20230611 cran (#144)

* update news and description

* update Roxygen

* - address issues to fix tests
- fix Vignette name

* rebuild 3.8

* bump GH actions

* pkg down yaml build and deploys the pages

* update news

---------

Co-authored-by: Zachary Charlop-Powers <zcpowers@Zacharys-MacBook-Air.local>

.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)'
-        
+

.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
 

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

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

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))
 }
 

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'))))
 }

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}
 ---