zachcp · Oct 19, 2026 · Oct 19, 2026 · Oct 19, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,15 +1,14 @@
-Makefile
 README.Rmd
 ^cran-comments.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^README_DEV.md$
-cdk/
-cdk.zip
 revdep/
 ^CRAN-SUBMISSION$
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
 ^\.github$
 ^cran-comments\.md$
+^Makefile$
+^build$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rcdklibs
-Version: 2.11
-Date: 2025-09-10
+Version: 2.13
+Date: 2026-10-19
 Authors@R: c(
   person('Rajarshi', 'Guha', ,'rajarshi.guha@gmail.com', role=c('aut'),
     comment = c(ORCID = "0000-0001-7403-8819")),

diff --git a/Makefile b/Makefile
@@ -1,30 +1,18 @@
-
-CDK_VERSION=2.11
-JAR_DIR=cdk/cdk-cdk-$(CDK_VERSION)/bundle/target/cdk-bundle-$(CDK_VERSION)/WEB-INF/lib
-
-cdk.zip:
-	wget -O cdk.zip https://github.com/cdk/cdk/archive/refs/tags/cdk-$(CDK_VERSION).zip
-
-
-build: cdk.zip
-	unzip cdk.zip -d cdk
-	# 88 - 92 is cdk-pdb
-	# 148-157 is cdk-builder3d and builder3d-tools
-	# 248-252 is cdk-pdbcml
-	# 372-378 is cdk-iordf 
-	sed -i .bak -e '88,92d;148,157d;248,252d;372,378d;' cdk/cdk-cdk-$(CDK_VERSION)/bundle/pom.xml
-	cd cdk/cdk-cdk-$(CDK_VERSION)/bundle && mvn compile war:war -P jdk11-plus && cd ../../..
-
-
-prepare: build
-	# find cdk/ -name "*.jar" | parallel "cp {}  inst/cont/{/}"	
-	cp $(JAR_DIR)/*jar inst/cont/
-
+CDK_VERSION=2.13
+BASE_URL=https://github.com/cdk/cdk/releases/download/cdk-$(CDK_VERSION)
+JAR=cdk-$(CDK_VERSION).jar
+SUMS=cdk-$(CDK_VERSION)-checksums-sha256.txt
+
+# Download the CDK release uberjar, verify it, and install it in inst/cont
+prepare:
+	mkdir -p build
+	curl -fL -o build/$(JAR) $(BASE_URL)/$(JAR)
+	curl -fL -o build/$(SUMS) $(BASE_URL)/$(SUMS)
+	cd build && grep " $(JAR)$$" $(SUMS) | shasum -a 256 -c -
+	rm -f inst/cont/*.jar
+	cp build/$(JAR) inst/cont/
 
 clean:
-	rm cdk.zip
-	rm -rf cdk/
-
+	rm -rf build
 
 all: clean prepare
-
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# v2.13
+
+- Update to CDK 2.13 libraries.
+- Bundle the official CDK release uberjar (`cdk-2.13.jar`) instead of ~90 individual jars; the Makefile now just downloads and verifies it.
+
 # v2.11
 
 - Update to CDK 2.11 libraries.

diff --git a/README.Rmd b/README.Rmd
@@ -25,7 +25,7 @@ The goal of rcdklibs is to provide the [CDK](https://github.com/cdk/cdk) jarfile
 and thereby facilitate chemoinformatic analysis within the R ecosystem. The 
 primary consumer of `rcdklibs` is the [rcdk](https://github.com/CDK-R/cdkr) package
 but all of CDK's functionality can be accessed by the standard [rJava]( https://CRAN.R-project.org/package=rJava)
-API. The libs provided in this release correspond to the [2.9 Release](https://github.com/cdk/cdk/releases/tag/cdk-2.9)
+API. The libs provided in this release correspond to the [2.13 Release](https://github.com/cdk/cdk/releases/tag/cdk-2.13)
 
