Two Cytoscape 3.3 build questions

[Adam Treister]

1)  I’m trying to install the developers' implementation of Cytoscape 3.3 on OSX 10.10.4, but not getting very far into the clone.    Download of the entire program (dmg) and sample apps worked fine.  I’m able to use github normally, but am generally doing so thru eclipse. The script appears to have execute privileges (I think on the server side). Permission error shown below.  I’ve tried this at different locations within my home directory.

AdamMac:~ adam$ git clone https://github.com/cytoscape/cytoscape.git

Cloning into 'cytoscape'...

remote: Counting objects: 242, done.

remote: Total 242 (delta 0), reused 0 (delta 0), pack-reused 242

Receiving objects: 100% (242/242), 50.09 KiB | 0 bytes/s, done.

Resolving deltas: 100% (97/97), done.

Checking connectivity... done.

AdamMac:~ adam$ cd ./cytoscape

AdamMac:cytoscape adam$ ./cy.sh init

Target directory = 

Cytoscape project will be cloned to: /Users/adam/cytoscape

Cloning into 'cytoscape'...

Permission denied (publickey).

fatal: Could not read from remote repository.

Please make sure you have the correct access rights

and the repository exists.

Could not clone remote repository: /Users/adam/cytoscape

AdamMac:cytoscape adam$ ls -l cy.sh

-rwxr-xr-x  1 adam  staff  5633 Feb 22 19:15 cy.sh

2) I was able to get pretty far by just downloading the source and building the entire project from scratch, but although I used maven to install the third-party jars, I am missing the correct jars for reading Excel files (WorkbookFactory, DataFormatter and FormulaEvaluator are examples of missing methods.) and for supporting the JGraph library (JGraphLayoutAlgorihtm, JGraphLayoutSettings).  Has anyone used Cytoscape to make a directed graph of its own code dependencies?

Thanks for the help,

Adam Treister

[Scooter Morris]

Hi Adam,
   Looks like you missed the "third-party" jar file.  That's one of the target modules in gui-distribution.  The easiest way to get everything built though is to change the cy.sh script and replace the "g...@github.com:" with "http://github.com/" in BASE_URL and APP_URL.  Then everything should pull down just fine and you can use maven from the top level.  I certainly wouldn't recommend trying to build all of cytoscape from within eclipse, though.  We all generally use maven from the command line for the full builds.

-- scooter

[Adam Treister]

Scooter,

I appreciate the fast help.  It got me past the download, build & launch.  

Somewhere in the process it must have clobbered JAVA_HOME, as now when I run the samples in Eclipse, I was seeing this:

Exception in thread "main" java.lang.UnsupportedClassVersionError: org/apache/maven/cli/MavenCli : Unsupported major.minor version 51.0

There are many suggestions at:  http://stackoverflow.com/questions/20313453/java-home-on-osx-with-eclipse-and-maven

but none worked at the time but somehow I’ve move past that one.

The current error I see is:

Exception in thread "main" java.lang.Error: java.io.FileNotFoundException: /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/lib/tzdb.dat (No such file or directory)

at sun.util.calendar.ZoneInfoFile$1.run(ZoneInfoFile.java:261)

If I make changes to a java file and rerun Maven Install, the console says there’s nothing to compile.  Is there a trick to dirty the files and start the next compile?

Thanks,

Adam

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