More Problems Building/Running Cytoscape 3.2

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michael...@non.agilent.com

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Jul 22, 2014, 12:01:36 PM7/22/14
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After "successfully" building Cy3, I tried running the result and it blow up. I tried running from Win7 command prompt (cytoscape.bat) and also GitBash (cytoscape.sh). Both get the same set of errors. The splash screen comes up, then it dies claiming Exported package names can't be zero length and then a whole bunch of missing requirement errors:

 

/c/work/Cy3.1.2-src/cytoscape/gui-distribution/assembly/target/cytoscape 527%>cytoscape.sh

cat: /proc/meminfo: No such file or directory

ERROR: Error parsing system bundle export statement: org.osgi.framework.startlevel;uses:="org.osgi.framework";version="1

.0", org.osgi.framework.wiring;uses:="org.osgi.framework";version="1.1", org.osgi.framework.hooks.bundle;uses:="org.osgi

.framework";version="1.1", org.osgi.framework.hooks.service;uses:="org.osgi.framework";version="1.1", org.osgi.framework

.hooks.resolver;uses:="org.osgi.framework.wiring";version="1.0", org.osgi.framework.launch;uses:="org.osgi.framework";ve

rsion="1.1", org.osgi.framework.namespace;uses:="org.osgi.resource";version="1.0", org.osgi.framework;version="1.7", org

.osgi.framework.hooks.weaving;uses:="org.osgi.framework.wiring";version="1.0",org.osgi.resource;version="1.0",org.osgi.s

ervice.url;version="1.0",org.osgi.service.startlevel;uses:="org.osgi.framework";version="1.1",org.osgi.service.packagead

min;uses:="org.osgi.framework";version="1.2",org.osgi.service.url;version="1.0", org.osgi.util.tracker;uses:="org.osgi.f

ramework";version="1.5.1", org.apache.karaf.jaas.boot;version="3.0.1", org.apache.karaf.jaas.boot.principal;version="3.0

.1", org.apache.karaf.management.boot;version="3.0.1", org.apache.karaf.version;version="3.0.1", javax.accessibility, ja

vax.activation, javax.activity, javax.annotation;version="1.1", javax.annotation.processing;version="1.1", javax.crypto,

javax.crypto.interfaces, javax.crypto.spec, javax.imageio, javax.imageio.event, javax.imageio.metadata, javax.imageio.p

lugins.bmp, javax.imageio.plugins.jpeg, javax.imageio.spi, javax.imageio.stream, javax.jws, javax.jws.soap, javax.lang.m

odel, javax.lang.model.element, javax.lang.model.type, javax.lang.model.util, javax.management, javax.management.loading

, javax.management.modelmbean, javax.management.monitor, javax.management.openmbean, javax.management.relation, javax.ma

nagement.remote, javax.management.remote.rmi, javax.management.timer, javax.naming, javax.naming.directory, javax.naming

.event, javax.naming.ldap, javax.naming.spi, javax.net, javax.net.ssl, javax.print, javax.print.attribute, javax.print.a

ttribute.standard, javax.print.event, javax.rmi, javax.rmi.CORBA, javax.rmi.ssl, javax.script, javax.security.auth, java

x.security.auth.callback, javax.security.auth.kerberos, javax.security.auth.login, javax.security.auth.spi, javax.securi

ty.auth.x500, javax.security.cert, javax.security.sasl, javax.sound.midi, javax.sound.midi.spi, javax.sound.sampled, jav

ax.sound.sampled.spi, javax.sql, javax.sql.rowset, javax.sql.rowset.serial, javax.sql.rowset.spi, javax.swing, javax.swi

ng.border, javax.swing.colorchooser, javax.swing.event, javax.swing.filechooser, javax.swing.plaf, javax.swing.plaf.basi

c, javax.swing.plaf.metal, javax.swing.plaf.multi, javax.swing.plaf.synth, javax.swing.table, javax.swing.text, javax.sw

ing.text.html, javax.swing.text.html.parser, javax.swing.text.rtf, javax.swing.tree, javax.swing.undo, javax.tools, java

x.transaction; javax.transaction.xa; partial=true; mandatory:=partial, javax.xml, javax.xml.bind, javax.xml.bind.annotat

ion, javax.xml.bind.annotation.adapters, javax.xml.bind.attachment, javax.xml.bind.helpers, javax.xml.bind.util, javax.x

ml.crypto, javax.xml.crypto.dom, javax.xml.crypto.dsig, javax.xml.crypto.dsig.dom, javax.xml.crypto.dsig.keyinfo, javax.