 
 ```
@@ -62,4 +62,3 @@ And the development version from [GitHub](https://github.com/) with:
 # install.packages("devtools")
 devtools::install_github("https://github.com/CDK-R/rcdklibs")
 ```
-
diff --git a/README.md b/README.md
@@ -18,8 +18,8 @@ ecosystem. The primary consumer of `rcdklibs` is the
 [rcdk](https://github.com/CDK-R/cdkr) package but all of CDK’s
 functionality can be accessed by the standard
 [rJava](https://CRAN.R-project.org/package=rJava) API. The libs provided
-in this release correspond to the [2.9
-Release](https://github.com/cdk/cdk/releases/tag/cdk-2.9)
+in this release correspond to the [2.13
+Release](https://github.com/cdk/cdk/releases/tag/cdk-2.13)
 
     # Example
     library(rcdklibs)

diff --git a/README_DEV.md b/README_DEV.md
@@ -1,26 +1,13 @@
 # Packaging CDK
 
-The CDK2.0 release is 25MB. To try to reduce this size we built a version of the CDK libs that removes several sub-libraries.
-
-```
-git clone https://github.com/cdk/cdk.git
-
-cd cdk/bundle
-
-#checkout the tag of the released version
-git checkout -b rcdk2 cdk2-2.0
-
-vi pox.xml
-
-# remove the entries for:
-# builder3d
-# builder3d-tools
-# cdk-pdb
-# cdk-pdbcml
-
-mvn package
-```
-
-You can now use the target/cdk-2.0.jar for inclusion in rcdklibs
+rcdklibs bundles the official CDK release uberjar (`cdk-<version>.jar`, published
+with each [CDK release](https://github.com/cdk/cdk/releases)) as the only jar in
+`inst/cont/`. It already includes all CDK modules and their dependencies, so no
+custom build is needed.
 
+To update to a new CDK release:
 
