Merge pull request #280 from tidymodels/rc-1-4-1

RC 1.4.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hardhat
 Title: Construct Modeling Packages
-Version: 1.4.0.9003
+Version: 1.4.1
 Authors@R: c(
     person("Hannah", "Frick", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6049-5258")),
@@ -25,7 +25,7 @@ Imports:
     cli (>= 3.6.0),
     glue (>= 1.6.2),
     rlang (>= 1.1.0),
-    sparsevctrs (>= 0.1.0.9000),
+    sparsevctrs (>= 0.2.0),
     tibble (>= 3.2.1),
     vctrs (>= 0.6.0)
 Suggests:
@@ -41,8 +41,6 @@ Suggests:
     testthat (>= 3.0.0),
     usethis (>= 2.1.5),
     withr (>= 3.0.0)
-Remotes:  
-    r-lib/sparsevctrs
 VignetteBuilder:
     knitr
 Config/Needs/website: tidyverse/tidytemplate

NEWS.md

@@ -1,9 +1,11 @@
-# hardhat (development version)
+# hardhat 1.4.1
 
 * Added a new vector class called `quantile_pred()` to house predictions made from a quantile regression model (tidymodels/parsnip#1191, @dajmcdon). 
 
 * Several functions gained a `call` argument for passing the call used in errors and warnings (#275).
 
+* Errors and warnings are now generated with the cli package (#272).
+
 # hardhat 1.4.0
 
 * Added `extract_postprocessor()` generic (#247).

R/quantile-pred.R

@@ -1,25 +1,25 @@
 #' Create a vector containing sets of quantiles
 #'
-#' [quantile_pred()] is a special vector class used to efficiently store
+#' `quantile_pred()` is a special vector class used to efficiently store
 #' predictions from a quantile regression model. It requires the same quantile
 #' levels for each row being predicted.
 #'
 #' @param values A matrix of values. Each column should correspond to one of
 #'   the quantile levels.
 #' @param quantile_levels A vector of probabilities corresponding to `values`.
-#' @param x An object produced by [quantile_pred()].
+#' @param x An object produced by `quantile_pred()`.
 #' @param .rows,.name_repair,rownames Arguments not used but required by the
 #' original S3 method.
 #' @param ... Not currently used.
 #'
 #' @export
 #' @return
-#'   * [quantile_pred()] returns a vector of values associated with the
+#'   * `quantile_pred()` returns a vector of values associated with the
 #' quantile levels.
-#'   * [extract_quantile_levels()] returns a numeric vector of levels.
-#'   * [as_tibble()] returns a tibble with rows `".pred_quantile"`,
+#'   * `extract_quantile_levels()` returns a numeric vector of levels.
+#'   * `as_tibble()` returns a tibble with rows `".pred_quantile"`,
 #'   `".quantile_levels"`, and `".row"`.
-#'   * [as.matrix()] returns an unnamed matrix with rows as samples, columns as
+#'   * `as.matrix()` returns an unnamed matrix with rows as samples, columns as
 #'   quantile levels, and entries are predictions.
 #' @examples
 #' .pred_quantile <- quantile_pred(matrix(rnorm(20), 5), c(.2, .4, .6, .8))

cran-comments.md

@@ -1 +0,0 @@
-There are no expected revdep failures.

revdep/README.md

@@ -1,34 +1,15 @@
-# Platform
+# Revdeps
 
-|field    |value                                                                                    |
-|:--------|:----------------------------------------------------------------------------------------|
-|version  |R version 4.3.3 (2024-02-29)                                                             |
-|os       |macOS Sonoma 14.4.1                                                                      |
-|system   |aarch64, darwin20                                                                        |
-|ui       |X11                                                                                      |
-|language |(EN)                                                                                     |
-|collate  |en_US.UTF-8                                                                              |
-|ctype    |en_US.UTF-8                                                                              |
-|tz       |America/Los_Angeles                                                                      |
-|date     |2024-05-30                                                                               |
-|pandoc   |3.1.12.3 @ /Applications/Positron.app/Contents/Resources/app/bin/pandoc/ (via rmarkdown) |
+## Failed to check (2)
 
-# Dependencies
+|package   |version |error |warning |note |
+|:---------|:-------|:-----|:-------|:----|
+|censored  |?       |      |        |     |
+|lnmixsurv |?       |      |        |     |
 