xml.crypto.dsig.spec, javax.xml.datatype, javax.xml.namespace, javax.xml.parsers, javax.xml.soap, javax.xml.transform, j

avax.xml.transform.dom, javax.xml.transform.sax, javax.xml.transform.stax, javax.xml.transform.stream, javax.xml.validat

ion, javax.xml.ws, javax.xml.ws.handler, javax.xml.ws.handler.soap, javax.xml.ws.http, javax.xml.ws.soap, javax.xml.ws.s

pi, javax.xml.ws.wsaddressing, javax.xml.xpath, org.ietf.jgss, org.omg.CORBA, org.omg.CORBA_2_3, org.omg.CORBA_2_3.porta

ble, org.omg.CORBA.DynAnyPackage, org.omg.CORBA.ORBPackage, org.omg.CORBA.portable, org.omg.CORBA.TypeCodePackage, org.o

mg.CosNaming, org.omg.CosNaming.NamingContextExtPackage, org.omg.CosNaming.NamingContextPackage, org.omg.Dynamic, org.om

g.DynamicAny, org.omg.DynamicAny.DynAnyFactoryPackage, org.omg.DynamicAny.DynAnyPackage, org.omg.IOP, org.omg.IOP.CodecF

actoryPackage, org.omg.IOP.CodecPackage, org.omg.Messaging, org.omg.PortableInterceptor, org.omg.PortableInterceptor.ORB

InitInfoPackage, org.omg.PortableServer, org.omg.PortableServer.CurrentPackage, org.omg.PortableServer.POAManagerPackage

, org.omg.PortableServer.POAPackage, org.omg.PortableServer.portable, org.omg.PortableServer.ServantLocatorPackage, org.

omg.SendingContext, org.omg.stub.java.rmi, org.omg.stub.javax.management.remote.rmi, org.w3c.dom, org.w3c.dom.bootstrap,

org.w3c.dom.css, org.w3c.dom.events, org.w3c.dom.html, org.w3c.dom.ls, org.w3c.dom.ranges, org.w3c.dom.stylesheets, org

.w3c.dom.traversal, org.w3c.dom.views, org.w3c.dom.xpath, org.xml.sax, org.xml.sax.ext, org.xml.sax.helpers,org.apache.k

araf.branding,org.cytoscape.launcher.internal,com.sun.xml.internal.bind,com.apple.eawt; (org.osgi.framework.BundleExcept

ion: Exported package names cannot be zero length.)

org.osgi.framework.BundleException: Exported package names cannot be zero length.

        at org.apache.felix.framework.util.manifestparser.ManifestParser.normalizeExportClauses(ManifestParser.java:744)

 

        at org.apache.felix.framework.util.manifestparser.ManifestParser.<init>(ManifestParser.java:191)

        at org.apache.felix.framework.ExtensionManager.<init>(ExtensionManager.java:221)

        at org.apache.felix.framework.Felix.<init>(Felix.java:385)

        at org.apache.felix.framework.FrameworkFactory.newFramework(FrameworkFactory.java:28)

        at org.apache.karaf.main.Main.launch(Main.java:236)

        at org.apache.karaf.main.Main.main(Main.java:171)

        at org.cytoscape.launcher.internal.Launcher.main(Launcher.java:76)

ERROR: Bundle org.ops4j.pax.url.mvn [1] Error starting org/ops4j/pax/url/pax-url-mvn/1.2.8/pax-url-mvn-1.2.8.jar (org.os

gi.framework.BundleException: Unresolved constraint in bundle org.ops4j.pax.url.mvn [1]: Unable to resolve 1.0: missing

requirement [1.0] osgi.wiring.package; (osgi.wiring.package=javax.net.ssl))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.ops4j.pax.url.mvn [1]: Unable to resolve 1.0: mi

ssing requirement [1.0] osgi.wiring.package; (osgi.wiring.package=javax.net.ssl)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.ops4j.pax.url.wrap [2] Error starting org/ops4j/pax/url/pax-url-wrap/1.2.8/pax-url-wrap-1.2.8.jar (org

