CDK-R · zachcp · Sep 11, 2025 · Sep 11, 2025 · Sep 11, 2025 · Sep 11, 2025
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@ revdep/
 ^docs$
 ^pkgdown$
 ^\.github$
+^cran-comments\.md$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,13 @@
 Package: rcdklibs
-Version: 2.9
-Date: 2024-03-02
+Version: 2.11
+Date: 2025-09-10
 Authors@R: c(
   person('Rajarshi', 'Guha', ,'[email protected]', role=c('aut'),
     comment = c(ORCID = "0000-0001-7403-8819")),
   person('Zachary', 'Charlop-Powers', ,'[email protected]',role=c('cre'), 
       comment = c(ORCID = "0000-0001-8816-4680")),
+  person('Egon', 'Willighagen', ,'[email protected]', role=c('ctb'), 
+      comment = c(ORCID = "0000-0001-7542-0286")),
   person('CDK Project', '', role=c('ctb', 'cph'), comment='CDK Java library contained in multiple jar files'))
 Depends:
     R (>= 2.0.0),
@@ -19,5 +21,5 @@ Description: An R interface to the Chemistry Development Kit, a Java library
     interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more
     idiomatic way. The CDK library itself is released as LGPL and the sources can be
     obtained from <https://github.com/cdk/cdk>.
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 URL: https://cdk-r.github.io/rcdklibs/
diff --git a/Makefile b/Makefile
@@ -1,5 +1,5 @@
 
-CDK_VERSION=2.9
+CDK_VERSION=2.11
 JAR_DIR=cdk/cdk-cdk-$(CDK_VERSION)/bundle/target/cdk-bundle-$(CDK_VERSION)/WEB-INF/lib
 
 cdk.zip:
@@ -11,8 +11,8 @@ build: cdk.zip
 	# 88 - 92 is cdk-pdb
 	# 148-157 is cdk-builder3d and builder3d-tools
 	# 248-252 is cdk-pdbcml
-	# 372-376 is cdk-iordf 
-	sed -i .bak -e '88,92d;148,157d;248,252d;372,376d;' cdk/cdk-cdk-$(CDK_VERSION)/bundle/pom.xml
+	# 372-378 is cdk-iordf 
+	sed -i .bak -e '88,92d;148,157d;248,252d;372,378d;' cdk/cdk-cdk-$(CDK_VERSION)/bundle/pom.xml
 	cd cdk/cdk-cdk-$(CDK_VERSION)/bundle && mvn compile war:war -P jdk11-plus && cd ../../..
 
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# v2.11
+
+- Update to CDK 2.11 libraries.
+- Add Egon as contributor
+
+
 # v2.9
 
 - Update to CDK 2.9 libraries.

diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,6 @@ knitr::opts_chunk$set(
 # rcdklibs
 
 <!-- badges: start -->
-[![Build Status](https://api.travis-ci.org/CDK-R/rcdklibs.svg?branch=master)](https://travis-ci.org/CDK-R/rcdklibs)
 [![CRAN Version](https://www.r-pkg.org/badges/version/rcdklibs?color=green)](https://cran.r-project.org/package=rcdklibs)
 [![CRAN Downloads](http://cranlogs.r-pkg.org/badges/grand-total/rcdklibs?color=green)](https://cran.r-project.org/package=rcdklibs)
 [![CRAN Downloads Monthyl](http://cranlogs.r-pkg.org/badges/last-month/rcdklibs?color=green)](https://cran.r-project.org/package=rcdklibs)

diff --git a/README.md b/README.md
@@ -5,8 +5,6 @@
 
 <!-- badges: start -->
 
-[![Build
-Status](https://api.travis-ci.org/CDK-R/rcdklibs.svg?branch=master)](https://travis-ci.org/CDK-R/rcdklibs)
 [![CRAN
 Version](https://www.r-pkg.org/badges/version/rcdklibs?color=green)](https://cran.r-project.org/package=rcdklibs)
 [![CRAN