-|package   |old   |new        |Δ  |
-|:---------|:-----|:----------|:--|
-|hardhat   |1.3.1 |1.3.1.9000 |*  |
-|cli       |3.6.2 |3.6.2      |   |
-|fansi     |1.0.6 |1.0.6      |   |
-|glue      |1.7.0 |1.7.0      |   |
-|lifecycle |1.0.4 |1.0.4      |   |
-|magrittr  |2.0.3 |2.0.3      |   |
-|pillar    |1.9.0 |1.9.0      |   |
-|pkgconfig |2.0.3 |2.0.3      |   |
-|rlang     |1.1.3 |1.1.3      |   |
-|tibble    |3.2.1 |3.2.1      |   |
-|utf8      |1.2.4 |1.2.4      |   |
-|vctrs     |0.6.5 |0.6.5      |   |
+## New problems (1)
 
-# Revdeps
+|package     |version |error |warning |note |
+|:-----------|:-------|:-----|:-------|:----|
+|[viralmodels](problems.md#viralmodels)|1.3.1   |      |__+1__  |     |
 

revdep/cran.md

@@ -1,7 +1,19 @@
 ## revdepcheck results
 
-We checked 33 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 37 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 saw 1 new problems
+ * We failed to check 2 packages
 
+Issues with CRAN packages are summarised below.
+
+### New problems
+(This reports the first line of each new failure)
+
+* viralmodels
+  checking whether package ‘viralmodels’ can be installed ... WARNING
+
+### Failed to check
+
+* censored  (NA)
+* lnmixsurv (NA)

revdep/failures.md

@@ -1 +1,152 @@
-*Wow, no problems at all. :)*
+# censored
+
+<details>
+
+* Version: 0.3.2
+* GitHub: https://github.com/tidymodels/censored
+* Source code: https://github.com/cran/censored
+* Date/Publication: 2024-06-11 18:10:02 UTC
+* Number of recursive dependencies: 163
+
+Run `revdepcheck::cloud_details(, "censored")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/censored/new/censored.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
+    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
+* running under: Ubuntu 24.04.1 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘censored/DESCRIPTION’ ... OK
+...
+* this is package ‘censored’ version ‘0.3.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required and available but unsuitable version: ‘survival’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/censored/old/censored.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
+    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
+* running under: Ubuntu 24.04.1 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘censored/DESCRIPTION’ ... OK
+...
+* this is package ‘censored’ version ‘0.3.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required and available but unsuitable version: ‘survival’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# lnmixsurv
+
+<details>
+
+* Version: 3.1.6
+* GitHub: NA
+* Source code: https://github.com/cran/lnmixsurv
+* Date/Publication: 2024-09-03 15:20:08 UTC
+* Number of recursive dependencies: 195
+
+Run `revdepcheck::cloud_details(, "lnmixsurv")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/lnmixsurv/new/lnmixsurv.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
+    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
+* running under: Ubuntu 24.04.1 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘lnmixsurv/DESCRIPTION’ ... OK
+...
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+  ‘compare.Rmd’ using ‘UTF-8’... OK
+  ‘expectation_maximization.Rmd’ using ‘UTF-8’... OK
+  ‘intercept_only.Rmd’ using ‘UTF-8’... OK
+  ‘lnmixsurv.Rmd’ using ‘UTF-8’... OK
+  ‘parallel_computation.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 4 NOTEs
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/lnmixsurv/old/lnmixsurv.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
+    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
+* running under: Ubuntu 24.04.1 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘lnmixsurv/DESCRIPTION’ ... OK
+...
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+  ‘compare.Rmd’ using ‘UTF-8’... OK
+  ‘expectation_maximization.Rmd’ using ‘UTF-8’... OK
+  ‘intercept_only.Rmd’ using ‘UTF-8’... OK
+  ‘lnmixsurv.Rmd’ using ‘UTF-8’... OK
+  ‘parallel_computation.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 4 NOTEs
+
+
+
+
+
+```

revdep/problems.md

@@ -1 +1,23 @@
-*Wow, no problems at all. :)*
+# viralmodels
+
+<details>
+
+* Version: 1.3.1
+* GitHub: https://github.com/juanv66x/viralmodels
+* Source code: https://github.com/cran/viralmodels
+* Date/Publication: 2024-10-18 12:00:02 UTC
+* Number of recursive dependencies: 185
+
+Run `revdepcheck::cloud_details(, "viralmodels")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking whether package ‘viralmodels’ can be installed ... WARNING
+    ```
+    Found the following significant warnings:
+      Warning: replacing previous import ‘hardhat::contr_one_hot’ by ‘parsnip::contr_one_hot’ when loading ‘viralmodels’
+    See ‘/tmp/workdir/viralmodels/new/viralmodels.Rcheck/00install.out’ for details.
+    ```
+