20250910 vbump (#156)

* - fix links to fingerprint package and update the docs

* Add Egon and bump version

* Fix a few test fns and lints

* update news file and Cran comments for submission

* update cache

* http->https URL Updates

* update description and Vignetter

* ignore the vignette that uses depict, which is not on CRAN and is causing problems

* add cran

* Clean build

* simplify examples for CRAN tests

* Remove expensive tests when on CRAN

* Using MACCs in our examples to speed calculation

* update cran_comments

* update the linux CRAN detection

* fix one more URL

* update CRAN submission markdown

* fix: URL moved permanently

* fix: set CPUs to 1 inside of CHECK environments

* fix: run all tests during the check now that CPU usage has been limited in CHECK envs

* fix update CRAN submission docs

* spelling

* update the date

* Correct first name

* Setup JAVA for single threaded testing to avoid triggering warning on CRAN

* prep for resubmission

* rebuild docs

---------

Co-authored-by: Egon Willighagen <egon.willighagen@gmail.com>

Author: zachcp

.github/workflows/R-CMD-check.yaml

@@ -46,7 +46,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

README.Rmd

@@ -11,7 +11,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-[![Build Status](https://api.travis-ci.org/CDK-R/cdkr.svg?branch=master)](https://travis-ci.org/CDK-R/cdkr)
+
 [![CRAN Version](https://www.r-pkg.org/badges/version/rcdk?color=green)](https://cran.r-project.org/package=rcdk)
 [![CRAN Downloads](http://cranlogs.r-pkg.org/badges/grand-total/rcdk?color=green)](https://cran.r-project.org/package=rcdk)
 [![CRAN Downloads Monthyl](http://cranlogs.r-pkg.org/badges/last-month/rcdk?color=green)](https://cran.r-project.org/package=rcdk)

rcdk/.Rbuildignore

@@ -6,3 +6,6 @@
 ^pkgdown$
 ^revdep$
 README.Rmd
+vignettes/Features_29.Rmd
+^doc$
+^Meta$

rcdk/.gitignore

@@ -5,4 +5,6 @@ revdep/
 .Rhistory
 .Rproj
 *.Rmd
-*.png
+*.png
+/doc/
+/Meta/

rcdk/DESCRIPTION

@@ -1,14 +1,16 @@
 Package: rcdk
-Version: 3.9.0
-Date: 2024-03-02
+Version: 3.8.2
+Date: 2025-11-30
 Title: Interface to the 'CDK' Libraries
 Authors@R: c(
   person('Rajarshi', 'Guha', ,'rajarshi.guha@gmail.com', role=c('aut',"cph"),
     comment = c(ORCID = "0000-0001-7403-8819")),
-  person('Zachary', 'Charlop-Powers', ,'zach.charlop.powers@gmail.com',role=c('cre'), 
+  person('Zachary', 'Charlop-Powers', ,'zach.charlop.powers@gmail.com',role=c('cre'),
       comment = c(ORCID = "0000-0001-8816-4680")),
-  person('Emma', 'Schymanski', ,'schymane@gmail.com', role=c('ctb'), 
-      comment = c(ORCID = "0000-0001-6868-8145")))
+  person('Emma', 'Schymanski', ,'schymane@gmail.com', role=c('ctb'),
+      comment = c(ORCID = "0000-0001-6868-8145")),
+  person('Egon', 'Willighagen', ,'egon.willighagen@maastrichtuniversity.nl', role=c('ctb'),
+      comment = c(ORCID = "0000-0001-7542-0286")))
 Depends:
     rcdklibs (>= 2.9)
 Imports:
@@ -23,19 +25,18 @@ Suggests:
     RUnit,
     knitr,
     rmarkdown,
-    devtools,
-    depict
+    devtools
 License: LGPL
 URL: https://github.com/CDK-R/cdkr
 LazyLoad: yes
 LazyData: true
 SystemRequirements: Java (>= 8)
 BugReports: https://github.com/CDK-R/cdkr/issues
 Description: Allows the user to access functionality in the
-    'CDK', a Java framework for chemoinformatics. This allows the user to load
+    'CDK', a Java framework for cheminformatics. 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: 7.3.1
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 Encoding: UTF-8
-Remotes: CDK-R/depict
+

rcdk/NEWS.md

@@ -1,6 +1,6 @@
-# rcdk 3.9.0
+# rcdk 3.8.2
 
-* Update rCDK to work with rcdklibs 2.9
+* Update rCDK to work with rcdklibs 2.11
 