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,25 +1,12 @@
-## General Comments
-
-- This is a resubmission of rcdklibs-2.8. I have fixed a few NOTES relates to R code quality or inactive URLs. 
-- I have also updates a few types found in the docs.
-- I'd like to reiterate that this package is submitted with rcdk v3.7 and they should be evaluated together.
-
-
 ## R CMD check results
-There were no ERRORs or WARNINGs. 
-
-There was 1 NOTE:
 
-* checking installed package size ... NOTE
-    installed size is 24.3Mb
+❯ checking installed package size ... NOTE
+    installed size is 42.7Mb
     sub-directories of 1Mb or more:
-      cont  24.2Mb
+      cont  42.6Mb
 
 0 errors ✔ | 0 warnings ✔ | 1 note ✖
 
-
-
-## Downstream dependencies
-
-The primary downstream dependency of rcdklibs is rcdk, which is being
-submitted at the same time.
+* This is patch release to update the cdklibs jars to 2.11
+* The note is related to size and we ask that rcdklibs continue to be granted a size exception.
+* this is the second submission of this package where we have fixed an incorrect link
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diff --git a/inst/cont/jna-inchi-linux-x86-1.2.jar b/inst/cont/jna-inchi-linux-x86-1.2.jar
diff --git a/inst/cont/jna-inchi-linux-x86-1.3.1.jar b/inst/cont/jna-inchi-linux-x86-1.3.1.jar
diff --git a/inst/cont/jna-inchi-linux-x86-64-1.2.jar b/inst/cont/jna-inchi-linux-x86-64-1.2.jar
diff --git a/inst/cont/jna-inchi-linux-x86-64-1.3.1.jar b/inst/cont/jna-inchi-linux-x86-64-1.3.1.jar
diff --git a/inst/cont/jna-inchi-win32-x86-1.2.jar b/inst/cont/jna-inchi-win32-x86-1.2.jar
diff --git a/inst/cont/jna-inchi-win32-x86-1.3.1.jar b/inst/cont/jna-inchi-win32-x86-1.3.1.jar
diff --git a/inst/cont/jna-inchi-win32-x86-64-1.2.jar b/inst/cont/jna-inchi-win32-x86-64-1.2.jar
diff --git a/inst/cont/jna-inchi-win32-x86-64-1.3.1.jar b/inst/cont/jna-inchi-win32-x86-64-1.3.1.jar
diff --git a/inst/cont/joda-time-2.12.5.jar → inst/cont/joda-time-2.13.0.jar b/inst/cont/joda-time-2.12.5.jar → inst/cont/joda-time-2.13.0.jar
diff --git a/inst/cont/jsonld-java-0.13.4.jar b/inst/cont/jsonld-java-0.13.4.jar
diff --git a/inst/cont/libthrift-0.19.0.jar b/inst/cont/libthrift-0.19.0.jar
diff --git a/inst/cont/log4j-1.2-api-2.20.0.jar b/inst/cont/log4j-1.2-api-2.20.0.jar
diff --git a/inst/cont/log4j-1.2-api-2.24.3.jar b/inst/cont/log4j-1.2-api-2.24.3.jar
diff --git a/inst/cont/log4j-api-2.20.0.jar b/inst/cont/log4j-api-2.20.0.jar
diff --git a/inst/cont/log4j-api-2.24.3.jar b/inst/cont/log4j-api-2.24.3.jar
diff --git a/inst/cont/log4j-core-2.20.0.jar b/inst/cont/log4j-core-2.20.0.jar
diff --git a/inst/cont/log4j-core-2.24.3.jar b/inst/cont/log4j-core-2.24.3.jar
diff --git a/inst/cont/protobuf-java-3.24.3.jar b/inst/cont/protobuf-java-3.24.3.jar
diff --git a/inst/cont/slf4j-api-1.7.36.jar b/inst/cont/slf4j-api-1.7.36.jar
diff --git a/inst/cont/titanium-json-ld-1.3.2.jar b/inst/cont/titanium-json-ld-1.3.2.jar