.osgi.framework.BundleException: Unresolved constraint in bundle org.ops4j.pax.url.wrap [2]: Unable to resolve 2.0: miss

ing requirement [2.0] osgi.wiring.package; (osgi.wiring.package=javax.net.ssl))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.ops4j.pax.url.wrap [2]: Unable to resolve 2.0: m

issing requirement [2.0] osgi.wiring.package; (osgi.wiring.package=javax.net.ssl)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.ops4j.pax.logging.pax-logging-api [3] Error starting org/ops4j/pax/logging/pax-logging-api/1.6.10/pax-

logging-api-1.6.10.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.ops4j.pax.logging.pax-lo

gging-api [3]: Unable to resolve 3.0: missing requirement [3.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.pars

ers))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.ops4j.pax.logging.pax-logging-api [3]: Unable to

resolve 3.0: missing requirement [3.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.ops4j.pax.logging.pax-logging-service [4] Error starting org/ops4j/pax/logging/pax-logging-service/1.6

.10/pax-logging-service-1.6.10.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.ops4j.pax.lo

gging.pax-logging-service [4]: Unable to resolve 4.0: missing requirement [4.0] osgi.wiring.package; (osgi.wiring.packag

e=javax.xml.parsers))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.ops4j.pax.logging.pax-logging-service [4]: Unabl

e to resolve 4.0: missing requirement [4.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.felix.configadmin [5] Error starting org/apache/felix/org.apache.felix.configadmin/1.2.8/org.ap

ache.felix.configadmin-1.2.8.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.felix.c

onfigadmin [5]: Unable to resolve 5.0: missing requirement [5.0] osgi.wiring.package; (&(osgi.wiring.package=org.osgi.fr

amework)(version>=1.3.0)))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.felix.configadmin [5]: Unable to resolve

5.0: missing requirement [5.0] osgi.wiring.package; (&(osgi.wiring.package=org.osgi.framework)(version>=1.3.0))

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.felix.fileinstall [6] Error starting org/apache/felix/org.apache.felix.fileinstall/3.2.4/org.ap

ache.felix.fileinstall-3.2.4.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.felix.f

ileinstall [6]: Unable to resolve 6.0: missing requirement [6.0] osgi.wiring.package; (&(osgi.wiring.package=org.osgi.fr

amework)(version>=1.4.0)(!(version>=2.0.0))))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.felix.fileinstall [6]: Unable to resolve

6.0: missing requirement [6.0] osgi.wiring.package; (&(osgi.wiring.package=org.osgi.framework)(version>=1.4.0)(!(version

>=2.0.0)))

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.aries.util [8] Error starting org/apache/aries/org.apache.aries.util/0.3.1/org.apache.aries.uti

l-0.3.1.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.util [8]: Unable to re

solve 8.0: missing requirement [8.0] osgi.wiring.package; (&(osgi.wiring.package=org.osgi.framework)(version>=1.5.0)(!(v

ersion>=2.0.0))))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.util [8]: Unable to resolve 8.0: mi

ssing requirement [8.0] osgi.wiring.package; (&(osgi.wiring.package=org.osgi.framework)(version>=1.5.0)(!(version>=2.0.0

)))

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.aries.proxy [9] Error starting org/apache/aries/proxy/org.apache.aries.proxy/0.3.1/org.apache.a

ries.proxy-0.3.1.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.proxy [9]: Un

able to resolve 9.0: missing requirement [9.0] osgi.wiring.package; (&(osgi.wiring.package=org.apache.aries.util)(versio

n>=0.3.0)(!(version>=1.0.0))) [caused by: Unable to resolve 8.0: missing requirement [8.0] osgi.wiring.package; (&(osgi.

wiring.package=org.osgi.framework)(version>=1.5.0)(!(version>=2.0.0)))])

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.proxy [9]: Unable to resolve 9.0: m

issing requirement [9.0] osgi.wiring.package; (&(osgi.wiring.package=org.apache.aries.util)(version>=0.3.0)(!(version>=1

.0.0))) [caused by: Unable to resolve 8.0: missing requirement [8.0] osgi.wiring.package; (&(osgi.wiring.package=org.osg

i.framework)(version>=1.5.0)(!(version>=2.0.0)))]