+1. Set `CDK_VERSION` in the `Makefile`.
+2. Run `make all`. This downloads the uberjar, verifies its SHA-256 checksum and
+   replaces the contents of `inst/cont/`.
+3. Update `Version`/`Date` in `DESCRIPTION` and add an entry to `NEWS.md`.
diff --git a/inst/cont/RoaringBitmap-1.0.0.jar b/inst/cont/RoaringBitmap-1.0.0.jar
diff --git a/inst/cont/beam-core-1.3.8.jar b/inst/cont/beam-core-1.3.8.jar
diff --git a/inst/cont/beam-func-1.3.8.jar b/inst/cont/beam-func-1.3.8.jar
diff --git a/inst/cont/caffeine-3.1.8.jar b/inst/cont/caffeine-3.1.8.jar
diff --git a/inst/cont/cdk-2.13.jar b/inst/cont/cdk-2.13.jar
diff --git a/inst/cont/cdk-atomtype-2.11.jar b/inst/cont/cdk-atomtype-2.11.jar
diff --git a/inst/cont/cdk-builder3d-2.11.jar b/inst/cont/cdk-builder3d-2.11.jar
diff --git a/inst/cont/cdk-builder3dtools-2.11.jar b/inst/cont/cdk-builder3dtools-2.11.jar
diff --git a/inst/cont/cdk-charges-2.11.jar b/inst/cont/cdk-charges-2.11.jar
diff --git a/inst/cont/cdk-cip-2.11.jar b/inst/cont/cdk-cip-2.11.jar
diff --git a/inst/cont/cdk-control-2.11.jar b/inst/cont/cdk-control-2.11.jar
diff --git a/inst/cont/cdk-core-2.11.jar b/inst/cont/cdk-core-2.11.jar
diff --git a/inst/cont/cdk-ctab-2.11.jar b/inst/cont/cdk-ctab-2.11.jar
diff --git a/inst/cont/cdk-data-2.11.jar b/inst/cont/cdk-data-2.11.jar
diff --git a/inst/cont/cdk-datadebug-2.11.jar b/inst/cont/cdk-datadebug-2.11.jar
diff --git a/inst/cont/cdk-depict-2.11.jar b/inst/cont/cdk-depict-2.11.jar
diff --git a/inst/cont/cdk-dict-2.11.jar b/inst/cont/cdk-dict-2.11.jar
diff --git a/inst/cont/cdk-diff-2.11.jar b/inst/cont/cdk-diff-2.11.jar
diff --git a/inst/cont/cdk-extra-2.11.jar b/inst/cont/cdk-extra-2.11.jar
diff --git a/inst/cont/cdk-fingerprint-2.11.jar b/inst/cont/cdk-fingerprint-2.11.jar
diff --git a/inst/cont/cdk-forcefield-2.11.jar b/inst/cont/cdk-forcefield-2.11.jar
diff --git a/inst/cont/cdk-formula-2.11.jar b/inst/cont/cdk-formula-2.11.jar
diff --git a/inst/cont/cdk-fragment-2.11.jar b/inst/cont/cdk-fragment-2.11.jar
diff --git a/inst/cont/cdk-group-2.11.jar b/inst/cont/cdk-group-2.11.jar
diff --git a/inst/cont/cdk-hash-2.11.jar b/inst/cont/cdk-hash-2.11.jar
diff --git a/inst/cont/cdk-inchi-2.11.jar b/inst/cont/cdk-inchi-2.11.jar
diff --git a/inst/cont/cdk-interfaces-2.11.jar b/inst/cont/cdk-interfaces-2.11.jar
diff --git a/inst/cont/cdk-io-2.11.jar b/inst/cont/cdk-io-2.11.jar
diff --git a/inst/cont/cdk-ioformats-2.11.jar b/inst/cont/cdk-ioformats-2.11.jar
diff --git a/inst/cont/cdk-ionpot-2.11.jar b/inst/cont/cdk-ionpot-2.11.jar
diff --git a/inst/cont/cdk-iordf-2.11.jar b/inst/cont/cdk-iordf-2.11.jar
diff --git a/inst/cont/cdk-isomorphism-2.11.jar b/inst/cont/cdk-isomorphism-2.11.jar
diff --git a/inst/cont/cdk-jniinchi-support-2.11.jar b/inst/cont/cdk-jniinchi-support-2.11.jar
diff --git a/inst/cont/cdk-legacy-2.11.jar b/inst/cont/cdk-legacy-2.11.jar
diff --git a/inst/cont/cdk-libiocml-2.11.jar b/inst/cont/cdk-libiocml-2.11.jar
diff --git a/inst/cont/cdk-libiomd-2.11.jar b/inst/cont/cdk-libiomd-2.11.jar
diff --git a/inst/cont/cdk-model-2.11.jar b/inst/cont/cdk-model-2.11.jar
diff --git a/inst/cont/cdk-pcore-2.11.jar b/inst/cont/cdk-pcore-2.11.jar
diff --git a/inst/cont/cdk-pdb-2.11.jar b/inst/cont/cdk-pdb-2.11.jar
