From 33bc9dfe0f3b3109405648e10b513396260927c6 Mon Sep 17 00:00:00 2001 From: Hannah Frick Date: Wed, 29 Jan 2025 09:14:36 +0000 Subject: [PATCH 1/6] Polish NEWS --- NEWS.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index c5797e7e..a73eb4f3 100644 --- a/NEWS.md +++ b/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). From ef0a0524bdc4ab59208d95f10cde3a70c98040b1 Mon Sep 17 00:00:00 2001 From: Hannah Frick Date: Wed, 29 Jan 2025 09:17:53 +0000 Subject: [PATCH 2/6] Remove remote for sparsevctrs --- DESCRIPTION | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3ad382a5..539175f4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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 From 538b99a822c4466481a282b773c2489698af69ca Mon Sep 17 00:00:00 2001 From: Hannah Frick Date: Wed, 29 Jan 2025 10:34:12 +0000 Subject: [PATCH 3/6] clean out cran-comments --- cran-comments.md | 1 - 1 file changed, 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 3b175523..e69de29b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1 +0,0 @@ -There are no expected revdep failures. From 4e66fca0c33620b1a010d8d358eeb5a9ea096e10 Mon Sep 17 00:00:00 2001 From: Hannah Frick Date: Wed, 29 Jan 2025 10:34:58 +0000 Subject: [PATCH 4/6] update revdep checks --- revdep/README.md | 39 +++--------- revdep/cran.md | 18 +++++- revdep/failures.md | 153 ++++++++++++++++++++++++++++++++++++++++++++- revdep/problems.md | 24 ++++++- 4 files changed, 200 insertions(+), 34 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 4e6d5342..8f3a02b0 100644 --- a/revdep/README.md +++ b/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__ | | diff --git a/revdep/cran.md b/revdep/cran.md index e90c0b12..a1f65fb8 100644 --- a/revdep/cran.md +++ b/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) diff --git a/revdep/failures.md b/revdep/failures.md index 9a207363..8991f2fb 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -1 +1,152 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# censored + +
+ +* 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 + +
+ +## 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 + +
+ +* 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 + +
+ +## 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 + + + + + +``` diff --git a/revdep/problems.md b/revdep/problems.md index 9a207363..7c2ad410 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1 +1,23 @@ -*Wow, no problems at all. :)* \ No newline at end of file +# viralmodels + +
+ +* 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 + +
+ +## 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. + ``` + From d5ccff0cc3eea7ee60cbce91c1d63add7be3f185 Mon Sep 17 00:00:00 2001 From: Hannah Frick Date: Wed, 29 Jan 2025 10:39:12 +0000 Subject: [PATCH 5/6] Increment version number to 1.4.1 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 539175f4..8b12b6c3 100644 --- a/DESCRIPTION +++ b/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", , "hannah@posit.co", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6049-5258")), From b3b5ebb908c1a18946433d99fb6b5c220e3a02fe Mon Sep 17 00:00:00 2001 From: Hannah Frick Date: Wed, 29 Jan 2025 15:01:45 +0000 Subject: [PATCH 6/6] no need to link to the page itself --- R/quantile-pred.R | 12 ++++++------ man/quantile_pred.Rd | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/R/quantile-pred.R b/R/quantile-pred.R index 9695c577..d4c2b9dc 100644 --- a/R/quantile-pred.R +++ b/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)) diff --git a/man/quantile_pred.Rd b/man/quantile_pred.Rd index b73166a3..f9ac7cf3 100644 --- a/man/quantile_pred.Rd +++ b/man/quantile_pred.Rd @@ -21,7 +21,7 @@ the quantile levels.} \item{quantile_levels}{A vector of probabilities corresponding to \code{values}.} -\item{x}{An object produced by \code{\link[=quantile_pred]{quantile_pred()}}.} +\item{x}{An object produced by \code{quantile_pred()}.} \item{...}{Not currently used.} @@ -30,17 +30,17 @@ original S3 method.} } \value{ \itemize{ -\item \code{\link[=quantile_pred]{quantile_pred()}} returns a vector of values associated with the +\item \code{quantile_pred()} returns a vector of values associated with the quantile levels. -\item \code{\link[=extract_quantile_levels]{extract_quantile_levels()}} returns a numeric vector of levels. -\item \code{\link[=as_tibble]{as_tibble()}} returns a tibble with rows \code{".pred_quantile"}, +\item \code{extract_quantile_levels()} returns a numeric vector of levels. +\item \code{as_tibble()} returns a tibble with rows \code{".pred_quantile"}, \code{".quantile_levels"}, and \code{".row"}. -\item \code{\link[=as.matrix]{as.matrix()}} returns an unnamed matrix with rows as samples, columns as +\item \code{as.matrix()} returns an unnamed matrix with rows as samples, columns as quantile levels, and entries are predictions. } } \description{ -\code{\link[=quantile_pred]{quantile_pred()}} is a special vector class used to efficiently store +\code{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. }