From ba4903780d218faaaafd3b346ed79fa8ed8bd526 Mon Sep 17 00:00:00 2001 From: aloctavodia Date: Fri, 5 Dec 2025 14:10:55 +0200 Subject: [PATCH 1/2] Bump release --- DESCRIPTION | 4 +- NEWS.md | 4 +- cran-comments.md | 84 ++++-------------------------------------- vignettes/projpred.Rmd | 2 +- 4 files changed, 13 insertions(+), 81 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7dd5e80f0..becd7be78 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: projpred Encoding: UTF-8 Title: Projection Predictive Feature Selection -Version: 2.9.1.9001 -Date: 2025-11-02 +Version: 2.10.0 +Date: 2025-12-05 Authors@R: c(person("Juho", "Piironen", role = c("aut"), email = "juho.t.piironen@gmail.com"), person("Markus", "Paasiniemi", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 6ca8b6572..4f78f7c29 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,13 +2,15 @@ If you read this from a place other than , please consider switching to that website since it features better formatting and cross-linking. -# projpred 2.9.1.9000 (development) +# projpred 2.10.0 ## Major changes * Added support for censored observations when using the latent projection (with response-scale analyses). This makes it possible, e.g., to use the latent projection for time-to-event models (also known as models for survival analysis). Due to this new feature, the function passed to argument `latent_ll_oscale` of `extend_family()` now needs to have an argument `cens`. See `?extend_family` (section "Latent projection") as well as the latent-projection vignette (section ["Censored observations (survival analysis)"](https://mc-stan.org/projpred/articles/latent.html#cens)) for more information and examples. Note that only the performance statistics `"elpd"`, `"mlpd"`, and `"gmpd"` take censoring into account (on response scale). (GitHub: #528) ## Minor changes + +* `suggest_size()` returns `nterms_max` instead of NA when no model satisfies the criterion * Use `reformulas` package directly for formula processing functions. This package is already a dependency of `lme4` >= v1.1-38. ## Bug fixes diff --git a/cran-comments.md b/cran-comments.md index 2f009dc71..948c80916 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,13 +1,14 @@ ## Test environments * Local: - + R version 4.5.1 (2025-06-13) on Ubuntu 25.04 system (platform: + + R version 4.5.1 (2025-06-13) on Ubuntu 24.04.3 LTS system (platform: x86_64-pc-linux-gnu (64-bit)) * win-builder: + R-devel (R Under development (unstable) (2025-07-02 r88374 ucrt)) - + R-release (R version 4.5.1 (2025-06-13 ucrt)) + + R-release (R version 4.5.2 (2025-10-31 ucrt)) + R-oldrelease (R version 4.4.3 (2025-02-28 ucrt)) + ## R CMD check results All checks gave neither ERRORs nor WARNINGs. @@ -16,76 +17,23 @@ All checks gave neither ERRORs nor WARNINGs. The local check on a Linux system gave the following NOTEs: - * checking CRAN incoming feasibility ... [10s/60s] NOTE - Maintainer: ‘Osvaldo Martin <[e-mail address]>’ - - New maintainer: - Osvaldo Martin <[e-mail address]> - Old maintainer(s): - Frank Weber <[e-mail address]> - Suggests or Enhances not in mainstream repositories: cmdstanr Availability using Additional_repositories specification: cmdstanr yes https://stan-dev.r-universe.dev/ - Found the following (possibly) invalid URLs: - URL: https://sites.stat.columbia.edu/gelman/arm/ - From: man/mesquite.Rd - Status: Error - Message: libcurl error code 60: - SSL certificate problem: unable to get local issuer certificate - (Status without verification: OK) - URL: https://sites.stat.columbia.edu/gelman/arm/examples/mesquite/mesquite.dat - From: man/mesquite.Rd - Status: Error - Message: libcurl error code 60: - SSL certificate problem: unable to get local issuer certificate - (Status without verification: OK) - - * checking compilation flags used ... NOTE - Compilation used the following non-portable flag(s): - ‘-mno-omit-leaf-frame-pointer’ - - * checking examples ... [27s/28s] NOTE - Examples with CPU (user + system) or elapsed time > 5s - user system elapsed - as.matrix.projection 8.788 0.437 9.376 - -As stated in the first NOTE, we would like to change the maintainer in this -release. - -As also stated in the first NOTE, the 'cmdstanr' package +As stated in the first NOTE, the 'cmdstanr' package () is not available on CRAN. The 'cmdstanr' backend can be used in 'projpred''s unit tests, but it is not necessary for 'projpred' to work. As this NOTE says, we have added the repository URL for the 'cmdstanr' package to the 'DESCRIPTION' file (field 'Additional_repositories'). -The URLs reported as possibly invalid in the first NOTE are in fact accessible. -The certificate problems are not related to 'projpred'. - -The compilation flag