 # rcdk 3.8.0
 
@@ -13,9 +13,11 @@
 * Update rCDK to work with rcdklibs 2.8
 
 
+
+
 # rcdk 3.6.0
 
-* Fix code to handle changes to JDK17. Notably, I needed to reduce the use of the J notation in a nubmer of places in favor of direct calls.
+* Fix code to handle changes to JDK17. Notably, I needed to reduce the use of the J notation in a number of places in favor of direct calls.
 * formally deprecated `do.typing` in favor of `set.atom.types`
 * Updated handling of atomic descriptors to resolve a name mismatch bug
 * Added a test case for atomic descriptors (thanks to Francesca Di Cesare)
@@ -30,7 +32,7 @@
 
 # rcdk  3.5.0
 
-* update to RCDKlibs 2.3. This changes uderlying AtomContainer defualt to Atomcontainer2 and also has new support for mass spec mass functions. On the rcdk side we have moved to a tidyverse documentation and build system.
+* update to RCDKlibs 2.3. This changes underlying AtomContainer default to Atomcontainer2 and also has new support for mass spec mass functions. On the rcdk side we have moved to a tidyverse documentation and build system.
 
 # rcdk  3.4.7 
 

rcdk/R/deprecated_functions.R

@@ -1,20 +1,19 @@
 ################################################################################
 #' Deprecated functions in the rcdk package.
-#' 
+#'
 #' These functions are provided for compatibility with older version of
 #' the phyloseq package.  They may eventually be completely
 #' removed.
-#' 
+#'
 #' @usage deprecated_rcdk_function(x, value, ...)
 #' @rdname rcdk-deprecated
 #' @name rcdk-deprecated
 #' @param x For assignment operators, the object that will undergo a replacement
 #'  (object inside parenthesis).
-#' @param value For assignment operators, the value to replace with 
+#' @param value For assignment operators, the value to replace with
 #'  (the right side of the assignment).
-#' @param ... For functions other than assignment operators, 
+#' @param ... For functions other than assignment operators,
 #'  parameters to be passed to the modern version of the function (see table).
-#' @docType package
 #' @export do.typing
 #' @aliases deprecated_rcdk_function do.typing
 #' @details
@@ -24,4 +23,4 @@
 #'
 deprecated_rcdk_function <- function(x, value, ...){return(NULL)}
 do.typing <- function(...){.Deprecated("set.atom.types", package="rcdk");return(set.atom.types(...))}
-################################################################################
+################################################################################

