From 8266f05e600bea47b504a5c2e95e6d007ba07469 Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 17:26:37 +0100 Subject: [PATCH 1/9] ignore check folder --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 4e3c4c7..69ebb98 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,4 @@ tags /doc/ /Meta/ +check From de8aee5ee343e2d9a2423f6f240e7356b04f7a0c Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 17:55:12 +0100 Subject: [PATCH 2/9] put linux CI in separate yml to install Tcl --- .github/workflows/check-linux.yaml | 50 +++++++++++++++++++++++++++ .github/workflows/check-standard.yaml | 3 -- 2 files changed, 50 insertions(+), 3 deletions(-) create mode 100644 .github/workflows/check-linux.yaml diff --git a/.github/workflows/check-linux.yaml b/.github/workflows/check-linux.yaml new file mode 100644 index 0000000..c72c60a --- /dev/null +++ b/.github/workflows/check-linux.yaml @@ -0,0 +1,50 @@ +# 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 + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {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@v3 + + - 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 + + - name: Install Tcl + run: sudo apt-get install -y tcl8.6-dev + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true \ No newline at end of file diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml index 2c39720..667023d 100644 --- a/.github/workflows/check-standard.yaml +++ b/.github/workflows/check-standard.yaml @@ -20,9 +20,6 @@ jobs: 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 }} From a6aaff1542dba2acb8f37910b00522a41b27a3b6 Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 17:55:33 +0100 Subject: [PATCH 3/9] update badge --- README.Rmd | 2 +- README.md | 12 +++++++----- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/README.Rmd b/README.Rmd index 6601033..cfc868a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -27,7 +27,7 @@ old <- options(width = 100L, digits = 10) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/GroupSeq)](https://cran.r-project.org/package=GroupSeq) -[![R-CMD-check](https://github.com/rpahl/GroupSeq/workflows/R-CMD-check/badge.svg)](https://github.com/rpahl/GroupSeq/actions) +[![R-CMD-check](https://github.com/rpahl/GroupSeq/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/rpahl/GroupSeq/actions/workflows/check-standard.yaml) [![dependencies](https://tinyverse.netlify.com/badge/GroupSeq)](https://CRAN.R-project.org/package=GroupSeq) [![Lifecycle_Badge](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://cran.r-project.org/package=GroupSeq) [![downloads](https://cranlogs.r-pkg.org/badges/GroupSeq?color=3aa9e8)](https://www.r-pkg.org:443/pkg/GroupSeq) diff --git a/README.md b/README.md index d820424..df8c228 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/GroupSeq)](https://cran.r-project.org/package=GroupSeq) -[![R-CMD-check](https://github.com/rpahl/GroupSeq/workflows/R-CMD-check/badge.svg)](https://github.com/rpahl/GroupSeq/actions) +[![R-CMD-check](https://github.com/rpahl/GroupSeq/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/rpahl/GroupSeq/actions/workflows/check-standard.yaml) [![dependencies](https://tinyverse.netlify.com/badge/GroupSeq)](https://CRAN.R-project.org/package=GroupSeq) [![Lifecycle_Badge](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://cran.r-project.org/package=GroupSeq) [![downloads](https://cranlogs.r-pkg.org/badges/GroupSeq?color=3aa9e8)](https://www.r-pkg.org:443/pkg/GroupSeq) @@ -55,9 +55,11 @@ page. Since the package was written back in 2005, the graphical user interface may appear a bit outdated. Still, it does it’s job and at least has -stood the test of time[1](#refs). Luckily in recent years -others have started to develop R-based tools with graphical user -interface and similar (and more) statistical functionality: +stood the test of +time[![^1](https://latex.codecogs.com/png.image?%5Cdpi%7B110%7D&space;%5Cbg_white&space;%5E1 "^1")](#refs). +Luckily in recent years others have started to develop R-based tools +with graphical user interface and similar (and more) statistical +functionality: - [gsDesign](https://CRAN.R-project.org/package=gsDesign) with a free [shiny web interface](https://gsdesign.shinyapps.io/prod/) including @@ -74,7 +76,7 @@ interface and similar (and more) statistical functionality: DeMets, D. L., and K. K. Lan. 1994. “Interim analysis: the alpha spending function approach.” *Stat Med* 13 -(13-14): 1341–52. . +(13-14): 1341–52. . From 756ef5907260757f17a31dd2ec723481870c0c2c Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 19:16:44 +0100 Subject: [PATCH 4/9] install non-dev tcl --- .github/workflows/check-linux.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-linux.yaml b/.github/workflows/check-linux.yaml index c72c60a..7e4949a 100644 --- a/.github/workflows/check-linux.yaml +++ b/.github/workflows/check-linux.yaml @@ -38,7 +38,7 @@ jobs: use-public-rspm: true - name: Install Tcl - run: sudo apt-get install -y tcl8.6-dev + run: sudo apt-get install -y tcl - uses: r-lib/actions/setup-r-dependencies@v2 with: From 85ee1544aded7bd3292fed9de26b27d079651c8e Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 19:31:09 +0100 Subject: [PATCH 5/9] remove tcl install as it seems already to be installed --- .github/workflows/check-linux.