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There are ~20 JavaDoc errors in the project which are all quite easy to fix.
/Users/john/Workspace/GitHub/cdk/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java:57: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java:77: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java:87: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/storage/ctab/src/main/java/org/openscience/cdk/io/RdfileRecord.java:31: error: text not allowed in <ul> element
/Users/john/Workspace/GitHub/cdk/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java:69: error: self-closing element not allowed
/Users/john/Workspace/GitHub/cdk/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java:69: error: element not closed: b
/Users/john/Workspace/GitHub/cdk/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java:69: error: element not closed: b
/Users/john/Workspace/GitHub/cdk/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java:34: error: attribute not supported in HTML5: summary
/Users/john/Workspace/GitHub/cdk/storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIToReaction.java:43: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIGenerator.java:60: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIGenerator.java:90: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/tool/structgen/src/main/java/org/openscience/cdk/structgen/maygen/Maygen.java:76: error: malformed HTML
/Users/john/Workspace/GitHub/cdk/tool/structgen/src/main/java/org/openscience/cdk/structgen/maygen/Maygen.java:76: error: malformed HTML
/Users/john/Workspace/GitHub/cdk/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java:468: error: syntax error in reference
/Users/john/Workspace/GitHub/cdk/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java:513: error: syntax error in reference
/Users/john/Workspace/GitHub/cdk/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java:294: error: unknown tag: cdoe
/Users/john/Workspace/GitHub/cdk/base/core/src/main/java/org/openscience/cdk/config/Elements.java:562: error: malformed HTML
/Users/john/Workspace/GitHub/cdk/base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java:149: error: unexpected heading used: <H1>, compared to implicit preceding heading: <H3>
/Users/john/Workspace/GitHub/cdk/base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java:171: error: unexpected heading used: <H1>, compared to implicit preceding heading: <H3>
/Users/john/Workspace/GitHub/cdk/base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java:177: error: unknown tag: cdoe
/Users/john/Workspace/GitHub/cdk/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java:57: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java:77: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java:87: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/storage/ctab/src/main/java/org/openscience/cdk/io/RdfileRecord.java:31: error: text not allowed in <ul> element
/Users/john/Workspace/GitHub/cdk/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java:69: error: self-closing element not allowed
/Users/john/Workspace/GitHub/cdk/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java:69: error: element not closed: b
/Users/john/Workspace/GitHub/cdk/storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java:69: error: element not closed: b
/Users/john/Workspace/GitHub/cdk/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java:34: error: attribute not supported in HTML5: summary
/Users/john/Workspace/GitHub/cdk/storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIToReaction.java:43: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIGenerator.java:60: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIGenerator.java:90: error: unexpected end tag: </p>
/Users/john/Workspace/GitHub/cdk/tool/structgen/src/main/java/org/openscience/cdk/structgen/maygen/Maygen.java:76: error: malformed HTML
/Users/john/Workspace/GitHub/cdk/tool/structgen/src/main/java/org/openscience/cdk/structgen/maygen/Maygen.java:76: error: malformed HTML
/Users/john/Workspace/GitHub/cdk/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java:468: error: syntax error in reference
/Users/john/Workspace/GitHub/cdk/base/core/src/main/java/org/openscience/cdk/graph/Cycles.java:513: error: syntax error in reference
/Users/john/Workspace/GitHub/cdk/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java:294: error: unknown tag: cdoe
/Users/john/Workspace/GitHub/cdk/base/core/src/main/java/org/openscience/cdk/config/Elements.java:562: error: malformed HTML
/Users/john/Workspace/GitHub/cdk/base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java:149: error: unexpected heading used: <H1>, compared to implicit preceding heading: <H3>
/Users/john/Workspace/GitHub/cdk/base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java:171: error: unexpected heading used: <H1>, compared to implicit preceding heading: <H3>
/Users/john/Workspace/GitHub/cdk/base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java:177: error: unknown tag: cdoe
```
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