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Merge pull request #124 from mrc-ide/develop
Updating version prior to training workshop. Will try and get this version going on the mrc runiverse for ease of installation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,14 +1,15 @@ | ||
| ^data-raw$ | ||
| ^Meta$ | ||
| ^doc$ | ||
| ^docs$ | ||
| ^_pkgdown\.yml$ | ||
| ^codecov\.yml$ | ||
| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
| ignore/ | ||
| R_ignore/ | ||
| ^index.md | ||
| ^\.github$ | ||
| ^README\.Rmd$ | ||
| test_scripts/ | ||
| ^data-raw$ | ||
| ^Meta$ | ||
| ^doc$ | ||
| ^docs$ | ||
| ^_pkgdown\.yml$ | ||
| ^codecov\.yml$ | ||
| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ | ||
| ignore/ | ||
| R_ignore/ | ||
| ^index.md | ||
| ^\.github$ | ||
| ^README\.Rmd$ | ||
| test_scripts/ | ||
| LICENSE.md |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,81 +1,81 @@ | ||
| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | ||
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | ||
| on: | ||
| push: | ||
| branches: | ||
| - develop | ||
| pull_request: | ||
| branches: | ||
| - develop | ||
|
|
||
| name: develop_build | ||
|
|
||
| jobs: | ||
| R-CMD-check: | ||
| runs-on: ${{ matrix.config.os }} | ||
|
|
||
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: macOS-latest, r: 'release'} | ||
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
|
|
||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v1 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v1 | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| if: runner.os != 'Windows' | ||
| 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 system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| - name: Install dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran("rcmdcheck") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Upload check results | ||
| if: failure() | ||
| uses: actions/upload-artifact@main | ||
| with: | ||
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | ||
| path: check | ||
| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | ||
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | ||
| on: | ||
| push: | ||
| branches: | ||
| - develop | ||
| pull_request: | ||
| branches: | ||
| - develop | ||
|
|
||
| name: develop_build | ||
|
|
||
| jobs: | ||
| R-CMD-check: | ||
| runs-on: ${{ matrix.config.os }} | ||
|
|
||
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: macOS-latest, r: 'release'} | ||
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
|
|
||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v1 | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| if: runner.os != 'Windows' | ||
| 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 system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| - name: Install dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran("rcmdcheck") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Upload check results | ||
| if: failure() | ||
| uses: actions/upload-artifact@main | ||
| with: | ||
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | ||
| path: check |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,81 +1,81 @@ | ||
| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | ||
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: | ||
| - master | ||
|
|
||
| name: master_build | ||
|
|
||
| jobs: | ||
| R-CMD-check: | ||
| runs-on: ${{ matrix.config.os }} | ||
|
|
||
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: macOS-latest, r: 'release'} | ||
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
|
|
||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v1 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v1 | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| if: runner.os != 'Windows' | ||
| 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 system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| - name: Install dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran("rcmdcheck") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Upload check results | ||
| if: failure() | ||
| uses: actions/upload-artifact@main | ||
| with: | ||
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | ||
| path: check | ||
| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | ||
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | ||
| on: | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
| branches: | ||
| - master | ||
|
|
||
| name: master_build | ||
|
|
||
| jobs: | ||
| R-CMD-check: | ||
| runs-on: ${{ matrix.config.os }} | ||
|
|
||
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
|
|
||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - {os: windows-latest, r: 'release'} | ||
| - {os: macOS-latest, r: 'release'} | ||
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||
|
|
||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| RSPM: ${{ matrix.config.rspm }} | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v2 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
|
|
||
| - uses: r-lib/actions/setup-pandoc@v1 | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| install.packages('remotes') | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| if: runner.os != 'Windows' | ||
| 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 system dependencies | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| while read -r cmd | ||
| do | ||
| eval sudo $cmd | ||
| done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') | ||
| - name: Install dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE) | ||
| remotes::install_cran("rcmdcheck") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Check | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Upload check results | ||
| if: failure() | ||
| uses: actions/upload-artifact@main | ||
| with: | ||
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | ||
| path: check |
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Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| Package: drjacoby | ||
| Type: Package | ||
| Title: Flexible Markov Chain Monte Carlo via Reparameterization | ||
| Version: 1.5.2 | ||
| Version: 1.5.3 | ||
| Authors@R: c( | ||
| person("Bob", "Verity", email = "[email protected]", role = c("aut", "cre")), | ||
| person("Pete", "Winskill", email = "[email protected]", role = c("aut")) | ||
|
|
@@ -13,24 +13,20 @@ Description: drjacoby is an R package for performing Bayesian inference via | |
| License: MIT + file LICENSE | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 7.1.1 | ||
| RoxygenNote: 7.3.1 | ||
| LinkingTo: | ||
| Rcpp | ||
| Imports: | ||
| Rcpp, | ||
| coda, | ||
| parallel, | ||
| ggplot2, | ||
| RcppXPtrUtils, | ||
| usethis, | ||
| tools, | ||
| rlang, | ||
| cowplot, | ||
| dplyr, | ||
| magrittr, | ||
| readr, | ||
| data.table | ||
| SystemRequirements: C++11 | ||
| magrittr | ||
| Suggests: | ||
| testthat, | ||
| covr, | ||
|
|
||
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