Merge pull request #104 from zachcp/cranchecks23

More small fixes to R for CRAN release

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='[email protected]'),
  person('Zachary', 'Charlop-Powers', role=c('cre'), email='[email protected]'),
  person('Emma', 'Schymanski', role=c('ctb'), email='[email protected]'))
 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/unitTests/runit.match.R

@@ -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/vignettes/molform.Rmd

@@ -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}

rcdk/vignettes/using-rcdk.Rmd

@@ -26,7 +26,7 @@ chemical information with the R environment.
 The [CDK](https://cdk.github.io) is a Java library for cheminformatics that supports a wide variety
 of cheminformatics functionality ranging from reading molecular file
 formats, performing ring perception and armaticity detection to fingerprint
-generation and molecular descriptors. The CDK website provides links to useful documentation as well as complete [Javadocs](https://cdk.github.io/cdk/2.0/docs/api/index.html?overview-summary.html)
+generation and molecular descriptors. The CDK website provides links to useful documentation as well as complete [Javadocs](https://cdk.github.io/cdk/2.3/docs/api/index.html?overview-summary.html)
 
 ## Getting started
 
@@ -136,7 +136,7 @@ unlist(lapply(mols, get.smiles))
 ```
 
 
- The [CDK](https://cdk.github.io) supports a number of _flavors_ when generating SMILES. For example, you can generate a SMILES with or without chirality information or generate SMILES in [Kekule form](https://www.chemguide.co.uk/basicorg/bonding/benzene1.html). The `smiles.flavors` generates an object that represents the various flavors desired for SMILES output. See the [SmiFlavor javadocs](https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html) for the full list of possible flavors. Example usage is
+ The [CDK](https://cdk.github.io) supports a number of _flavors_ when generating SMILES. For example, you can generate a SMILES with or without chirality information or generate SMILES in [Kekule form](https://www.chemguide.co.uk/basicorg/bonding/benzene1.html). The `smiles.flavors` generates an object that represents the various flavors desired for SMILES output. See the [SmiFlavor javadocs](https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html) for the full list of possible flavors. Example usage is
 
  ```{r}
 smiles <- c('CCC', 'c1ccccc1', 'CCc1ccccc1CC(C)(C)CC(=O)NC')
@@ -145,7 +145,7 @@ get.smiles(mols[[3]], smiles.flavors(c('UseAromaticSymbols')))
 get.smiles(mols[[3]], smiles.flavors(c('Generic','CxSmiles')))
 ```
 
-Using the [CxSmiles](https://www.chemaxon.com/marvin-archive/latest/help/formats/cxsmiles-doc.html) flavors allows the user to encode a variety of information in the SMILES string, such as 2D or 3D coordinates.
+Using the [CxSmiles](http://www.chemeddl.org/tools/marvin/help/formats/cxsmiles-doc.html) flavors allows the user to encode a variety of information in the SMILES string, such as 2D or 3D coordinates.
 
 ```{r}
 m <- parse.smiles('CCC')[[1]]