Lositan freezing when producing selection table
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0
Entering edit mode
9.6 years ago
carolw1 ▴ 10

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 • 2.5k views
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Can you send me your input file (to my email address)? I need to have a look at that.

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I have sent the file to you, thanks.

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

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same with me, has anyone solved this problem?

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