rcdk/R/fingerprint.R

@@ -1,8 +1,8 @@
 #' Generate molecular fingerprints
-#' 
+#'
 #' `get.fingerprint` returns a `fingerprint` object representing molecular fingerprint of
 #' the input molecule.
-#' 
+#'
 #' @param molecule A \code{jobjRef} object to an \code{IAtomContaine}
 #' @param type The type of fingerprint. Possible values are:
 #'   \itemize{
@@ -18,52 +18,50 @@
 #' \item pubchem - 881 bit fingerprints defined by PubChem
 #' \item kr - 4860 bit fingerprint defined by Klekota and Roth
 #' \item shortestpath - A fingerprint based on the shortest paths between pairs of atoms and takes into account ring systems, charges etc.
-#' \item signature - A feature,count type of fingerprint, similar in nature to circular fingerprints, but based on the signature 
+#' \item signature - A feature,count type of fingerprint, similar in nature to circular fingerprints, but based on the signature
 #' descriptor
 #' \item circular - An implementation of the ECFP6 (default) fingerprint. Other circular types can be chosen by modifying the \code{circular.type} parameter.
 #' \item substructure - Fingerprint based on list of SMARTS pattern. By default a set of functional groups is tested.
 #' }
 #' @param fp.mode The style of fingerprint. Specifying "`bit`" will return a binary fingerprint,
-#' "`raw`" returns the the original representation (usually sequence of integers) and 
+#' "`raw`" returns the the original representation (usually sequence of integers) and
 #' "`count`" returns the fingerprint as a sequence of counts.
 #' @param depth The search depth. This argument is ignored for the
 #' `pubchem`, `maccs`, `kr` and `estate` fingerprints
-#' @param size The final length of the fingerprint. 
-#' This argument is ignored for the `pubchem`, `maccs`, `kr`, `signature`, `circular` and 
+#' @param size The final length of the fingerprint.
+#' This argument is ignored for the `pubchem`, `maccs`, `kr`, `signature`, `circular` and
 #' `estate` fingerprints
 #' @param substructure.pattern List of characters containing the SMARTS pattern to match. If the an empty list is provided (default) than the functional groups substructures (default in CDK) are used.
 #' @param circular.type Name of the circular fingerprint type that should be computed given as string. Possible values are: 'ECFP0', 'ECFP2', 'ECFP4', 'ECFP6' (default), 'FCFP0', 'FCFP2', 'FCFP4' and 'FCFP6'.
 #' @param verbose Verbose output if \code{TRUE}
-#' @return an S4 object of class \code{\link{fingerprint-class}} or \code{\link{featvec-class}}, 
+#' @return an S4 object of class \code{\link[fingerprint]{fingerprint-class}} or \code{\link[fingerprint]{featvec-class}},
 #' which can be manipulated with the fingerprint package.
 #' @export
 #' @author Rajarshi Guha (\email{rajarshi.guha@@gmail.com})
-#' @examples 
+#' @examples
 #' ## get some molecules
-#' sp <- get.smiles.parser()
-#' smiles <- c('CCC', 'CCN', 'CCN(C)(C)', 'c1ccccc1Cc1ccccc1','C1CCC1CC(CN(C)(C))CC(=O)CC')
+#' smiles <- c('CCC', 'CCN')
 #' mols <- parse.smiles(smiles)
-#' 
-#' ## get a single fingerprint using the standard
-#' ## (hashed, path based) fingerprinter
-#' fp <- get.fingerprint(mols[[1]])
-#' 
-#' ## get MACCS keys for all the molecules
+#'
+#' ## get a single fingerprint using MACCS (fast)
+#' fp <- get.fingerprint(mols[[1]], type='maccs')
+#'
+#' ## get MACCS keys for both molecules
 #' fps <- lapply(mols, get.fingerprint, type='maccs')
-#' 
+#'
 #' ## get Signature fingerprint
 #' ## feature, count fingerprinter
 #' fps <- lapply(mols, get.fingerprint, type='signature', fp.mode='raw')
 #' ## get Substructure fingerprint for functional group fragments
 #' fps <- lapply(mols, get.fingerprint, type='substructure')
-#' 
+#'
 #' ## get Substructure count fingerprint for user defined fragments
 #' mol1 <- parse.smiles("c1ccccc1CCC")[[1]]
 #' smarts <- c("c1ccccc1", "[CX4H3][#6]", "[CX2]#[CX2]")
 #' fps <- get.fingerprint(mol1, type='substructure', fp.mode='count',
 #'     substructure.pattern=smarts)
-#' 
-#' ## get ECFP0 count fingerprints 
+#'
+#' ## get ECFP0 count fingerprints
 #' mol2 <- parse.smiles("C1=CC=CC(=C1)CCCC2=CC=CC=C2")[[1]]
 #' fps <- get.fingerprint(mol2, type='circular', fp.mode='count', circular.type='ECFP0')
 get.fingerprint <- function(molecule, type = 'standard', fp.mode = 'bit', depth=6, size=1024, substructure.pattern=character(), circular.type = "ECFP6", verbose=FALSE) {
@@ -75,17 +73,17 @@ get.fingerprint <- function(molecule, type = 'standard', fp.mode = 'bit', depth=
 
   mode(size) <- 'integer'
   mode(depth) <- 'integer'
-  
+
   # Determine integer ID for the circular fingerprint given its desired type.
-  # This allows us to use also ECFP4, ... 
+  # This allows us to use also ECFP4, ...
   if (type == 'circular') {
-        circular.type.id <- switch(circular.type, 
+        circular.type.id <- switch(circular.type,
              ECFP0 = 1, ECFP2 = 2, ECFP4 = 3, ECFP6 = 4,
              FCFP0 = 5, FCFP2 = 6, FCFP4 = 7, FCFP6 = 8,
              NULL)
-        
+
         if (is.null(circular.type.id)) stop(paste('Invalid circular fingerprint type: ', circular.type))
-        
+
         mode(circular.type.id) <- 'integer'
   }
 