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.aries.blueprint [10] Error starting org/apache/aries/blueprint/org.apache.aries.blueprint/0.3.2

/org.apache.aries.blueprint-0.3.2.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.ar

ies.blueprint [10]: Unable to resolve 10.0: missing requirement [10.0] osgi.wiring.package; (osgi.wiring.package=javax.x

ml.parsers))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.blueprint [10]: Unable to resolve 1

0.0: missing requirement [10.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.deployer.spring [33] Error starting org/apache/karaf/deployer/org.apache.karaf.deployer.s

pring/2.2.11/org.apache.karaf.deployer.spring-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in b

undle org.apache.karaf.deployer.spring [33]: Unable to resolve 33.0: missing requirement [33.0] osgi.wiring.package; (os

gi.wiring.package=javax.xml.parsers))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.deployer.spring [33]: Unable to res

olve 33.0: missing requirement [33.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.deployer.blueprint [34] Error starting org/apache/karaf/deployer/org.apache.karaf.deploye

r.blueprint/2.2.11/org.apache.karaf.deployer.blueprint-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constr

aint in bundle org.apache.karaf.deployer.blueprint [34]: Unable to resolve 34.0: missing requirement [34.0] osgi.wiring.

package; (osgi.wiring.package=javax.xml.parsers))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.deployer.blueprint [34]: Unable to

resolve 34.0: missing requirement [34.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

       at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.shell.console [11] Error starting org/apache/karaf/shell/org.apache.karaf.shell.console/2

.2.11/org.apache.karaf.shell.console-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org

.apache.karaf.shell.console [11]: Unable to resolve 11.0: missing requirement [11.0] osgi.wiring.package; (osgi.wiring.p

ackage=javax.security.auth))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.shell.console [11]: Unable to resol

ve 11.0: missing requirement [11.0] osgi.wiring.package; (osgi.wiring.package=javax.security.auth)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.shell.osgi [12] Error starting org/apache/karaf/shell/org.apache.karaf.shell.osgi/2.2.11/

org.apache.karaf.shell.osgi-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.k

araf.shell.osgi [12]: Unable to resolve 12.0: missing requirement [12.0] osgi.wiring.package; (&(osgi.wiring.package=jli

ne)(version>=2.9.0)(!(version>=3.0.0))) [caused by: Unable to resolve 11.0: missing requirement [11.0] osgi.wiring.packa

ge; (osgi.wiring.package=javax.security.auth)])

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.shell.osgi [12]: Unable to resolve

12.0: missing requirement [12.0] osgi.wiring.package; (&(osgi.wiring.package=jline)(version>=2.9.0)(!(version>=3.0.0)))

[caused by: Unable to resolve 11.0: missing requirement [11.0] osgi.wiring.package; (osgi.wiring.package=javax.security.

auth)]

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.shell.log [13] Error starting org/apache/karaf/shell/org.apache.karaf.shell.log/2.2.11/or

g.apache.karaf.shell.log-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.kara

f.shell.log [13]: Unable to resolve 13.0: missing requirement [13.0] osgi.wiring.package; (&(osgi.wiring.package=org.apa

che.felix.gogo.commands)(version>=0.10.0)(!(version>=1.0.0))) [caused by: Unable to resolve 11.0: missing requirement [1

1.0] osgi.wiring.package; (osgi.wiring.package=javax.security.auth)])

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.shell.log [13]: Unable to resolve 1

3.0: missing requirement [13.0] osgi.wiring.package; (&(osgi.wiring.package=org.apache.felix.gogo.commands)(version>=0.1

0.0)(!(version>=1.0.0))) [caused by: Unable to resolve 11.0: missing requirement [11.0] osgi.wiring.package; (osgi.wirin

g.package=javax.security.auth)]

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.shell.packages [14] Error starting org/apache/karaf/shell/org.apache.karaf.shell.packages

/2.2.11/org.apache.karaf.shell.packages-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle

org.apache.karaf.shell.packages [14]: Unable to resolve 14.0: missing requirement [14.0] osgi.wiring.package; (&(osgi.wi

ring.package=org.apache.felix.gogo.commands)(version>=0.10.0)(!(version>=1.0.0))) [caused by: Unable to resolve 11.0: mi

ssing requirement [11.0] osgi.wiring.package; (osgi.wiring.package=javax.security.auth)])

