From 27425394f3a4c04a53348c1d05c470fee729b78d Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 11:58:13 +1100 Subject: [PATCH 01/13] updating yml --- .github/workflows/pkgdown.yml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index b7de09e..e9c5f34 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -9,10 +9,13 @@ on: jobs: pkgdown: - runs-on: macOS-latest + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: + - name: Install R + uses: r-lib/actions/setup-r@v1.0.0 + - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@master @@ -40,11 +43,11 @@ jobs: remotes::install_deps(dependencies = TRUE, type="binary") shell: Rscript {0} - - name: Install pkgdown + - name: Install pkgdown run: | install.packages("pkgdown", type = "binary") shell: Rscript {0} - + - name: Install package run: R CMD INSTALL . From 30d44a87ac599df6e289fae7fe6c12288ba0a2cd Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 12:01:17 +1100 Subject: [PATCH 02/13] updating yml --- .github/workflows/pkgdown.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index e9c5f34..8a4bf8d 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -18,8 +18,6 @@ jobs: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@master - - uses: r-lib/actions/setup-pandoc@master - name: Query dependencies From c79fe7161f55dd7acae39ea74ba2301aa19df4ae Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 12:05:26 +1100 Subject: [PATCH 03/13] Update of the YML file --- .github/workflows/pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 8a4bf8d..c49d742 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -14,7 +14,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - name: Install R - uses: r-lib/actions/setup-r@v1.0.0 + uses: r-lib/actions/setup-r@v1 - uses: actions/checkout@v2 From 3869a91d590c108b23e071e5f8ba470859f3b509 Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 12:14:30 +1100 Subject: [PATCH 04/13] updating yml file --- .github/workflows/pkgdown.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index c49d742..dd90858 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -14,11 +14,11 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - name: Install R - uses: r-lib/actions/setup-r@v1 - - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-pandoc@master + uses: r-lib/actions/setup-r@v1 + + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-pandoc@v1.0.0 - name: Query dependencies run: | From c3a56015418a581752feb641a4d1de905cbb4f99 Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 12:18:10 +1100 Subject: [PATCH 05/13] updating yml file --- .github/workflows/pkgdown.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index dd90858..9891ef6 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -14,11 +14,11 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - name: Install R - uses: r-lib/actions/setup-r@v1 + uses: r-lib/actions/setup-r@v1 - - uses: actions/checkout@v2 + - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-pandoc@v1.0.0 + - uses: r-lib/actions/setup-pandoc@v1.0.0 - name: Query dependencies run: | From f49c9cd39362247e6c83b9a86e1e42c85ffabc7a Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 12:20:33 +1100 Subject: [PATCH 06/13] New YML --- .github/workflows/pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 9891ef6..879009a 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -18,7 +18,7 @@ jobs: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-pandoc@v1.0.0 + - uses: r-lib/actions/setup-pandoc@v2 - name: Query dependencies run: | From 695feaac274d660001ca6335745d2baeeca5dfbe Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 14:17:22 +1100 Subject: [PATCH 07/13] updating ghpages --- .github/workflows/pkgdown.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 879009a..5a16202 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -40,6 +40,11 @@ jobs: run: | remotes::install_deps(dependencies = TRUE, type="binary") shell: Rscript {0} + + - name: Install R + run: | + sudo apt-get update + sudo apt-get install r-base - name: Install pkgdown run: | From 253c320d74f04c9d7b0bbdbae883b5557e38bc71 Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 14:25:53 +1100 Subject: [PATCH 08/13] New version --- .github/workflows/pkgdown.