From d98ef8afc3739068e56e6d33632f38690ca006d2 Mon Sep 17 00:00:00 2001 From: Valerio Gherardi Date: Fri, 28 Nov 2025 10:57:16 +0100 Subject: [PATCH 1/7] Increment version number to 1.0.1.9000 --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 619f775..e00db40 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: fcci Type: Package Title: Feldman-Cousins Confidence Intervals -Version: 1.0.1 +Version: 1.0.1.9000 Authors@R: person(given = "Valerio", family = "Gherardi", diff --git a/NEWS.md b/NEWS.md index fa4c0d6..6062c40 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# fcci (development version) + # fcci 1.0.1 * Set correct tolerance in algorithm tests. From ef48a805996e838407e3e0757e096e22c3b182d5 Mon Sep 17 00:00:00 2001 From: Valerio Gherardi Date: Fri, 28 Nov 2025 11:00:00 +0100 Subject: [PATCH 2/7] Remove C++11 spec from package dependencies --- DESCRIPTION | 1 - NEWS.md | 3 +++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index e00db40..314556b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,7 +19,6 @@ LinkingTo: Rcpp Imports: Rcpp, assertthat, rlang -SystemRequirements: C++11 URL: https://github.com/vgherard/fcci, https://vgherard.github.io/fcci/ BugReports: https://github.com/vgherard/fcci/issues diff --git a/NEWS.md b/NEWS.md index 6062c40..262657f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,8 @@ # fcci (development version) +* Removed C++11 specification in dependencies: the default C++17 suffices. + + # fcci 1.0.1 * Set correct tolerance in algorithm tests. From aacd5f7f54470726b04f6f6419124bba31d78f32 Mon Sep 17 00:00:00 2001 From: Valerio Gherardi Date: Fri, 28 Nov 2025 11:08:21 +0100 Subject: [PATCH 3/7] Update GH actions --- .github/workflows/R-CMD-check.yaml | 41 ++++++++++++---- .github/workflows/test-coverage.yaml | 72 +++++++++++++++++----------- DESCRIPTION | 2 +- README.Rmd | 4 +- README.md | 7 +-- man/fcci-package.Rd | 6 +-- 6 files changed, 85 insertions(+), 47 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 5bef95c..562fe0f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,28 +1,51 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: branches: [main, master] pull_request: - branches: [main, master] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: - runs-on: ubuntu-latest + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes + steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: rcmdcheck + extra-packages: any::rcmdcheck + needs: check - - uses: r-lib/actions/check-r-package@v1 + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index ba1f94f..0ab748d 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,48 +1,62 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: - - main - - master + branches: [main, master] pull_request: - branches: - - main - - master -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: - runs-on: macOS-latest + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage - - name: Query dependencies + - name: Test coverage run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + print(cov) + covr::to_cobertura(cov) shell: Rscript {0} - - name: Restore R package cache - uses: actions/cache@v2 + - uses: codecov/codecov-action@v5 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install dependencies + # Fail if error if not on PR, or if on PR and token is given + fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} + files: ./cobertura.xml + plugins: noop + disable_search: true + token: ${{ secrets.CODECOV_TOKEN }} + + - name: Show testthat output + if: always() run: | - install.packages(c("remotes")) - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("covr") - shell: Rscript {0} + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash - - name: Test coverage - run: covr::codecov() - shell: Rscript {0} + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package diff --git a/DESCRIPTION b/DESCRIPTION index 314556b..df5b987 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -14,7 +14,7 @@ Description: [G. J. Feldman and R. D. Cousins (1998) ]. License: GPL (>= 3) Encoding: UTF-8 -RoxygenNote: 7.1.1 +RoxygenNote: 7.3.3 LinkingTo: Rcpp