diff --git a/inst/cont/cdk-pdbcml-2.11.jar b/inst/cont/cdk-pdbcml-2.11.jar
diff --git a/inst/cont/cdk-qm-2.11.jar b/inst/cont/cdk-qm-2.11.jar
diff --git a/inst/cont/cdk-qsar-2.11.jar b/inst/cont/cdk-qsar-2.11.jar
diff --git a/inst/cont/cdk-qsaratomic-2.11.jar b/inst/cont/cdk-qsaratomic-2.11.jar
diff --git a/inst/cont/cdk-qsarbond-2.11.jar b/inst/cont/cdk-qsarbond-2.11.jar
diff --git a/inst/cont/cdk-qsarcml-2.11.jar b/inst/cont/cdk-qsarcml-2.11.jar
diff --git a/inst/cont/cdk-qsarionpot-2.11.jar b/inst/cont/cdk-qsarionpot-2.11.jar
diff --git a/inst/cont/cdk-qsarmolecular-2.11.jar b/inst/cont/cdk-qsarmolecular-2.11.jar
diff --git a/inst/cont/cdk-qsarprotein-2.11.jar b/inst/cont/cdk-qsarprotein-2.11.jar
diff --git a/inst/cont/cdk-reaction-2.11.jar b/inst/cont/cdk-reaction-2.11.jar
diff --git a/inst/cont/cdk-render-2.11.jar b/inst/cont/cdk-render-2.11.jar
diff --git a/inst/cont/cdk-renderawt-2.11.jar b/inst/cont/cdk-renderawt-2.11.jar
diff --git a/inst/cont/cdk-renderbasic-2.11.jar b/inst/cont/cdk-renderbasic-2.11.jar
diff --git a/inst/cont/cdk-renderextra-2.11.jar b/inst/cont/cdk-renderextra-2.11.jar
diff --git a/inst/cont/cdk-sdg-2.11.jar b/inst/cont/cdk-sdg-2.11.jar
diff --git a/inst/cont/cdk-signature-2.11.jar b/inst/cont/cdk-signature-2.11.jar
diff --git a/inst/cont/cdk-silent-2.11.jar b/inst/cont/cdk-silent-2.11.jar
diff --git a/inst/cont/cdk-smarts-2.11.jar b/inst/cont/cdk-smarts-2.11.jar
diff --git a/inst/cont/cdk-smiles-2.11.jar b/inst/cont/cdk-smiles-2.11.jar
diff --git a/inst/cont/cdk-standard-2.11.jar b/inst/cont/cdk-standard-2.11.jar
diff --git a/inst/cont/cdk-structgen-2.11.jar b/inst/cont/cdk-structgen-2.11.jar
diff --git a/inst/cont/cdk-tautomer-2.11.jar b/inst/cont/cdk-tautomer-2.11.jar
diff --git a/inst/cont/cdk-valencycheck-2.11.jar b/inst/cont/cdk-valencycheck-2.11.jar
diff --git a/inst/cont/checker-qual-3.37.0.jar b/inst/cont/checker-qual-3.37.0.jar
diff --git a/inst/cont/cmlxom-4.10.jar b/inst/cont/cmlxom-4.10.jar
diff --git a/inst/cont/collection-0.7.jar b/inst/cont/collection-0.7.jar
diff --git a/inst/cont/commons-cli-1.5.0.jar b/inst/cont/commons-cli-1.5.0.jar
diff --git a/inst/cont/commons-codec-1.16.0.jar b/inst/cont/commons-codec-1.16.0.jar
diff --git a/inst/cont/commons-collections4-4.4.jar b/inst/cont/commons-collections4-4.4.jar
diff --git a/inst/cont/commons-compress-1.24.0.jar b/inst/cont/commons-compress-1.24.0.jar
diff --git a/inst/cont/commons-csv-1.10.0.jar b/inst/cont/commons-csv-1.10.0.jar
diff --git a/inst/cont/commons-io-2.18.0.jar b/inst/cont/commons-io-2.18.0.jar
diff --git a/inst/cont/commons-lang3-3.13.0.jar b/inst/cont/commons-lang3-3.13.0.jar
diff --git a/inst/cont/commons-lang3-3.17.0.jar b/inst/cont/commons-lang3-3.17.0.jar
diff --git a/inst/cont/commons-math-2.2.jar b/inst/cont/commons-math-2.2.jar
diff --git a/inst/cont/error_prone_annotations-2.21.1.jar b/inst/cont/error_prone_annotations-2.21.1.jar
diff --git a/inst/cont/euclid-2.10.jar b/inst/cont/euclid-2.10.jar
diff --git a/inst/cont/freehep-graphics2d-2.4.jar b/inst/cont/freehep-graphics2d-2.4.jar
diff --git a/inst/cont/freehep-graphicsbase-2.4.jar b/inst/cont/freehep-graphicsbase-2.4.jar
diff --git a/inst/cont/freehep-graphicsio-2.4.jar b/inst/cont/freehep-graphicsio-2.4.jar