@@ -103,8 +101,8 @@ get.fingerprint <- function(molecule, type = 'standard', fp.mode = 'bit', depth=
            shortestpath = .jnew('org/openscience/cdk/fingerprint/ShortestPathFingerprinter', size),
            signature = .jnew('org/openscience/cdk/fingerprint/SignatureFingerprinter', depth),
            circular = .jnew('org/openscience/cdk/fingerprint/CircularFingerprinter', circular.type.id),
-           substructure = 
-               if (length(substructure.pattern) == 0) 
+           substructure =
+               if (length(substructure.pattern) == 0)
                    # Loads the default group substructures
                    { .jnew('org/openscience/cdk/fingerprint/SubstructureFingerprinter') }
                else
@@ -125,11 +123,11 @@ get.fingerprint <- function(molecule, type = 'standard', fp.mode = 'bit', depth=
   } else if (fp.mode == 'count') {
     jfp <- .jcall(fingerprinter,
                   "Lorg/openscience/cdk/fingerprint/ICountFingerprint;",
-                  "getCountFingerprint", molecule, check=FALSE)    
+                  "getCountFingerprint", molecule, check=FALSE)
   }
-  
+
   e <- .jgetEx()
-  if (.jcheck(silent=TRUE)) { 
+  if (.jcheck(silent=TRUE)) {
     if (verbose) print(e)
     return(NULL)
   }
@@ -139,15 +137,15 @@ get.fingerprint <- function(molecule, type = 'standard', fp.mode = 'bit', depth=
 
   if (fp.mode == 'bit') {
     bitset <- .jcall(jfp, "Ljava/util/BitSet;", "asBitSet")
-    
+
     if (type == 'maccs') nbit <- 166
     else if (type == 'estate') nbit <- 79
     else if (type == 'pubchem') nbit <- 881
     else if (type == 'kr') nbit <- 4860
     else if (type == 'substructure') nbit <- .jcall(fingerprinter, "I", "getSize")
     else if (type == 'circular') nbit <- .jcall(fingerprinter, "I", "getSize")
     else nbit <- size
-    
+
     bitset <- .jcall(bitset, "S", "toString")
     s <- gsub('[{}]','', bitset)
     s <- strsplit(s, split=',')[[1]]
@@ -166,7 +164,7 @@ get.fingerprint <- function(molecule, type = 'standard', fp.mode = 'bit', depth=
         tempkey <- .jsimplify(tempkey)
       }
       keys[[i]] <- tempkey
-    
+
     }
 
     values <- list()

rcdk/R/formula.R

@@ -528,7 +528,7 @@ generate.formula <- function(mass,
 #' @param tol The tolerance
 #' @return A \code{jobjRef} corresponding to an instance of \code{IsotopePatternSimilarity}
 #' @seealso \code{\link{compare.isotope.pattern}}
-#' @references \url{http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html}
+#' @references \url{https://cdk.github.io/cdk/2.10/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html}
 #' @author Miguel Rojas Cherto
 get.isotope.pattern.similarity <- function(tol = NULL) {
     ips <- .jnew("org/openscience/cdk/formula/IsotopePatternSimilarity")
@@ -544,7 +544,7 @@ get.isotope.pattern.similarity <- function(tol = NULL) {
 #'
 #' @param minAbundance The minimum abundance
 #' @return A \code{jobjRef} corresponding to an instance of \code{IsotopePatternGenerator}
-#' @references \url{http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/formula/IsotopePatternGenerator.html}
+#' @references \url{https://cdk.github.io/cdk/2.10/docs/api/org/openscience/cdk/formula/IsotopePatternGenerator.html}
 #' @author Miguel Rojas Cherto
 get.isotope.pattern.generator <- function(minAbundance = NULL) {
     if (is.null(minAbundance))
@@ -564,7 +564,7 @@ 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/2.3/docs/api/org/openscience/cdk/formula/IsotopePatternSimilarity.html}
+#' @references \url{https://cdk.github.io/cdk/2.10/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/frags.R

@@ -22,7 +22,7 @@
 #' `frameworks`. Each of these elements is either a character vector of SMILES strings or a list of
 #' `IAtomContainer` objects.
 #' @author Rajarshi Guha (\email{rajarshi.guha@@gmail.com})
-#' @seealso [get.exhuastive.fragments()]
+#' @seealso [get.exhaustive.fragments()]
 #' @export
 #' @examples 
 #' mol <- parse.smiles('c1ccc(cc1)CN(c2cc(ccc2[N+](=O)[O-])c3c(nc(nc3CC)N)N)C')[[1]]