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 5a16202..0d38e03 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -34,14 +34,13 @@ jobs: key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - name: Install binary dependencies if: runner.os != 'Linux' run: | remotes::install_deps(dependencies = TRUE, type="binary") shell: Rscript {0} - - - name: Install R + + - name: Install R run: | sudo apt-get update sudo apt-get install r-base From 72b890704e628d83dd16b3a3944fb161db590440 Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 14:29:07 +1100 Subject: [PATCH 09/13] new yml` file --- .github/workflows/pkgdown.yml | 55 ++++++++--------------------------- 1 file changed, 12 insertions(+), 43 deletions(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 0d38e03..ce2ea1f 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -6,55 +6,24 @@ on: - main - master - jobs: - pkgdown: + deploy: runs-on: ubuntu-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - name: Install R + - name: Checkout code + uses: actions/checkout@v2 + + - name: Setup R uses: r-lib/actions/setup-r@v1 - - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-pandoc@v2 - - name: Query dependencies + - name: Install dependencies run: | install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - uses: actions/cache@v2 - 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 binary dependencies - if: runner.os != 'Linux' - run: | - remotes::install_deps(dependencies = TRUE, type="binary") - shell: Rscript {0} - - - name: Install R - run: | - sudo apt-get update - sudo apt-get install r-base - - - name: Install pkgdown - run: | - install.packages("pkgdown", type = "binary") - shell: Rscript {0} - - - name: Install package - run: R CMD INSTALL . + remotes::install_deps(dependencies = TRUE) - - name: Deploy package + - name: Build and deploy run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' + Rscript -e "pkgdown::build_site()" + bash deploy.sh + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} \ No newline at end of file From b4695ce39678ac8ab7c948331bf47321abe91d50 Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 14:33:02 +1100 Subject: [PATCH 10/13] ready --- .github/workflows/pkgdown.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index ce2ea1f..8fb23a3 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -10,11 +10,15 @@ jobs: deploy: runs-on: ubuntu-latest steps: + - name: Install R + run: | + sudo apt-get update + sudo apt-get install r-base - name: Checkout code uses: actions/checkout@v2 - name: Setup R - uses: r-lib/actions/setup-r@v1 + uses: r-lib/actions/setup-r@v2 - name: Install dependencies run: | From d0564ab79fcbb29b0ae5cb7e9e1d8003f12cfddf Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 14:36:38 +1100 Subject: [PATCH 11/13] new page --- .github/workflows/pkgdown.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index 8fb23a3..beb6fd7 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -22,8 +22,8 @@ jobs: - name: Install dependencies run: | - install.packages('remotes') - remotes::install_deps(dependencies = TRUE) + Rscript -e "install.packages('remotes')" + Rscript -e "remotes::install_deps(dependencies = TRUE)" - name: Build and deploy run: | From a80007b21c138163f7d3a038453bfbe9af7622a8 Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Wed, 18 Oct 2023 14:55:38 +1100 Subject: [PATCH 12/13] yml: .github/workflows/pkgdown.yml --- .github/workflows/pkgdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml index beb6fd7..80387fc 100644 --- a/.github/workflows/pkgdown.yml +++ b/.github/workflows/pkgdown.yml @@ -24,6 +24,7 @@ jobs: run: | Rscript -e "install.packages('remotes')" Rscript -e "remotes::install_deps(dependencies = TRUE)" + Rscript -e "install.packages('pkgdown')" - name: Build and deploy run: | From a834ad88a6a631fb8d362fd0cfec37296999181d Mon Sep 17 00:00:00 2001 From: "Porobic Garate, Javier Porobic (Environment, Hobart)" Date: Mon, 30 Oct 2023 11:11:26 +1100 Subject: [PATCH 13/13] solved problem with naming of variables --- R/initGen.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/initGen.R b/R/initGen.R index c3b1e84..1130a83 100755 --- a/R/initGen.R +++ b/R/initGen.R @@ -172,7 +172,7 @@ generate.vars.init <- function(grp.file, cum.depths, df.atts, ice_model) { att.index <- c(att.index, indx) } if (df.grp$needsLight[grp]) { ## single light adaptation group - Variable <- c(Variable, paste("Light_Adaptn_", df.grp$Code[grp], + Variable <- c(Variable, paste("Light_Adaptn_", df.grp$code[grp], sep = "")) indx <- which(df.atts$name == "Light3D") long_name <- c(long_name, paste("Light adaption of",