reported in the second NOTE is not set within 'projpred', -so it is probably due to the system that this local check ran on. In CRAN -checks, this NOTE has never appeared yet (but it is shown when checking the -previous CRAN version 2.8.0 locally). - -The runtime of the 'as.matrix.projection' example (see the third NOTE) may -sometimes be slightly > 5s. - ### win-builder checks #### R-devel The R-devel check on win-builder gave the following NOTE: - - * checking CRAN incoming feasibility ... [15s] NOTE - Maintainer: 'Osvaldo Martin <[e-mail address]>' - - New maintainer: - Osvaldo Martin <[e-mail address]> - Old maintainer(s): - Frank Weber <[e-mail address]> - + Suggests or Enhances not in mainstream repositories: cmdstanr Availability using Additional_repositories specification: @@ -97,14 +45,6 @@ For an explanation of this NOTE, see the explanations for the local check above. The R-release check on win-builder gave the following NOTEs: - * checking CRAN incoming feasibility ... [14s] NOTE - Maintainer: 'Osvaldo Martin <[e-mail address]>' - - New maintainer: - Osvaldo Martin <[e-mail address]> - Old maintainer(s): - Frank Weber <[e-mail address]> - Suggests or Enhances not in mainstream repositories: cmdstanr Availability using Additional_repositories specification: @@ -115,26 +55,16 @@ For an explanation of this NOTE, see the explanations for the local check above. #### R-oldrelease The R-oldrelease check on win-builder gave the following NOTEs: - - * checking CRAN incoming feasibility ... [20s] NOTE - Maintainer: 'Osvaldo Martin <[e-mail address]>' - - New maintainer: - Osvaldo Martin <[e-mail address]> - Old maintainer(s): - Frank Weber <[e-mail address]> + Suggests or Enhances not in mainstream repositories: cmdstanr Availability using Additional_repositories specification: cmdstanr yes https://stan-dev.r-universe.dev/ - * checking package dependencies ... NOTE - Packages suggested but not available for checking: 'unix', 'cmdstanr' For an explanation of the first NOTE, see the explanations for the local check -above. The unavailability of some "suggested" dependencies mentioned in the -second NOTE is not due to 'projpred'. +above. ## Downstream dependencies diff --git a/vignettes/projpred.Rmd b/vignettes/projpred.Rmd index c37e87455..04830bc6f 100755 --- a/vignettes/projpred.Rmd +++ b/vignettes/projpred.Rmd @@ -81,7 +81,7 @@ tau0 <- p0 / (D - p0) * 1 / sqrt(N) We now fit the reference model to the data. To make this vignette build faster, we use only 2 MCMC chains and 1000 iterations per chain (with half of them being discarded as warmup draws). In practice, 4 chains and 2000 iterations per chain are reasonable defaults. -Furthermore, we make use of [**rstan**](https://mc-stan.org/rstan/)'s parallelization, which means to run each chain on a separate CPU core^[More generally, the number of chains is split up as evenly as possible among the number of CPU cores.]. +Furthermore, we make use of [**rstan**](https://mc-stan.org/)'s parallelization, which means to run each chain on a separate CPU core^[More generally, the number of chains is split up as evenly as possible among the number of CPU cores.]. If you run the following code yourself, you can either rely on an automatic mechanism to detect the number of CPU cores (like the `parallel::detectCores()` function shown below) or adapt `ncores` manually to your system. ```{r ref_fit} # Set this manually if desired: From ac8290ad9800bda85bdf4b9a0240cf83cc0abca5 Mon Sep 17 00:00:00 2001 From: aloctavodia Date: Fri, 5 Dec 2025 16:11:38 +0200 Subject: [PATCH 2/2] update comments --- cran-comments.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 948c80916..ec92ce6bd 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -4,9 +4,9 @@ + R version 4.5.1 (2025-06-13) on Ubuntu 24.04.3 LTS system (platform: x86_64-pc-linux-gnu (64-bit)) * win-builder: - + R-devel (R Under development (unstable) (2025-07-02 r88374 ucrt)) + + R-devel R Under development (unstable) (2025-12-04 r89100 ucrt) + R-release (R version 4.5.2 (2025-10-31 ucrt)) - + R-oldrelease (R version 4.4.3 (2025-02-28 ucrt)) + + R-oldrelease (version 4.4.3 (2025-02-28 ucrt)) ## R CMD check results @@ -61,10 +61,13 @@ The R-oldrelease check on win-builder gave the following NOTEs: cmdstanr Availability using Additional_repositories specification: cmdstanr yes https://stan-dev.r-universe.dev/ - + + * checking package dependencies ... NOTE + Packages suggested but not available for checking: 'unix', 'cmdstanr' For an explanation of the first NOTE, see the explanations for the local check -above. +above. The unavailability of some "suggested" dependencies mentioned in the +second NOTE is not due to 'projpred'. ## Downstream dependencies