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/check-linux.yaml b/.github/workflows/check-linux.yaml index 7e4949a..c9cc675 100644 --- a/.github/workflows/check-linux.yaml +++ b/.github/workflows/check-linux.yaml @@ -37,9 +37,6 @@ jobs: http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - - name: Install Tcl - run: sudo apt-get install -y tcl - - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::rcmdcheck From f2228e1e9accbdd1fb6fe5f91b2dff44ec220c7f Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 19:47:24 +0100 Subject: [PATCH 6/9] set display variable --- .github/workflows/check-linux.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/check-linux.yaml b/.github/workflows/check-linux.yaml index c9cc675..e0f58c5 100644 --- a/.github/workflows/check-linux.yaml +++ b/.github/workflows/check-linux.yaml @@ -37,6 +37,9 @@ jobs: http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true + - name: Set Display variable + run: export DISPLAY=:99 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: any::rcmdcheck From 04a5fd4acb8cccf03c6278de91a94d815040358d Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 20:04:48 +0100 Subject: [PATCH 7/9] set DISPLAY variable 2nd try --- .github/workflows/check-linux.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check-linux.yaml b/.github/workflows/check-linux.yaml index e0f58c5..7146c4f 100644 --- a/.github/workflows/check-linux.yaml +++ b/.github/workflows/check-linux.yaml @@ -38,7 +38,7 @@ jobs: use-public-rspm: true - name: Set Display variable - run: export DISPLAY=:99 + run: echo "export DISPLAY=:99" - uses: r-lib/actions/setup-r-dependencies@v2 with: From 3d56e3c41606435d082c90abdd6b74524c13b03f Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 20:17:48 +0100 Subject: [PATCH 8/9] only run pipeline for windows for now --- .github/workflows/check-linux.yaml | 50 --------------------------- .github/workflows/check-standard.yaml | 3 +- 2 files changed, 1 insertion(+), 52 deletions(-) delete mode 100644 .github/workflows/check-linux.yaml diff --git a/.github/workflows/check-linux.yaml b/.github/workflows/check-linux.yaml deleted file mode 100644 index 7146c4f..0000000 --- a/.github/workflows/check-linux.yaml +++ /dev/null @@ -1,50 +0,0 @@ -# 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 - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {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@v3 - - - 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 - - - name: Set Display variable - run: echo "export DISPLAY=:99" - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::rcmdcheck - needs: check - - - uses: r-lib/actions/check-r-package@v2 - with: - upload-snapshots: true \ No newline at end of file diff --git a/.github/workflows/check-standard.yaml b/.github/workflows/check-standard.yaml index 667023d..54ab5db 100644 --- a/.github/workflows/check-standard.yaml +++ b/.github/workflows/check-standard.yaml @@ -18,7 +18,6 @@ jobs: fail-fast: false matrix: config: - - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} env: @@ -43,4 +42,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: - upload-snapshots: true \ No newline at end of file + upload-snapshots: true From bc0b75509b350004e678794619f6c068661be9bf Mon Sep 17 00:00:00 2001 From: Roman Pahl Date: Mon, 6 Nov 2023 20:30:01 +0100 Subject: [PATCH 9/9] rebuild home --- docs/404.html | 178 ++++++++++++++++++---------------------------- docs/authors.html | 171 +++++++++++++++----------------------------- docs/index.html | 150 ++++++++++++++++++++------------------ 3 files changed, 207 insertions(+), 292 deletions(-) diff --git a/docs/404.html b/docs/404.html index 9e1e3b3..cd19137 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,74 +1,34 @@ - - - - + + + + - Page not found (404) • GroupSeq - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + - - - - -
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Page not found (404)

+
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+ + - - diff --git a/docs/authors.html b/docs/authors.html index 5f2cb74..44b9e2b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,74 +1,12 @@ - - - - - - - -Authors • GroupSeq - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Authors and Citation • GroupSeq - - + + - - - -
-
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-

Authors

+
+
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Authors

+
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Citation

+ Source: DESCRIPTION +
- + +

Pahl R (2023). +GroupSeq: Group Sequential Design Probabilities - With Graphical User Interface. +R package version 1.4.2, https://CRAN.R-project.org/package=GroupSeq. +

+ 
@Manual{,
+  title = {GroupSeq: Group Sequential Design Probabilities - With Graphical User Interface},
+  author = {Roman Pahl},
+  year = {2023},
+  note = {R package version 1.4.2},
+  url = {https://CRAN.R-project.org/package=GroupSeq},
+}
@@ -209,22 +156,20 @@

Authors

-
- - + + diff --git a/docs/index.html b/docs/index.html index ce20945..c0ea1f7 100644 --- a/docs/index.html +++ b/docs/index.html @@ -21,7 +21,8 @@ + Supports the alpha spending approach by Lan-DeMets (1994) + <doi:10.1002/sim.4780131308>"> + +