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idekerlab / dot-app

Cytoscape application for exporting to .dot file format
GNU General Public License v3.0
7 stars 4 forks source link

app not building after cloning repository #14

Closed matthiaskoenig closed 5 years ago

matthiaskoenig commented 7 years ago

When cloning the repository it is not possible to build with a clean install. The libs in lib must be available for the maven build.

mkoenig@core1:~/git/dot-app$ mvn clean install
[INFO] Scanning for projects...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building dot-app 0.9.4
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.734 s
[INFO] Finished at: 2017-07-27T09:48:43+02:00
[INFO] Final Memory: 10M/228M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project dot-app: Could not resolve dependencies for project org.cytoscape.intern:dot-app:bundle:0.9.4: Failed to collect dependencies at com.alexmerz:jpgd:jar:0.8.6: Failed to read artifact descriptor for com.alexmerz:jpgd:jar:0.8.6: Could not transfer artifact com.alexmerz:jpgd:pom:0.8.6 from/to lib-repo (/home/mkoenig/git/dot-app\lib\): Cannot access /home/mkoenig/git/dot-app\lib\ with type default using the available connector factories: BasicRepositoryConnectorFactory: Cannot access /home/mkoenig/git/dot-app\lib\ using the registered transporter factories: WagonTransporterFactory: Unsupported transport protocol -> [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/DependencyResolutionException
bdtfitts commented 7 years ago

For some reason, if you run mvn clean [initialize thru process-resources] first and then mvn clean install it works on my machine. I am unsure why it does not allow it to be built solely by running mvn clean install, as I am very novice when using Maven.

matthiaskoenig commented 7 years ago

Does not work for me. You should delete your mvn repository and try again. I am sure you installed the dependencies manually in the repository at some point there that is why they can be resolved.

If you delete com.alexmerz from ~/.m2/repository it will not work, because com.alexmerz:jpgd:jar:0.8.6 is not part of the repository lib folder.

Or the files are not commited to the repository and you only have them local. Clean your mvn repository and make a clean clone of the project than you will see the issue.

On Fri, Jul 28, 2017 at 5:09 AM, Braxton Fitts notifications@github.com wrote:

For some reason, if you run mvn clean [initialize thru process-resources] first and then mvn clean install it works on my machine. I am unsure why it does not allow it to be built solely by running mvn clean install.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/idekerlab/dot-app/issues/14#issuecomment-318544863, or mute the thread https://github.com/notifications/unsubscribe-auth/AA29usOJCtr7RM0jWqwNWMsl0zwHGtCPks5sSVDsgaJpZM4Ok6vi .

-- Dr. Matthias König Junior Group Leader LiSyM - Systems Medicine of the Liver Humboldt-University Berlin, Institute of Biology, Institute for Theoretical Biology https://www.livermetabolism.com konigmatt@googlemail.com Tel: +49 30 20938450 Tel: +49 176 81168480

bdtfitts commented 7 years ago

Can you download the latest commit for me and see if it fixes the build dependency? I'm fairly certain that it should now.

matthiaskoenig commented 7 years ago

Thanks for this.

I just tried but getting now the following UTF8 encoding errors. This is the copyright sign in your source files which is not UTF8. I am on Ubuntu which is native UTF8 encoding.

You should set the encoding in the compiler plugin https://stackoverflow.com/questions/8978013/error-unmappable-character-for-encoding-utf8-during-maven-compilation Or even better be more conservative with the characters you use in your java source files. Normally I am trying to restrict myself to ASCII or UTF-8. But the copyright sign is not needed in this location.

[INFO] Compiling 16 source files to /home/mkoenig/git/dot-app/target/classes
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 58.277 s
[INFO] Finished at: 2017-08-03T22:18:53+02:00
[INFO] Final Memory: 16M/394M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:2.0.2:compile (default-compile) on project dot-app: Compilation failure: Compilation failure:
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/NodeReader.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/write/mapper/NetworkPropertyMapper.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/write/mapper/Mapper.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/Reader.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/write/mapper/EdgePropertyMapper.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/DotActivator.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderFactory.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/write/DotWriterTask.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/DotReaderTask.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/GradientListener.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/write/mapper/NodePropertyMapper.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/NetworkReader.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/Notifier.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/EdgeReader.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/write/DotWriterFactory.java:[2,13] error: unmappable character for encoding UTF8
[ERROR] 
[ERROR] /home/mkoenig/git/dot-app/src/main/java/org/cytoscape/intern/read/reader/StringColor.java:[2,13] error: unmappable character for encoding UTF8
[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
bdtfitts commented 7 years ago

I've set the encoding in the pom like you suggested