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This repository contains material helping you to set up a ContentMine workshop. It also includes tutorials for learning the ContentMine tools on your own.
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norma installation java error #57

Open teatree1212 opened 8 years ago

teatree1212 commented 8 years ago

I get the following error message, when installing norma: mvn clean install

[INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.xml-cml:norma:jar:0.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for com.mycila.maven-license-plugin:maven-license-plugin is missing. @ line 92, column 12 [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:cobertura-maven-plugin is missing. @ line 53, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO]
[INFO] ------------------------------------------------------------------------ [INFO] Building norma 0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ norma --- [INFO] Deleting /Users/hildegaa/Documents/sra_upload/map_papers/norma/target [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ norma --- [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 46 resources [INFO] [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ norma --- [INFO] Changes detected - recompiling the module! [WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent! [INFO] Compiling 85 source files to /Users/hildegaa/Documents/sra_upload/map_papers/norma/target/classes [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/pubstyle/getpapers/GetPapers.java:[14,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/html/HtmlCleaner.java:[8,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[22,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[28,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[269,42] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[315,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[347,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[354,57] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[375,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[445,16] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[25,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[82,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaTransformer [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[171,38] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.util.TransformerWrapper [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[14,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[36,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[42,35] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [INFO] 16 errors [INFO] ------------------------------------------------------------- [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.497 s [INFO] Finished at: 2016-04-08T11:46:06+01:00 [INFO] Final Memory: 23M/316M [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project norma: Compilation failure: Compilation failure: [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/pubstyle/getpapers/GetPapers.java:[14,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/html/HtmlCleaner.java:[8,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[22,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[28,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[269,42] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[315,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[347,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[354,57] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[375,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[445,16] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[25,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[82,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaTransformer [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[171,38] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.util.TransformerWrapper [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[14,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[36,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[42,35] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

petermr commented 8 years ago

This is due to out of date jar files. make sure you have the latest versions and then rebuild. If you have problems contact Tom Arrow who is putting together updated instructions

On Fri, Apr 8, 2016 at 11:58 AM, teatree1212 notifications@github.com wrote:

I get the following error message, when installing norma: mvn clean install

[INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.xml-cml:norma:jar:0.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for com.mycila.maven-license-plugin:maven-license-plugin is missing. @ line 92, column 12 [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:cobertura-maven-plugin is missing. @ line 53, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO]

[INFO]

[INFO] Building norma 0.1-SNAPSHOT

[INFO]

[INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ norma --- [INFO] Deleting /Users/hildegaa/Documents/sra_upload/map_papers/norma/target [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ norma --- [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 46 resources [INFO] [INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ norma --- [INFO] Changes detected - recompiling the module! [WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent! [INFO] Compiling 85 source files to /Users/hildegaa/Documents/sra_upload/map_papers/norma/target/classes [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/pubstyle/getpapers/GetPapers.java:[14,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/html/HtmlCleaner.java:[8,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[22,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[28,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[269,42] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[315,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[347,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[354,57] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[375,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[445,16] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[25,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[82,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaTransformer [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[171,38] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.util.TransformerWrapper [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[14,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[36,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[42,35] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [INFO] 16 errors [INFO] -------------------------------------------------------------

[INFO]

[INFO] BUILD FAILURE

[INFO]

[INFO] Total time: 1.497 s [INFO] Finished at: 2016-04-08T11:46:06+01:00 [INFO] Final Memory: 23M/316M

[INFO]

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project norma: Compilation failure: Compilation failure: [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/pubstyle/getpapers/GetPapers.java:[14,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/html/HtmlCleaner.java:[8,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[22,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[28,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[269,42] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[315,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[347,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[354,57] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[375,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[445,16] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[25,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[82,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaTransformer [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[171,38] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.util.TransformerWrapper [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[14,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[36,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR] /Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[42,35] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/ContentMine/workshop-resources/issues/57

Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069

tarrow commented 8 years ago

You probably don't need to build anything. Have you taken a look at our installation instructions at http://contentmine.github.io ? That shows how to download and install already built binaries.

On Fri, Apr 8, 2016 at 9:09 PM, petermr notifications@github.com wrote:

This is due to out of date jar files. make sure you have the latest versions and then rebuild. If you have problems contact Tom Arrow who is putting together updated instructions

On Fri, Apr 8, 2016 at 11:58 AM, teatree1212 notifications@github.com wrote:

I get the following error message, when installing norma: mvn clean install

[INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.xml-cml:norma:jar:0.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for com.mycila.maven-license-plugin:maven-license-plugin is missing. @ line 92, column 12 [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:cobertura-maven-plugin is missing. @ line 53, column 12 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO]

[INFO]

[INFO] Building norma 0.1-SNAPSHOT

[INFO]

[INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ norma --- [INFO] Deleting /Users/hildegaa/Documents/sra_upload/map_papers/norma/target [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ norma --- [WARNING] Using platform encoding (UTF-8 actually) to copy filtered resources, i.e. build is platform dependent! [INFO] Copying 46 resources [INFO]

[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ norma

[INFO] Changes detected - recompiling the module! [WARNING] File encoding has not been set, using platform encoding UTF-8, i.e. build is platform dependent! [INFO] Compiling 85 source files to /Users/hildegaa/Documents/sra_upload/map_papers/norma/target/classes [INFO] ------------------------------------------------------------- [ERROR] COMPILATION ERROR : [INFO] ------------------------------------------------------------- [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/pubstyle/getpapers/GetPapers.java:[14,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/html/HtmlCleaner.java:[8,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[22,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[28,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[269,42] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[315,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[347,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[354,57] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[375,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[445,16] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[25,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[82,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.NormaTransformer [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[171,38] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.util.TransformerWrapper [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[14,30] cannot find symbol symbol: class CMDir location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[36,17] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[42,35] cannot find symbol symbol: class CMDir location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [INFO] 16 errors [INFO] -------------------------------------------------------------

[INFO]

[INFO] BUILD FAILURE

[INFO]

[INFO] Total time: 1.497 s [INFO] Finished at: 2016-04-08T11:46:06+01:00 [INFO] Final Memory: 23M/316M

[INFO]

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project norma: Compilation failure: Compilation failure: [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/pubstyle/getpapers/GetPapers.java:[14,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/html/HtmlCleaner.java:[8,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[22,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[28,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[269,42] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[315,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[347,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[354,57] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[375,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaArgProcessor.java:[445,16] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaArgProcessor [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[25,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/NormaTransformer.java:[82,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.NormaTransformer [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/util/TransformerWrapper.java:[171,38] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.util.TransformerWrapper [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[14,30] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: package org.xmlcml.cmine.files [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[36,17] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR]

/Users/hildegaa/Documents/sra_upload/map_papers/norma/src/main/java/org/xmlcml/norma/input/pdf/PDF2XHTMLConverter.java:[42,35] cannot find symbol [ERROR] symbol: class CMDir [ERROR] location: class org.xmlcml.norma.input.pdf.PDF2XHTMLConverter [ERROR] -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

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Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069

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