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.shell.packages [14]: Unable to reso

lve 14.0: missing requirement [14.0] osgi.wiring.package; (&(osgi.wiring.package=org.apache.felix.gogo.commands)(version

>=0.10.0)(!(version>=1.0.0))) [caused by: Unable to resolve 11.0: missing requirement [11.0] osgi.wiring.package; (osgi.

wiring.package=javax.security.auth)]

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.shell.commands [15] Error starting org/apache/karaf/shell/org.apache.karaf.shell.commands

/2.2.11/org.apache.karaf.shell.commands-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle

org.apache.karaf.shell.commands [15]: Unable to resolve 15.0: missing requirement [15.0] osgi.wiring.package; (&(osgi.wi

ring.package=jline)(version>=2.9.0)(!(version>=3.0.0))) [caused by: Unable to resolve 11.0: missing requirement [11.0] o

sgi.wiring.package; (osgi.wiring.package=javax.security.auth)])

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.shell.commands [15]: Unable to reso

lve 15.0: missing requirement [15.0] osgi.wiring.package; (&(osgi.wiring.package=jline)(version>=2.9.0)(!(version>=3.0.0

))) [caused by: Unable to resolve 11.0: missing requirement [11.0] osgi.wiring.package; (osgi.wiring.package=javax.secur

ity.auth)]

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.shell.dev [16] Error starting org/apache/karaf/shell/org.apache.karaf.shell.dev/2.2.11/or

g.apache.karaf.shell.dev-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.kara

f.shell.dev [16]: Unable to resolve 16.0: missing requirement [16.0] osgi.wiring.package; (osgi.wiring.package=javax.net

.ssl))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.shell.dev [16]: Unable to resolve 1

6.0: missing requirement [16.0] osgi.wiring.package; (osgi.wiring.package=javax.net.ssl)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.jaas.config [17] Error starting org/apache/karaf/jaas/org.apache.karaf.jaas.config/2.2.11

/org.apache.karaf.jaas.config-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache

.karaf.jaas.config [17]: Unable to resolve 17.0: missing requirement [17.0] osgi.wiring.package; (osgi.wiring.package=ja

vax.net.ssl))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.jaas.config [17]: Unable to resolve

17.0: missing requirement [17.0] osgi.wiring.package; (osgi.wiring.package=javax.net.ssl)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.jaas.modules [18] Error starting org/apache/karaf/jaas/org.apache.karaf.jaas.modules/2.2.

11/org.apache.karaf.jaas.modules-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apa

che.karaf.jaas.modules [18]: Unable to resolve 18.0: missing requirement [18.0] osgi.wiring.package; (osgi.wiring.packag

e=javax.naming))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.jaas.modules [18]: Unable to resolv

e 18.0: missing requirement [18.0] osgi.wiring.package; (osgi.wiring.package=javax.naming)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.jaas.command [19] Error starting org/apache/karaf/jaas/org.apache.karaf.jaas.command/2.2.

11/org.apache.karaf.jaas.command-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apa

che.karaf.jaas.command [19]: Unable to resolve 19.0: missing requirement [19.0] osgi.wiring.package; (osgi.wiring.packag

e=javax.management))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.jaas.command [19]: Unable to resolv

e 19.0: missing requirement [19.0] osgi.wiring.package; (osgi.wiring.package=javax.management)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.features.core [20] Error starting org/apache/karaf/features/org.apache.karaf.features.cor

e/2.2.11/org.apache.karaf.features.core-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle

org.apache.karaf.features.core [20]: Unable to resolve 20.0: missing requirement [20.0] osgi.wiring.package; (osgi.wirin

g.package=javax.xml.parsers))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.features.core [20]: Unable to resol

ve 20.0: missing requirement [20.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.features.command [21] Error starting org/apache/karaf/features/org.apache.karaf.features.

command/2.2.11/org.apache.karaf.features.command-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint i

n bundle org.apache.karaf.features.command [21]: Unable to resolve 21.0: missing requirement [21.0] osgi.wiring.package;

