Leiningen has problems building a working uberjar

Question

We're trying to build our Clojure project with Leiningen. We've succeeded in creating an uberjar by doing the following:

preconditions:

• project.clj file lists dependencies
• :main my-project.core in project.clj
• a core.clj file with a -main function
• (:gen-class :main true) in core.clj

procedure:

• ran lein test; completed with no failures
• ran lein deps; completed successfully
• from project.clj's directory: rain lein uberjar
• This created two jar files: My-Project-1.0.0-SNAPSHOT-standalone.jar, and My-Project-1.0.0-SNAPSHOT.jar.
• ran java -jar BioClojure-1.0.0-SNAPSHOT-standalone.jar, which resulted in this exception:

Exception in thread "main" java.lang.SecurityException: Invalid signature file digest for Manifest main attributes

My research into this problem has not been fruitful. Apparently, it's a known problem with no good solution. I do not understand the answers there.

What do we need to do to get our uberjar working?

• determine which of our dependencies is causing the problem?
• remove dependencies from our project?
• compile the project some other way?
• patch leiningen?
• use the suggested command: zip *-standalone.jar -d META-INF/DUMMY.SF (I have no idea what this does)
• do something with :uberjar-exclusions in the project.clj file? (if so, what?)

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Lein and java versions:

$ lein version
Leiningen 1.6.1 on Java 1.6.0_26 Java HotSpot(TM) 64-Bit Server VM

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Update: running the command suggested gives:

$ unzip -l BioClojure-1.0.0-SNAPSHOT-standalone.jar | grep -i -e "\.sf"
 49911  08-27-09 15:57   META-INF/RCSB-PDB.SF
     0  03-23-10 08:21   META-INF/maven/net.sf.alxa/
     0  03-23-10 08:21   META-INF/maven/net.sf.alxa/jlatexmath/
   929  03-23-10 08:20   META-INF/maven/net.sf.alxa/jlatexmath/pom.xml
   115  03-21-10 14:01   META-INF/maven/net.sf.alxa/jlatexmath/pom.properties
175241  08-17-11 20:25   META-INF/SELFSIGN.SF
     0  09-21-09 06:45   META-INF/maven/net.sf.opencsv/
     0  09-21-09 06:45   META-INF/maven/net.sf.opencsv/opencsv/
  5510  09-21-09 06:44   META-INF/maven/net.sf.opencsv/opencsv/pom.xml
   106  09-21-09 06:45   META-INF/maven/net.sf.opencsv/opencsv/pom.properties

Answer 1

My understanding from reading the comments in that issue is that your problem would go away if you add the following to your project.clj

:uberjar-exclusions [#"foo.sf"] 

where foo.sf is the particular .sf file you want to ignore from the jar. You can determine this by running:

unzip -l BioClojure-1.0.0-SNAPSHOT-standalone.jar | grep -i -e "\.sf"

The suggested zip command deletes the particular file from the jar (which is of the ZIP format).