Imports: diff --git a/README.Rmd b/README.Rmd index 41de7f7..c01c7c3 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,8 +17,8 @@ knitr::opts_chunk$set( [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![R-CMD-check](https://github.com/vgherard/fcci/workflows/R-CMD-check/badge.svg)](https://github.com/vgherard/fcci/actions) -[![Codecov test coverage](https://codecov.io/gh/vgherard/fcci/branch/master/graph/badge.svg)](https://app.codecov.io/gh/vgherard/fcci?branch=master) +[![R-CMD-check](https://github.com/vgherard/fcci/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/vgherard/fcci/actions/workflows/R-CMD-check.yaml) +[![Codecov test coverage](https://codecov.io/gh/vgherard/fcci/graph/badge.svg)](https://app.codecov.io/gh/vgherard/fcci) [![CRAN status](https://www.r-pkg.org/badges/version/fcci)](https://CRAN.R-project.org/package=fcci) [![R-universe status](https://vgherard.r-universe.dev/badges/fcci)](https://vgherard.r-universe.dev/) [![Website](https://img.shields.io/badge/Website-here-blue)](https://vgherard.github.io/fcci/) diff --git a/README.md b/README.md index 4e8e843..7e76f4f 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![R-CMD-check](https://github.com/vgherard/fcci/workflows/R-CMD-check/badge.svg)](https://github.com/vgherard/fcci/actions) +[![R-CMD-check](https://github.com/vgherard/fcci/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/vgherard/fcci/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/vgherard/fcci/branch/master/graph/badge.svg)](https://app.codecov.io/gh/vgherard/fcci?branch=master) [![CRAN @@ -17,6 +17,7 @@ status](https://www.r-pkg.org/badges/version/fcci)](https://CRAN.R-project.org/p status](https://vgherard.r-universe.dev/badges/fcci)](https://vgherard.r-universe.dev/) [![Website](https://img.shields.io/badge/Website-here-blue)](https://vgherard.github.io/fcci/) [![Tweet](https://img.shields.io/twitter/url/http/shields.io.svg?style=social)](https://twitter.com/intent/tweet?text=%7Bfcci%7D:%20Feldman-Cousins%20Confidence%20Intervals%20in%20R&url=https://vgherard.github.io/r2r&via=ValerioGherardi&hashtags=rstats,statistics,physics,confidenceintervals) + `fcci` is an R package providing support for building @@ -79,8 +80,8 @@ confint_pois(n = 10, b = 2, cl = 0.95) #> [1] 0.95 ``` -Let us compare the 68% C.L. intervals for *n* = 0 events and no -background obtained from `fcci` and from `stats::poisson.test()` +Let us compare the 68% C.L. intervals for $n=0$ events and no background +obtained from `fcci` and from `stats::poisson.test()` ``` r confint_pois(n = 0, cl = 0.68) diff --git a/man/fcci-package.Rd b/man/fcci-package.Rd index de74b08..e8be05a 100644 --- a/man/fcci-package.Rd +++ b/man/fcci-package.Rd @@ -6,19 +6,19 @@ \alias{fcci-package} \title{fcci: Feldman-Cousins Confidence Intervals} \description{ -Provides support for building Feldman-Cousins confidence intervals - [G. J. Feldman and R. D. Cousins (1998) ]. +Provides support for building Feldman-Cousins confidence intervals [G. J. Feldman and R. D. Cousins (1998) \doi{10.1103/PhysRevD.57.3873}]. } \seealso{ Useful links: \itemize{ \item \url{https://github.com/vgherard/fcci} + \item \url{https://vgherard.github.io/fcci/} \item Report bugs at \url{https://github.com/vgherard/fcci/issues} } } \author{ -\strong{Maintainer}: Valerio Gherardi \email{vgherard@sissa.it} (\href{https://orcid.org/0000-0002-8215-3013}{ORCID}) +\strong{Maintainer}: Valerio Gherardi \email{vgherard840@gmail.com} (\href{https://orcid.org/0000-0002-8215-3013}{ORCID}) } \keyword{internal} From 62108a7248de3b279c19a6054bfc046bc49f821f Mon Sep 17 00:00:00 2001 From: Valerio Gherardi Date: Fri, 28 Nov 2025 11:15:45 +0100 Subject: [PATCH 4/7] Increment version number to 1.0.2 --- DESCRIPTION | 2 +- NEWS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index df5b987..70157c5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: fcci Type: Package Title: Feldman-Cousins Confidence Intervals -Version: 1.0.1.9000 +Version: 1.0.2 Authors@R: person(given = "Valerio", family = "Gherardi", diff --git a/NEWS.md b/NEWS.md index 262657f..6bc01a7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# fcci (development version) +# fcci 1.0.2 * Removed C++11 specification in dependencies: the default C++17 suffices. From 4a3d3733e1f113cbf2437aa28122c87bcba25da6 Mon Sep 17 00:00:00 2001 From: Valerio Gherardi Date: Fri, 28 Nov 2025 11:21:15 +0100 Subject: [PATCH 5/7] Update CRAN comments for v1.0.2 release --- cran-comments.md | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 2da4f79..708ac87 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,14 +1,8 @@ -# fcci v1.0.1 +## v1.0.2 -This is a minor patch release fixing a test causing R CMD CHECK failure. +This is patch release with the only purpose of removing the C++11 specification +from package requirements (no longer needed as the current default is C++17). ## R CMD check results -0 errors | 0 warnings | 1 note - -``` -* New maintainer: - Valerio Gherardi -``` - -The maintainer has changed email address. +0 errors | 0 warnings | 0 note From 5a1dd22d2a48be3587bb1dbaef0de8dbb2ebce06 Mon Sep 17 00:00:00 2001 From: Valerio Gherardi Date: Fri, 28 Nov 2025 11:49:35 +0100 Subject: [PATCH 6/7] Remove Twitter badge from README --- README.Rmd | 1 - README.md | 4 +--- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/README.Rmd b/README.Rmd index c01c7c3..ad491a9 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,7 +22,6 @@ knitr::opts_chunk$set( [![CRAN status](https://www.r-pkg.org/badges/version/fcci)](https://CRAN.R-project.org/package=fcci) [![R-universe status](https://vgherard.r-universe.dev/badges/fcci)](https://vgherard.r-universe.dev/) [![Website](https://img.shields.io/badge/Website-here-blue)](https://vgherard.github.io/fcci/) -[![Tweet](https://img.shields.io/twitter/url/http/shields.io.svg?style=social)](https://twitter.com/intent/tweet?text={fcci}: Feldman-Cousins Confidence Intervals in R&url=https://vgherard.github.io/r2r&via=ValerioGherardi&hashtags=rstats,statistics,physics,confidenceintervals) `fcci` is an R package providing support for building [Feldman-Cousins](https://doi.org/10.1103/PhysRevD.57.3873) confidence diff --git a/README.md b/README.md index 7e76f4f..d2b816f 100644 --- a/README.md +++ b/README.md @@ -10,14 +10,12 @@ state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![R-CMD-check](https://github.com/vgherard/fcci/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/vgherard/fcci/actions/workflows/R-CMD-check.yaml) [![Codecov test -coverage](https://codecov.io/gh/vgherard/fcci/branch/master/graph/badge.svg)](https://app.codecov.io/gh/vgherard/fcci?branch=master) +coverage](https://codecov.io/gh/vgherard/fcci/graph/badge.svg)](https://app.codecov.io/gh/vgherard/fcci) [![CRAN status](https://www.r-pkg.org/badges/version/fcci)](https://CRAN.R-project.org/package=fcci) [![R-universe status](https://vgherard.r-universe.dev/badges/fcci)](https://vgherard.r-universe.dev/) [![Website](https://img.shields.io/badge/Website-here-blue)](https://vgherard.github.io/fcci/) -[![Tweet](https://img.shields.io/twitter/url/http/shields.io.svg?style=social)](https://twitter.com/intent/tweet?text=%7Bfcci%7D:%20Feldman-Cousins%20Confidence%20Intervals%20in%20R&url=https://vgherard.github.io/r2r&via=ValerioGherardi&hashtags=rstats,statistics,physics,confidenceintervals) - `fcci` is an R package providing support for building From 2e9b707f6384a5b3cfd1e1ee7254d9ed04a84a5c Mon Sep 17 00:00:00 2001 From: Valerio Gherardi Date: Fri, 28 Nov 2025 11:55:30 +0100 Subject: [PATCH 7/7] Add note to CRAN comments --- cran-comments.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 708ac87..121ac5e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -5,4 +5,12 @@ from package requirements (no longer needed as the current default is C++17). ## R CMD check results -0 errors | 0 warnings | 0 note +0 errors | 0 warnings | 1 note + +* checking DESCRIPTION meta-information ... NOTE +Author field differs from that derived from Authors@R + Author: 'Valerio Gherardi [aut, cre] (ORCID: )' + Authors@R: 'Valerio Gherardi [aut, cre] ()' + +I wasn't able to identify the source of this issue, as I don't have separate +Author and Authors@R fields. However, the issue looks innocuous.