(osgi.wiring.package=javax.management))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.features.command [21]: Unable to re

solve 21.0: missing requirement [21.0] osgi.wiring.package; (osgi.wiring.package=javax.management)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.diagnostic.common [23] Error starting org/apache/karaf/diagnostic/org.apache.karaf.diagno

stic.common/2.2.11/org.apache.karaf.diagnostic.common-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constra

int in bundle org.apache.karaf.diagnostic.common [23]: Unable to resolve 23.0: missing requirement [23.0] osgi.wiring.pa

ckage; (&(osgi.wiring.package=org.apache.karaf.features)(version>=2.2.0)(!(version>=3.0.0))) [caused by: Unable to resol

ve 20.0: missing requirement [20.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)])

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.diagnostic.common [23]: Unable to r

esolve 23.0: missing requirement [23.0] osgi.wiring.package; (&(osgi.wiring.package=org.apache.karaf.features)(version>=

2.2.0)(!(version>=3.0.0))) [caused by: Unable to resolve 20.0: missing requirement [20.0] osgi.wiring.package; (osgi.wir

ing.package=javax.xml.parsers)]

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.diagnostic.command [24] Error starting org/apache/karaf/diagnostic/org.apache.karaf.diagn

ostic.command/2.2.11/org.apache.karaf.diagnostic.command-2.2.11.jar (org.osgi.framework.BundleException: Unresolved cons

traint in bundle org.apache.karaf.diagnostic.command [24]: Unable to resolve 24.0: missing requirement [24.0] osgi.wirin

g.package; (&(osgi.wiring.package=org.apache.felix.gogo.commands)(version>=0.10.0)(!(version>=1.0.0))) [caused by: Unabl

e to resolve 11.0: missing requirement [11.0] osgi.wiring.package; (osgi.wiring.package=javax.security.auth)])

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.diagnostic.command [24]: Unable to

resolve 24.0: missing requirement [24.0] osgi.wiring.package; (&(osgi.wiring.package=org.apache.felix.gogo.commands)(ver

sion>=0.10.0)(!(version>=1.0.0))) [caused by: Unable to resolve 11.0: missing requirement [11.0] osgi.wiring.package; (o

sgi.wiring.package=javax.security.auth)]

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.aries.jmx.api [25] Error starting org/apache/aries/jmx/org.apache.aries.jmx.api/0.3/org.apache.

aries.jmx.api-0.3.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.jmx.api [25]

: Unable to resolve 25.0: missing requirement [25.0] osgi.wiring.package; (osgi.wiring.package=javax.management.openmbea

n))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.jmx.api [25]: Unable to resolve 25.

0: missing requirement [25.0] osgi.wiring.package; (osgi.wiring.package=javax.management.openmbean)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.aries.jmx.core [26] Error starting org/apache/aries/jmx/org.apache.aries.jmx.core/0.3.1/org.apa

che.aries.jmx.core-0.3.1.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.jmx.c

ore [26]: Unable to resolve 26.0: missing requirement [26.0] osgi.wiring.package; (osgi.wiring.package=javax.management)

)

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.jmx.core [26]: Unable to resolve 26

.0: missing requirement [26.0] osgi.wiring.package; (osgi.wiring.package=javax.management)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.aries.jmx.blueprint [27] Error starting org/apache/aries/jmx/org.apache.aries.jmx.blueprint/0.3

/org.apache.aries.jmx.blueprint-0.3.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.

aries.jmx.blueprint [27]: Unable to resolve 27.0: missing requirement [27.0] osgi.wiring.package; (osgi.wiring.package=j

avax.management))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.aries.jmx.blueprint [27]: Unable to resol

ve 27.0: missing requirement [27.0] osgi.wiring.package; (osgi.wiring.package=javax.management)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.admin.core [28] Error starting org/apache/karaf/admin/org.apache.karaf.admin.core/2.2.11/

org.apache.karaf.admin.core-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.k

araf.admin.core [28]: Unable to resolve 28.0: missing requirement [28.0] osgi.wiring.package; (osgi.wiring.package=javax

.management))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.admin.core [28]: Unable to resolve

28.0: missing requirement [28.0] osgi.wiring.package; (osgi.wiring.package=javax.management)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.admin.command [29] Error starting org/apache/karaf/admin/org.apache.karaf.admin.command/2

.2.11/org.apache.karaf.admin.command-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org