diff --git a/inst/cont/freehep-graphicsio-pdf-2.4.jar b/inst/cont/freehep-graphicsio-pdf-2.4.jar
diff --git a/inst/cont/freehep-graphicsio-ps-2.4.jar b/inst/cont/freehep-graphicsio-ps-2.4.jar
diff --git a/inst/cont/freehep-graphicsio-tests-2.4.jar b/inst/cont/freehep-graphicsio-tests-2.4.jar
diff --git a/inst/cont/freehep-io-2.2.2.jar b/inst/cont/freehep-io-2.2.2.jar
diff --git a/inst/cont/gson-2.10.1.jar b/inst/cont/gson-2.10.1.jar
diff --git a/inst/cont/httpclient-4.5.14.jar b/inst/cont/httpclient-4.5.14.jar
diff --git a/inst/cont/httpclient-cache-4.5.14.jar b/inst/cont/httpclient-cache-4.5.14.jar
diff --git a/inst/cont/httpcore-4.4.16.jar b/inst/cont/httpcore-4.4.16.jar
diff --git a/inst/cont/jackson-annotations-2.15.3.jar b/inst/cont/jackson-annotations-2.15.3.jar
diff --git a/inst/cont/jackson-core-2.15.3.jar b/inst/cont/jackson-core-2.15.3.jar
diff --git a/inst/cont/jackson-databind-2.15.3.jar b/inst/cont/jackson-databind-2.15.3.jar
diff --git a/inst/cont/jakarta.json-2.0.1.jar b/inst/cont/jakarta.json-2.0.1.jar
diff --git a/inst/cont/jama-1.0.3.jar b/inst/cont/jama-1.0.3.jar
diff --git a/inst/cont/jcl-over-slf4j-1.7.36.jar b/inst/cont/jcl-over-slf4j-1.7.36.jar
diff --git a/inst/cont/jena-arq-4.10.0.jar b/inst/cont/jena-arq-4.10.0.jar
diff --git a/inst/cont/jena-base-4.10.0.jar b/inst/cont/jena-base-4.10.0.jar
diff --git a/inst/cont/jena-core-4.10.0.jar b/inst/cont/jena-core-4.10.0.jar
diff --git a/inst/cont/jena-iri-4.10.0.jar b/inst/cont/jena-iri-4.10.0.jar
diff --git a/inst/cont/jgrapht-0.6.0.jar b/inst/cont/jgrapht-0.6.0.jar
diff --git a/inst/cont/jna-5.10.0.jar b/inst/cont/jna-5.10.0.jar
diff --git a/inst/cont/jna-inchi-api-1.3.1.jar b/inst/cont/jna-inchi-api-1.3.1.jar
diff --git a/inst/cont/jna-inchi-core-1.3.1.jar b/inst/cont/jna-inchi-core-1.3.1.jar
diff --git a/inst/cont/jna-inchi-darwin-aarch64-1.3.1.jar b/inst/cont/jna-inchi-darwin-aarch64-1.3.1.jar
diff --git a/inst/cont/jna-inchi-darwin-x86-64-1.3.1.jar b/inst/cont/jna-inchi-darwin-x86-64-1.3.1.jar
diff --git a/inst/cont/jna-inchi-linux-aarch64-1.3.1.jar b/inst/cont/jna-inchi-linux-aarch64-1.3.1.jar
diff --git a/inst/cont/jna-inchi-linux-arm-1.3.1.jar b/inst/cont/jna-inchi-linux-arm-1.3.1.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-x86-64-1.3.1.jar b/inst/cont/jna-inchi-linux-x86-64-1.3.1.jar
diff --git a/inst/cont/jna-inchi-win32-x86-1.3.1.jar b/inst/cont/jna-inchi-win32-x86-1.3.1.jar
diff --git a/inst/cont/jna-inchi-win32-x86-64-1.3.1.jar b/inst/cont/jna-inchi-win32-x86-64-1.3.1.jar
diff --git a/inst/cont/joda-time-2.13.0.jar b/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-2.24.3.jar b/inst/cont/log4j-1.2-api-2.24.3.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-2.24.3.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/signatures-1.1.jar b/inst/cont/signatures-1.1.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/tagsoup-1.2.1.jar b/inst/cont/tagsoup-1.2.1.jar
diff --git a/inst/cont/titanium-json-ld-1.3.2.jar b/inst/cont/titanium-json-ld-1.3.2.jar
diff --git a/inst/cont/vecmath-1.5.2.jar b/inst/cont/vecmath-1.5.2.jar
diff --git a/inst/cont/xml-apis-1.0.b2.jar b/inst/cont/xml-apis-1.0.b2.jar
diff --git a/inst/cont/xom-1.3.9.jar b/inst/cont/xom-1.3.9.jar