Merge branch 'master' into 202402-29

rcdk/DESCRIPTION

@@ -29,6 +29,8 @@ 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
     molecules, evaluate fingerprints, calculate molecular descriptors and so on.

rcdk/NEWS.md

@@ -5,6 +5,8 @@
 # rcdk 3.8.0
 
 * Change DESCRIPTION in accordance with CRAN rules about JDKs
+* Fix System Requirements line
+
 
 # rcdk 3.7.0
 

rcdk/R/formula.R

@@ -12,7 +12,7 @@
 #'   mass and window accuracy
 #' @author Miguel Rojas-Cherto (\email{miguelrojasch@@yahoo.es})
 #' @references A parallel effort to expand the Chemistry Development 
-#'   Kit: \url{http://cdk.sourceforge.net}
+#'   Kit: \url{https://cdk.github.io/}
 #' @seealso  
 #' \code{\link{get.formula}}
 #' \code{\link{set.charge.formula}}

rcdk/cran-comments.md

@@ -1,36 +1,5 @@
 ## General Comments
 
-- This is a resubmission of rcdk-3.7. I have fixed a few NOTES relates to R code quality.
-- There is an ERROR on the cloud system related to a difference between the primary dependency of this library, rcdklibs. 
-- This package should be co-evaluated with rcdklibs
-
-
-
-## Submission
-rCDK v 3.7.0
-
-## Test environments
-* local OS X install, R 4.2
-* win-builder (release)
-
-## R CMD check results
-
-0 errors | 0 warnings | 0 note
-
-
-## Reverse dependencies
-
-Using the latest rcdklibs (2.8) and this version of rcdk (3.7) I obtained the following
-results. 
-
----
-
-```
-✔ DeepPINCS 1.4.0                        ── E: 0     | W: 0     | N: 2
-✔ Rcpi 1.32.2                            ── E: 0     | W: 0     | N: 2
-✔ RMassBank 3.6.1                        ── E: 0     | W: 4     | N: 4
-✔ RxnSim 1.0.3                           ── E: 0     | W: 0     | N: 0
-✔ webchem 1.1.3                          ── E: 0     | W: 0     | N: 0
-```
-
-
+- submission of rcdk 3.8.1
+- fix to the SystemRequirements Field
+- update CITATION file

rcdk/inst/CITATION

@@ -1,6 +1,7 @@
 citHeader("To cite rcdk in publications use:")
-citEntry(entry = "article",
-	author = personList(person(given="Rajarshi",family="Guha", email="[email protected]")),
+bibentry(
+  bibtype = "article",
+	author = c(person(given="Rajarshi",family="Guha", email="[email protected]")),
 	journal = "Journal of Statistical Software",
 	number = 6,
 	title = "Chemical Informatics Functionality in R",