20230625 smallfix (#145)

* - Fix System Requirements
- bump version
- small doc update

* update submission

* Fixes for CRAN upload

* bibEntry --> bibentry

* fix citation

---------

Co-authored-by: Zachary Charlop-Powers <zcpowers@Zacharys-MacBook-Air.local>

rcdk/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rcdk
-Version: 3.8.0
-Date: 2023-06-11
+Version: 3.8.1
+Date: 2023-06-25
 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'),
@@ -23,6 +23,7 @@ Suggests:
 License: LGPL
 LazyLoad: yes
 LazyData: true
+SystemRequirements: Java (>= 8)
 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

@@ -1,6 +1,8 @@
 # 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="rajarshi.guha@gmail.com")),
+bibentry(
+  bibtype = "article",
+	author = c(person(given="Rajarshi",family="Guha", email="rajarshi.guha@gmail.com")),
 	journal = "Journal of Statistical Software",
 	number = 6,
 	title = "Chemical Informatics Functionality in R",