Merge pull request #104 from zachcp/cranchecks23

More small fixes to R for CRAN release

Author: rajarshi

rcdk/DESCRIPTION

@@ -1,12 +1,12 @@
 Package: rcdk
 Version: 3.5.0
-Date: 2019-01-21
+Date: 2020-03-06
 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'),
              person('Emma', 'Schymanski', role=c('ctb'), email='schymane@gmail.com'))
 Depends:
-    rcdklibs (>= 2.0)
+    rcdklibs (>= 2.3)
 Imports:
     fingerprint,
     rJava,
@@ -22,6 +22,7 @@ Suggests:
 SystemRequirements: Java JDK 8 or higher
 License: LGPL
 LazyLoad: yes
+LazyData: true
 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.

rcdk/R/formula.R

@@ -560,7 +560,7 @@ get.isotope.pattern.generator <- function(minAbundance = NULL) {
 #' @return A numeric value between 0 and 1 indicating the similarity between the two patterns
 #' @seealso \code{\link{get.isotope.pattern.similarity}}
 #' @export
-#' @references \url{http://cdk.github.io/cdk/2.0/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html}
+#' @references \url{http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html}
 #' @author Miguel Rojas Cherto
 compare.isotope.pattern <- function(iso1, iso2, ips = NULL) {
     cls <- unique(c(class(iso1), class(iso2)))

rcdk/R/rcdk.R

@@ -14,7 +14,7 @@
 #' Note that this is a static object that is created at package load time, 
 #' and the same instance is returned whenever this function is called.
 #' 
-#' @return An instance of \href{http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/silent/SilentChemObjectBuilder.html}{SilentChemObjectBuilder}
+#' @return An instance of \href{http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/silent/SilentChemObjectBuilder.html}{SilentChemObjectBuilder}
 #' @export
 #' @author Rajarshi Guha (\email{rajarshi.guha@@gmail.com})
 get.chem.object.builder <- function() {

rcdk/R/smiles.R

@@ -2,11 +2,11 @@
 #'
 #' The CDK supports a variety of customizations for SMILES generation including
 #' the use of lower case symbols for aromatic compounds to the use of the ChemAxon
-#' \href{https://www.chemaxon.com/marvin-archive/latest/help/formats/cxsmiles-doc.html}{CxSmiles}
+#' \href{http://www.chemeddl.org/tools/marvin/help/formats/cxsmiles-doc.html}{CxSmiles}
 #' format. Each 'flavor' is represented by an integer and multiple
 #' customizations are bitwise OR'ed. This method accepts the names of one or
 #' more customizations and returns the bitwise OR of them.
-#' See \href{https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation}
+#' See \href{https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation}
 #' for the list of flavors and what they mean.
 #'
 #' @param flavors A character vector of flavors. The default is \code{Generic} 
@@ -42,7 +42,7 @@
 #' @md
 #' @return A numeric representing the bitwise `OR`` of the specified flavors
 #' @seealso \code{\link{get.smiles}}
-#' @references \href{https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation}
+#' @references \href{https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation}
 #' @examples
 #' m <- parse.smiles('C1C=CCC1N(C)c1ccccc1')[[1]]
 #' get.smiles(m)

rcdk/inst/cont/rcdk.jar

@@ -64,7 +64,7 @@ test.mcs2 <- function() {
   lapply(mols, do.aromaticity)
   lapply(mols, do.typing) 
   mcs <- get.mcs(mols[[1]], mols[[2]], FALSE)
-  checkEquals("matrix", class(mcs))
+  checkTrue(inherits(mcs, "matrix"))
   checkEquals(9, nrow(mcs))
   checkEquals(2, ncol(mcs))
 }

rcdk/inst/unitTests/runit.match.R

@@ -44,7 +44,7 @@ formula <- get.mol2formula(molecule,charge=0)
 Note that the above formula object is a `CDKFormula-class`. This class
 contains some attributes that defines a molecular formula. For example,
 the mass, the charge, the isotopes, the character representation of the
-molecular formula and the [IMolecularFormula](https://cdk.github.io/cdk/2.0/docs/api/org/openscience/cdk/interfaces/IMolecularFormula.html) `jobjRef` object.
+molecular formula and the [IMolecularFormula](https://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/interfaces/IMolecularFormula.html) `jobjRef` object.
 
 The molecular mass, charge and string representation for this formula are given by
 ```{r}