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Merge pull request #125 from mrc-ide/feature/develop_fixnotes
Feature/develop fixnotes Failing CI checks on coverage, but otherwise passing
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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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,39 @@ | ||
| Package: drjacoby | ||
| Type: Package | ||
| Title: Flexible Markov Chain Monte Carlo via Reparameterization | ||
| 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")) | ||
| ) | ||
| Description: drjacoby is an R package for performing Bayesian inference via | ||
| Markov chain monte carlo (MCMC). In addition to being highly flexible it | ||
| implements some advanced techniques that can improve mixing in tricky | ||
| situations. | ||
| License: MIT + file LICENSE | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 7.1.2 | ||
| LinkingTo: | ||
| Rcpp | ||
| Imports: | ||
| Rcpp, | ||
| coda, | ||
| parallel, | ||
| ggplot2, | ||
| RcppXPtrUtils, | ||
| usethis, | ||
| tools, | ||
| rlang, | ||
| cowplot, | ||
| dplyr, | ||
| magrittr, | ||
| readr, | ||
| data.table | ||
| SystemRequirements: C++11 | ||
| Suggests: | ||
| testthat, | ||
| covr, | ||
| knitr, | ||
| rmarkdown, | ||
| microbenchmark, | ||
| gridExtra | ||
| BugReports: https://github.com/mrc-ide/drjacoby/issues | ||
| VignetteBuilder: knitr | ||
| Depends: R (>= 3.1.0) | ||
| Package: drjacoby | ||
| Type: Package | ||
| Title: Flexible Markov Chain Monte Carlo via Reparameterization | ||
| 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")) | ||
| ) | ||
| Description: drjacoby is an R package for performing Bayesian inference via | ||
| Markov chain monte carlo (MCMC). In addition to being highly flexible it | ||
| implements some advanced techniques that can improve mixing in tricky | ||
| situations. | ||
| License: MIT + file LICENSE | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 7.1.2 | ||
| LinkingTo: | ||
| Rcpp | ||
| Imports: | ||
| Rcpp, | ||
| coda, | ||
| parallel, | ||
| ggplot2, | ||
| usethis, | ||
| tools, | ||
| rlang, | ||
| cowplot, | ||
| dplyr, | ||
| magrittr | ||
| Suggests: | ||
| testthat, | ||
| covr, | ||
| knitr, | ||
| rmarkdown, | ||
| microbenchmark, | ||
| gridExtra | ||
| BugReports: https://github.com/mrc-ide/drjacoby/issues | ||
| VignetteBuilder: knitr | ||
| Depends: R (>= 3.1.0) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,2 @@ | ||
| MIT License | ||
|
|
||
| Copyright (c) 2019 MRC Centre for Outbreak Analysis and Modelling | ||
|
|
||
| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
|
|
||
| The above copyright notice and this permission notice shall be included in all | ||
| copies or substantial portions of the Software. | ||
|
|
||
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| SOFTWARE. | ||
| YEAR: 2024 | ||
| COPYRIGHT HOLDER: MRC Centre for Outbreak Analysis and Modelling |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| MIT License | ||
|
|
||
| Copyright (c) 2024 MRC Centre for Outbreak Analysis and Modelling | ||
|
|
||
| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
|
|
||
| The above copyright notice and this permission notice shall be included in all | ||
| copies or substantial portions of the Software. | ||
|
|
||
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| SOFTWARE. |
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