.apache.karaf.admin.command [29]: Unable to resolve 29.0: missing requirement [29.0] osgi.wiring.package; (osgi.wiring.p

ackage=javax.management))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.admin.command [29]: Unable to resol

ve 29.0: missing requirement [29.0] osgi.wiring.package; (osgi.wiring.package=javax.management)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.mina.core [30] Error starting org/apache/mina/mina-core/2.0.5/mina-core-2.0.5.jar (org.osgi.fra

mework.BundleException: Unresolved constraint in bundle org.apache.mina.core [30]: Unable to resolve 30.0: missing requi

rement [30.0] osgi.wiring.package; (osgi.wiring.package=javax.crypto))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.mina.core [30]: Unable to resolve 30.0: m

issing requirement [30.0] osgi.wiring.package; (osgi.wiring.package=javax.crypto)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.sshd.core [31] Error starting org/apache/sshd/sshd-core/0.8.0/sshd-core-0.8.0.jar (org.osgi.fra

mework.BundleException: Unresolved constraint in bundle org.apache.sshd.core [31]: Unable to resolve 31.0: missing requi

rement [31.0] osgi.wiring.package; (osgi.wiring.package=javax.crypto))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.sshd.core [31]: Unable to resolve 31.0: m

issing requirement [31.0] osgi.wiring.package; (osgi.wiring.package=javax.crypto)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.shell.ssh [32] Error starting org/apache/karaf/shell/org.apache.karaf.shell.ssh/2.2.11/or

g.apache.karaf.shell.ssh-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.kara

f.shell.ssh [32]: Unable to resolve 32.0: missing requirement [32.0] osgi.wiring.package; (osgi.wiring.package=javax.sec

urity.auth))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.shell.ssh [32]: Unable to resolve 3

2.0: missing requirement [32.0] osgi.wiring.package; (osgi.wiring.package=javax.security.auth)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.deployer.features [35] Error starting org/apache/karaf/deployer/org.apache.karaf.deployer

.features/2.2.11/org.apache.karaf.deployer.features-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constrain

t in bundle org.apache.karaf.deployer.features [35]: Unable to resolve 35.0: missing requirement [35.0] osgi.wiring.pack

age; (osgi.wiring.package=javax.xml.parsers))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.deployer.features [35]: Unable to r

esolve 35.0: missing requirement [35.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

ERROR: Bundle org.apache.karaf.deployer.kar [36] Error starting org/apache/karaf/deployer/org.apache.karaf.deployer.kar/

2.2.11/org.apache.karaf.deployer.kar-2.2.11.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org

.apache.karaf.deployer.kar [36]: Unable to resolve 36.0: missing requirement [36.0] osgi.wiring.package; (osgi.wiring.pa

ckage=javax.xml.parsers))

org.osgi.framework.BundleException: Unresolved constraint in bundle org.apache.karaf.deployer.kar [36]: Unable to resolv

e 36.0: missing requirement [36.0] osgi.wiring.package; (osgi.wiring.package=javax.xml.parsers)

        at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

        at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

        at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

        at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

        at java.lang.Thread.run(Thread.java:744)

michael...@non.agilent.com

unread,
Jul 23, 2014, 1:48:35 PM7/23/14
to cytoscape...@googlegroups.com

Since I'm not able to run a new build of Cy3, is there an easy way I can get a zip of the cy3.1.1 release source code (github?)? I only need to debug the app manager on Cy 3.1.1 to see why my app doesn't show up in the app manger but runs fine.

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michael...@non.agilent.com

unread,
Jul 23, 2014, 2:13:28 PM7/23/14
to cytoscape...@googlegroups.com

Okay, I think I found the source--would that be under https://github.com/cytoscape/cytoscape-impl/releases/tag/3.1.1?

Jason Montojo

unread,
Jul 23, 2014, 2:19:46 PM7/23/14
to cytoscape...@googlegroups.com
Hi Michael,

Yes, but you'll also need the corresponding source releases for all the other repos too:


The last one is suspiciously missing.  looks like it wasn't tagged during the last release.  Anyway, this repo contains the top-level pom file and all the other repos should be cloned into this one, with the "cytoscape-" prefix stripped from the front; i.e. "api" instead of "cytoscape-api".

Hope this helps,
Jason
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