diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index b660f011a..0041cccfb 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -20,31 +20,31 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@v1 - - - uses: r-lib/actions/setup-pandoc@v1 - + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-r@v2 + + - uses: r-lib/actions/setup-pandoc@v2 + - name: Set up JDK 17 uses: actions/setup-java@v1 with: java-version: 17 - + - name: Build with Ant run: | cd rcdkjar ant clean jar cd ../ - + - name: Install dependencies run: | install.packages(c("remotes", "rcmdcheck"), repos = "http://cran.us.r-project.org") install.packages("pkgdown", type = "binary", repos = "http://cran.us.r-project.org") remotes::install_deps("rcdk", dependencies = TRUE) shell: Rscript {0} - + - name: Cache R packages uses: actions/cache@v2 with: @@ -56,14 +56,8 @@ jobs: - name: Install run: devtools::install("rcdk") shell: Rscript {0} - + - name: Check run: rcmdcheck::rcmdcheck("rcdk", args = "--no-manual", error_on = "error") shell: Rscript {0} - - - name: Deploy Website - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - Rscript -e 'pkgdown::deploy_to_branch(pkg="rcdk", branch="gh-pages", new_process = FALSE)' - \ No newline at end of file + diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index e0c18d85e..82de6782e 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -20,7 +20,7 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - uses: r-lib/actions/setup-pandoc@v2 diff --git a/rcdk/DESCRIPTION b/rcdk/DESCRIPTION index 64ac822fc..5348689ee 100755 --- a/rcdk/DESCRIPTION +++ b/rcdk/DESCRIPTION @@ -1,6 +1,6 @@ Package: rcdk -Version: 3.7.0 -Date: 2022-09-21 +Version: 3.8.0 +Date: 2023-06-11 Title: Interface to the 'CDK' Libraries Authors@R: c(person('Rajarshi', 'Guha', role=c('aut',"cph"), email='rajarshi.guha@gmail.com'), person('Zachary', 'Charlop-Powers', role=c('cre'), email='zach.charlop.powers@gmail.com'), @@ -27,6 +27,6 @@ Description: Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D. -RoxygenNote: 7.2.1 +RoxygenNote: 7.2.3 VignetteBuilder: knitr Encoding: UTF-8 diff --git a/rcdk/NEWS.md b/rcdk/NEWS.md index 7f151ca0f..e41338dc7 100755 --- a/rcdk/NEWS.md +++ b/rcdk/NEWS.md @@ -1,3 +1,7 @@ +# rcdk 3.8.0 + +* Change DESCRIPTION in accordance with CRAN rules about JDKs + # rcdk 3.7.0 * Update rCDK to work with rcdklibs 2.8 diff --git a/rcdk/inst/cont/rcdk.jar b/rcdk/inst/cont/rcdk.jar new file mode 100644 index 000000000..a011d1e85 Binary files /dev/null and b/rcdk/inst/cont/rcdk.jar differ diff --git a/rcdk/inst/unitTests/runit.match.R b/rcdk/inst/unitTests/runit.match.R index 8f874514f..42aee2636 100755 --- a/rcdk/inst/unitTests/runit.match.R +++ b/rcdk/inst/unitTests/runit.match.R @@ -46,7 +46,7 @@ test.mcs1 <- function() { lapply(mols, do.aromaticity) lapply(mols, set.atom.types) mcs <- get.mcs(mols[[1]], mols[[2]], TRUE) - checkEquals("org.openscience.cdk.AtomContainer2", .jclass(mcs)) + checkEquals("org.openscience.cdk.silent.AtomContainer2", .jclass(mcs)) checkEquals(9, get.atom.count(mcs)) } @@ -55,7 +55,7 @@ test.mcs3 <- function() { lapply(mols, do.aromaticity) lapply(mols, set.atom.types) mcs <- get.mcs(mols[[1]], mols[[2]], TRUE) - checkEquals("org.openscience.cdk.AtomContainer2", .jclass(mcs)) + checkEquals("org.openscience.cdk.silent.AtomContainer2", .jclass(mcs)) checkEquals(21, get.atom.count(mcs)) } diff --git a/rcdk/inst/unitTests/runit.smiles.R b/rcdk/inst/unitTests/runit.smiles.R index f613e7edb..ac0262866 100755 --- a/rcdk/inst/unitTests/runit.smiles.R +++ b/rcdk/inst/unitTests/runit.smiles.R @@ -7,7 +7,7 @@ test.get.smiles <- function() test.get.smiles2 <- function() { m1 <- parse.smiles("CCCNCC")[[1]] - m2 <- parse.smiles("CNCCS")[[1]] + m2 <- parse.smiles("CCNCCS")[[1]] mcs <- get.mcs(m1, m2) - checkEquals("[CH2]NCC", get.smiles(mcs, smiles.flavors(c('Unique')))) + checkEquals("[CH2]CNCC", get.smiles(mcs, smiles.flavors(c('Unique')))) } diff --git a/rcdk/vignettes/PerformanceNotes.Rmd b/rcdk/vignettes/PerformanceNotes.Rmd index ae7a81c38..589a09839 100644 --- a/rcdk/vignettes/PerformanceNotes.Rmd +++ b/rcdk/vignettes/PerformanceNotes.Rmd @@ -6,7 +6,7 @@ output: rmarkdown::html_vignette: toc: true vignette: > - %\VignetteIndexEntry{Handling Molecular Formulae} + %\VignetteIndexEntry{Performance Notes} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} ---