Ok, the reason we're having problems with the master branch and the exact commit to pull from is as far as I can tell:

1) you are asking me to pull from the head of master.
2) the head of master has not been tested.
3) because the head of master has not been tested, there is no tag on it.
4) because there is no tag on it, the IRIS deploy process is pulling the last tagged commit.

I'll go ahead and tag the head of master, and run it through the test process. If it passes the service test process, then I'll add it to the iris deployment.

Sound good?


On Oct 3, 2013, at 6:29 AM, Thomas Brettin <brettin@mcs.anl.gov> wrote:

ugh!

I'll check, thanks for helping.

Tom


On Oct 3, 2013, at 6:28 AM, James Gurtowski <gurtowsk@cshl.edu> wrote:

I think you are back to the first error now. Is this from the master branch?

James


On Wed, Oct 2, 2013 at 9:26 PM, Thomas Brettin <brettin@mcs.anl.gov> wrote:
I upgraded to 1.7.0_25-b15.

Where's this at?

java -cp `find dist/jnomics-manager-*.jar` edu.cshl.schatz.jnomics.manager.client.CreateKbaseScripts jk bin
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/lang3/StringUtils
        at edu.cshl.schatz.jnomics.manager.client.CreateKbaseScripts.main(Unknown Source)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.lang3.StringUtils
        at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        ... 1 more
make[1]: *** [build-jnomics] Error 1
make[1]: Leaving directory `/kb/dev_container/modules/jnomics'
make: *** [deploy] Error 1


root@t12:/kb/dev_container# echo $CLASSPATH
/kb/runtime//lib/*:/kb/dev_container/modules/auth/dist/lib/*:/kb/dev_container/modules/idserver/dist/lib/*:/kb/dev_container/modules/invocation/dist/lib/*:/kb/dev_container/modules/kb_seed/dist/lib/*:/kb/dev_container/modules/kbapi_common/dist/lib/*:/kb/dev_container/modules/typecomp/dist/lib/*