.com/cran/ldmppr +* Date/Publication: 2025-02-24 21:00:02 UTC +* Number of recursive dependencies: 128 + +Run `revdepcheck::revdep_details(, "ldmppr")` for more info + +
+ +## In both + +* checking whether package ‘ldmppr’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/juliasilge/Work/posit/bundle/revdep/checks.noindex/ldmppr/new/ldmppr.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ldmppr’ ... +** this is package ‘ldmppr’ version ‘1.0.4’ +** package ‘ldmppr’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.4.4.1)’ +using C++17 +using SDK: ‘MacOSX26.1.sdk’ +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/juliasilge/Work/posit/bundle/revdep/library.noindex/ldmppr/Rcpp/include' -I'/Users/juliasilge/Work/posit/bundle/revdep/library.noindex/ldmppr/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/juliasilge/Work/posit/bundle/revdep/library.noindex/ldmppr/Rcpp/include' -I'/Users/juliasilge/Work/posit/bundle/revdep/library.noindex/ldmppr/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c self_correcting_model.cpp -o self_correcting_model.o +clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ldmppr.so RcppExports.o self_correcting_model.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R +ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0' not found +ld: warning: search path '/opt/gfortran/lib' not found +ld: library 'emutls_w' not found +clang++: error: linker command failed with exit code 1 (use -v to see invocation) +make: *** [ldmppr.so] Error 1 +ERROR: compilation failed for package ‘ldmppr’ +* removing ‘/Users/juliasilge/Work/posit/bundle/revdep/checks.noindex/ldmppr/new/ldmppr.Rcheck/ldmppr’ + + +``` +### CRAN + +``` +* installing *source* package ‘ldmppr’ ... +** this is package ‘ldmppr’ version ‘1.0.4’ +** package ‘ldmppr’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.4.4.1)’ +using C++17 +using SDK: ‘MacOSX26.1.sdk’ +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/juliasilge/Work/posit/bundle/revdep/library.noindex/ldmppr/Rcpp/include' -I'/Users/juliasilge/Work/posit/bundle/revdep/library.noindex/ldmppr/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o +clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/juliasilge/Work/posit/bundle/revdep/library.noindex/ldmppr/Rcpp/include' -I'/Users/juliasilge/Work/posit/bundle/revdep/library.noindex/ldmppr/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c self_correcting_model.cpp -o self_correcting_model.o +clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ldmppr.so RcppExports.o self_correcting_model.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R +ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0' not found +ld: warning: search path '/opt/gfortran/lib' not found +ld: library 'emutls_w' not found +clang++: error: linker command failed with exit code 1 (use -v to see invocation) +make: *** [ldmppr.so] Error 1 +ERROR: compilation failed for package ‘ldmppr’ +* removing ‘/Users/juliasilge/Work/posit/bundle/revdep/checks.noindex/ldmppr/old/ldmppr.Rcheck/ldmppr’ + + +```