diff --git a/rcdk/DESCRIPTION b/rcdk/DESCRIPTION
index 8d3bffacef..80361ea7ed 100644
--- a/rcdk/DESCRIPTION
+++ b/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.
diff --git a/rcdk/R/formula.R b/rcdk/R/formula.R
index 7eb0e93e24..7f96c3a14f 100644
--- a/rcdk/R/formula.R
+++ b/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)))
diff --git a/rcdk/R/rcdk.R b/rcdk/R/rcdk.R
index aefe4f142d..2f076d9a3f 100644
--- a/rcdk/R/rcdk.R
+++ b/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() {
diff --git a/rcdk/R/smiles.R b/rcdk/R/smiles.R
index b52b91520a..40b41f8447 100644
--- a/rcdk/R/smiles.R
+++ b/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)
diff --git a/rcdk/inst/cont/rcdk.jar b/rcdk/inst/cont/rcdk.jar
index bf252f59b9..edfd90b74b 100644
Binary files a/rcdk/inst/cont/rcdk.jar 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 51419f89f8..26fcc47edb 100644
--- a/rcdk/inst/unitTests/runit.match.R
+++ b/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))
 }
diff --git a/rcdk/man/compare.isotope.pattern.Rd b/rcdk/man/compare.isotope.pattern.Rd
index dcc672e73e..a31a2fb8a7 100644
--- a/rcdk/man/compare.isotope.pattern.Rd
+++ b/rcdk/man/compare.isotope.pattern.Rd
@@ -20,7 +20,7 @@ A numeric value between 0 and 1 indicating the similarity between the two patter
 Computes a similarity score between two different isotope abundance patterns.
 }
 \references{
-\url{http://cdk.github.io/cdk/2.0/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html}
+\url{http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html}
 }
 \seealso{
 \code{\link{get.isotope.pattern.similarity}}
diff --git a/rcdk/man/get.chem.object.builder.Rd b/rcdk/man/get.chem.object.builder.Rd
index 2fa0cd5fa0..72e5a7e089 100644
--- a/rcdk/man/get.chem.object.builder.Rd
+++ b/rcdk/man/get.chem.object.builder.Rd
@@ -7,7 +7,7 @@
 get.chem.object.builder()
 }
 \value{
-An instance of \href{http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/silent/SilentChemObjectBuilder.html}{SilentChemObjectBuilder}
+An instance of \href{http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/silent/SilentChemObjectBuilder.html}{SilentChemObjectBuilder}
 }
 \description{
 The CDK employs a builder design pattern to construct
diff --git a/rcdk/man/smiles.flavors.Rd b/rcdk/man/smiles.flavors.Rd
index b2c8f9390e..d45127ebd5 100644
--- a/rcdk/man/smiles.flavors.Rd
+++ b/rcdk/man/smiles.flavors.Rd
@@ -46,11 +46,11 @@ A numeric representing the bitwise `OR`` of the specified flavors
 \description{
 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.
 }
 \examples{
@@ -64,7 +64,7 @@ get.smiles(m,flavor = smiles.flavors(c("CxSmiles","UseAromaticSymbols")))
 
 }
 \references{
-\href{https://cdk.github.io/cdk/2.0/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation}
+\href{https://cdk.github.io/cdk/2.3/docs/api/index.html?org/openscience/cdk/smiles/SmiFlavor.html}{CDK documentation}
 }
 \seealso{
 \code{\link{get.smiles}}
diff --git a/rcdk/vignettes/molform.Rmd b/rcdk/vignettes/molform.Rmd
index 3dc596cecc..9685bc6f13 100644
--- a/rcdk/vignettes/molform.Rmd
+++ b/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}
diff --git a/rcdk/vignettes/using-rcdk.Rmd b/rcdk/vignettes/using-rcdk.Rmd
index 79c8bcee69..c41dac2c69 100644
--- a/rcdk/vignettes/using-rcdk.Rmd
+++ b/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]]