Merge pull request #4 from zachcp/2022-unbundle

Prepare for 2.8 release

Author: rajarshi

.Rbuildignore

@@ -1,4 +1,10 @@
+Makefile
+README.Rmd
 ^cran-comments.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^README_DEV.md$
+^README_DEV.md$
+cdk/
+cdk.zip
+revdep/
+^CRAN-SUBMISSION$

.gitignore

@@ -2,3 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
+cdk/
+revdep/

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 2.8
+Date: 2022-09-25 14:59:30 UTC
+SHA: 8ddc5f4711377a7064523221ce36f75b18a67110

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: rcdklibs
-Version: 2.3
-Date: 2020-02-22
+Version: 2.8
+Date: 2022-09-20
 Authors@R: c(person('Rajarshi', 'Guha', role=c('aut'), email='[email protected]'),
              person('Zachary', 'Charlop-Powers', role=c('cre'), email='[email protected]'),
              person('CDK Project', '', role=c('ctb', 'cph'), comment='CDK Java library contained in multiple jar files'))
 Depends:
     R (>= 2.0.0),
-    rJava (>= 0.9-8)
+    rJava
 License: LGPL
 Title: The CDK Libraries Packaged for R
 Description: An R interface to the Chemistry Development Kit, a Java library
@@ -16,4 +16,4 @@ 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: 7.0.2
+RoxygenNote: 7.2.1

Makefile

@@ -0,0 +1,34 @@
+
+CDK_VERSION=2.8
+JAR_DIR=cdk/cdk-cdk-$(CDK_VERSION)/bundle/target/cdk-bundle-2.8/WEB-INF/lib
+
+cdk.zip:
+	wget -O cdk.zip https://github.com/cdk/cdk/archive/refs/tags/cdk-$(CDK_VERSION).zip
+	
+
+build: cdk.zip
+	unzip cdk.zip -d cdk
+	# 88 - 92 is cdk-pdb
+	# 148-157 is cdk-builder3d and builder3d-tools
+	# 238-242 is cdk-pdbcml
+	# 343-337 is cdk-iordf 
+	sed -i .bak -e '88,92d;148,157d;238,242d;343,347d;' cdk/cdk-cdk-$(CDK_VERSION)/bundle/pom.xml
+	cd cdk/cdk-cdk-$(CDK_VERSION)/bundle && mvn compile war:war -P jdk11-plus && cd ../../..
+
+# guava:
+# 	wget -O inst/cont/guava-31.1-jre.jar https://repo1.maven.org/maven2/com/google/guava/guava/31.1-jre/guava-31.1-jre.jar
+# 	wget -O inst/cont/failureaccess-1.0.1.jar https://repo1.maven.org/maven2/com/google/guava/failureaccess/1.0.1/failureaccess-1.0.1.jar
+
+
+prepare: build guava
+	# find cdk/ -name "*.jar" | parallel "cp {}  inst/cont/{/}"	
+	cp $(JAR_DIR)/*jar inst/cont/
+
+
+clean:
+	rm cdk.zip
+	rm -rf cdk/
+
+
+all: clean prepare
+

NEWS

@@ -19,14 +19,14 @@ knitr::opts_chunk$set(
 [![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=rcdklbs)
+[![CRAN Downloads Monthyl](http://cranlogs.r-pkg.org/badges/last-month/rcdklibs?color=green)](https://cran.r-project.org/package=rcdklibs)
 <!-- badges: end -->
 
 The goal of rcdklibs is to provide the [CDK](https://github.com/cdk/cdk) jarfiles
-and therby facilitate chemoinformatic analysis within the R ecosystem. The 
+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/web/packages/rJava/index.html)
-API. The libs provided in this release correspond to the [2.3 Release](http://cdk.github.io/cdk/2.3/docs/api/org/openscience/cdk/AtomContainer.html)
+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 [2.8 Release](https://github.com/cdk/cdk/releases/tag/cdk-2.8)
 
 
 ```