Question: Lositan freezing when producing selection table
0
gravatar for carolw1
4.5 years ago by
carolw10
Australia
carolw10 wrote:

Hi Tiago or anyone who has (hopefully) encountered and solved this problem.

I've posted about this problem before but with no response or solution. But I find that LOSITAN again freezes when it is generating a selection table and this is a huge problem for me.

I've posted the java error from the java console, hopefully someone can understand what the problem is?

Thank you

Error script

Missing Permissions manifest attribute in main jar: http://popgen.net/soft/lositan/code2/lib/selwb.jar
Windows 7 C:\Users\Dell \
console: Failed to install '': java.nio.charset.UnsupportedCharsetException: cp0.
890
-0.026404 16
Apr 20, 2015 8:16:42 PM jnr.ffi.util.ref.FinalizableReferenceQueue$SystemLoader loadFinalizer
INFO: Not allowed to access system class loader.
Apr 20, 2015 8:16:45 PM jnr.ffi.util.ref.FinalizableReferenceQueue$DecoupledLoader loadFinalizer
WARNING: Could not load Finalizer in its own class loader.Loading Finalizer in the current class loader instead. As a result, you will not be ableto garbage collect this class loader. To support reclaiming this class loader, eitherresolve the underlying issue, or move Google Collections to your system class path.
java.security.AccessControlException: access denied ("java.lang.RuntimePermission" "createClassLoader")
    at java.security.AccessControlContext.checkPermission(Unknown Source)
    at java.security.AccessController.checkPermission(Unknown Source)
    at java.lang.SecurityManager.checkPermission(Unknown Source)
    at com.sun.javaws.security.JavaWebStartSecurity.checkPermission(Unknown Source)
    at java.lang.SecurityManager.checkCreateClassLoader(Unknown Source)
    at java.lang.ClassLoader.checkCreateClassLoader(Unknown Source)
    at java.lang.ClassLoader.<init>(Unknown Source)
    at java.security.SecureClassLoader.<init>(Unknown Source)
    at java.net.URLClassLoader.<init>(Unknown Source)
    at jnr.ffi.util.ref.FinalizableReferenceQueue$DecoupledLoader.newLoader(FinalizableReferenceQueue.java:257)
    at jnr.ffi.util.ref.FinalizableReferenceQueue$DecoupledLoader.loadFinalizer(FinalizableReferenceQueue.java:227)
    at jnr.ffi.util.ref.FinalizableReferenceQueue.loadFinalizer(FinalizableReferenceQueue.java:155)
    at jnr.ffi.util.ref.FinalizableReferenceQueue.<clinit>(FinalizableReferenceQueue.java:84)
    at jnr.ffi.provider.jffi.NativeFinalizer.<init>(NativeFinalizer.java:9)
    at jnr.ffi.provider.jffi.NativeFinalizer$SingletonHolder.<clinit>(NativeFinalizer.java:12)
    at jnr.ffi.provider.jffi.NativeFinalizer.getInstance(NativeFinalizer.java:16)
    at jnr.ffi.provider.jffi.TransientNativeMemory$Magazine.<init>(TransientNativeMemory.java:104)
    at jnr.ffi.provider.jffi.TransientNativeMemory.allocate(TransientNativeMemory.java:44)
    at jnr.ffi.provider.jffi.NativeMemoryManager.allocateDirect(NativeMemoryManager.java:43)
    at jnr.ffi.Memory.allocateDirect(Memory.java:88)
    at jnr.posix.WString$1.toNative(WString.java:33)
    at jnr.posix.WString$1.toNative(WString.java:26)
    at jnr.ffi.provider.jffi.ParameterConverter.toNative(ParameterConverter.java:41)
    at jnr.posix.WindowsLibC$jaffl$0._wmkdir(Unknown Source)
    at jnr.posix.WindowsPOSIX.mkdir(WindowsPOSIX.java:458)
    at jnr.posix.LazyPOSIX.mkdir(LazyPOSIX.java:207)
    at org.python.modules.posix.PosixModule.mkdir(PosixModule.java:521)
    at org.python.modules.posix.PosixModule.mkdir(PosixModule.java:517)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:186)
    at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:204)
    at org.python.core.PyObject.__call__(PyObject.java:403)
    at org.python.core.PyObject.__call__(PyObject.java:407)
    at Bio.PopGen.FDist.Async$py.run_fdist$9(C:\Users\Dell\.lositan\Bio\PopGen\FDist\Async.py:185)
    at Bio.PopGen.FDist.Async$py.call_function(C:\Users\Dell\.lositan\Bio\PopGen\FDist\Async.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:194)
    at org.python.core.PyFunction.__call__(PyFunction.java:417)
    at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:232)
    at org.python.core.PyMethod.__call__(PyMethod.java:223)
    at org.python.core.PyMethod.__call__(PyMethod.java:213)
    at org.python.pycode._pyx0.runFDistPart$30(C:\Users\Dell\.lositan\Main.py:786)
    at org.python.pycode._pyx0.call_function(C:\Users\Dell\.lositan\Main.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyFunction.function___call__(PyFunction.java:406)
    at org.python.core.PyFunction.__call__(PyFunction.java:401)
    at org.python.core.PyFunction.__call__(PyFunction.java:391)
    at org.python.pycode._pyx0.runFDist$28(C:\Users\Dell\.lositan\Main.py:743)
    at org.python.pycode._pyx0.call_function(C:\Users\Dell\.lositan\Main.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:114)
    at org.python.core.PyFunction.__call__(PyFunction.java:337)
    at org.python.pycode._pyx0.actionPerformed$36(C:\Users\Dell\.lositan\Main.py:900)
    at org.python.pycode._pyx0.call_function(C:\Users\Dell\.lositan\Main.py)
    at org.python.core.PyTableCode.call(PyTableCode.java:165)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:301)
    at org.python.core.PyBaseCode.call(PyBaseCode.java:194)
    at org.python.core.PyFunction.__call__(PyFunction.java:417)
    at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:232)
    at org.python.core.PyMethod.__call__(PyMethod.java:223)
    at org.python.core.PyMethod.__call__(PyMethod.java:213)
    at org.python.core.PyMethod.__call__(PyMethod.java:208)
    at org.python.core.PyObject._jcallexc(PyObject.java:3555)
    at org.python.core.PyObject._jcall(PyObject.java:3587)
    at org.python.proxies.__main__$doAction$16.actionPerformed(Unknown Source)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$500(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue$4.run(Unknown Source)
    at java.awt.EventQueue$4.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)

Apr 20, 2015 8:16:45 PM jnr.ffi.util.ref.internal.Finalizer getInheritableThreadLocalsField
INFO: Couldn't access Thread.inheritableThreadLocals. Reference finalizer threads will inherit thread local values.

 

lositan • 1.4k views
ADD COMMENTlink modified 3.4 years ago by ukrz0 • written 4.5 years ago by carolw10

Can you send me your input file (to my email address)? I need to have a look at that.

ADD REPLYlink written 4.5 years ago by tiagoantao660

I have sent the file to you, thanks.

 

 

 

ADD REPLYlink written 4.5 years ago by carolw10
0
gravatar for kang602839647
3.8 years ago by
kang6028396470 wrote:

have you solved this problem? I have met this same problem,it's so bored! 

ADD COMMENTlink written 3.8 years ago by kang6028396470
0
gravatar for ukrz
3.4 years ago by
ukrz0
ukrz0 wrote:

same with me, has anyone solved this problem?

ADD COMMENTlink written 3.4 years ago by ukrz0
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