From: hansonr Date: Tue, 27 Aug 2019 22:03:46 +0000 (-0500) Subject: headless tests on Windows X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8f66f871d7e0c6db502106a5668f4fdaf1448f2a;p=jalview.git headless tests on Windows --- diff --git a/ALIGN.png b/ALIGN.png new file mode 100644 index 0000000..ced5a9f Binary files /dev/null and b/ALIGN.png differ diff --git a/hs_err_pid20236.log b/hs_err_pid20236.log new file mode 100644 index 0000000..6ca6cf3 --- /dev/null +++ b/hs_err_pid20236.log @@ -0,0 +1,296 @@ +# +# A fatal error has been detected by the Java Runtime Environment: +# +# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x000000005f2da6eb, pid=20236, tid=0x0000000000003bf8 +# +# JRE version: Java(TM) SE Runtime Environment (8.0_191-b12) (build 1.8.0_191-b12) +# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.191-b12 mixed mode windows-amd64 compressed oops) +# Problematic frame: +# V [jvm.dll+0x14a6eb] +# +# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows +# +# If you would like to submit a bug report, please visit: +# http://bugreport.java.com/bugreport/crash.jsp +# + +--------------- T H R E A D --------------- + +Current thread (0x0000000003362800): JavaThread "main" [_thread_in_vm, id=15352, stack(0x0000000003260000,0x0000000003360000)] + +siginfo: ExceptionCode=0xc0000005, reading address 0x0000000000000000 + +Registers: +RAX=0x0000000017af8ec8, RBX=0x00000001000de0f0, RCX=0x0000000000000002, RDX=0x0000000017af8ec0 +RSP=0x000000000335eba0, RBP=0x0000000000000004, RSI=0x00000000033629f8, RDI=0x0000000003362800 +R8 =0x0000000000000004, R9 =0x0000000000000000, R10=0x0000000000000312, R11=0x0000000003363140 +R12=0x0000000000000000, R13=0x000000000335eca8, R14=0x000000000335ee18, R15=0x0000000003362800 +RIP=0x000000005f2da6eb, EFLAGS=0x0000000000010206 + +Top of Stack: (sp=0x000000000335eba0) +0x000000000335eba0: 00000000033629f8 00000001000de0f0 +0x000000000335ebb0: 0000000000000004 0000000003362800 +0x000000000335ebc0: 0000000000000001 00000001000de0f0 +0x000000000335ebd0: 000000000313e890 000000005f3a8465 +0x000000000335ebe0: 000000000313e890 000000005fecfff0 +0x000000000335ebf0: 0000000003362800 0000000000000000 +0x000000000335ec00: 0000000017af9560 000000005f3a79dc +0x000000000335ec10: 0000000017af8ec0 000000000313e890 +0x000000000335ec20: 0000000017af8ec0 0000000000000001 +0x000000000335ec30: 0000000003362800 000000005f2cecc2 +0x000000000335ec40: 000000001773b4f8 0000000000000000 +0x000000000335ec50: 0000000017af8ec0 000000005fe39df4 +0x000000000335ec60: 0000000000000004 00000000033629f8 +0x000000000335ec70: 0000000000000000 000000001773b4f8 +0x000000000335ec80: 0000000017af8ec0 000000005fe3cb34 +0x000000000335ec90: 00000000033629f8 0000000000000004 + +Instructions: (pc=0x000000005f2da6eb) +0x000000005f2da6cb: cf e8 0f 04 0e 00 33 c0 e9 dd 01 00 00 48 8b d0 +0x000000005f2da6db: 48 8b ce 48 89 ac 24 c0 00 00 00 e8 55 d2 0c 00 +0x000000005f2da6eb: 49 8b 0c 24 c7 44 24 40 0e 00 00 00 48 8b 51 08 +0x000000005f2da6fb: 48 8b e8 0f b7 4a 24 48 8b 52 08 48 8b 54 ca 50 + + +Register to memory mapping: + +RAX=0x0000000017af8ec8 is an unknown value +RBX=0x00000001000de0f0 is pointing into metadata +RCX=0x0000000000000002 is an unknown value +RDX=0x0000000017af8ec0 is an unknown value +RSP=0x000000000335eba0 is pointing into the stack for thread: 0x0000000003362800 +RBP=0x0000000000000004 is an unknown value +RSI=0x00000000033629f8 is an unknown value +RDI=0x0000000003362800 is a thread +R8 =0x0000000000000004 is an unknown value +R9 =0x0000000000000000 is an unknown value +R10=0x0000000000000312 is an unknown value +R11=0x0000000003363140 is an unknown value +R12=0x0000000000000000 is an unknown value +R13=0x000000000335eca8 is pointing into the stack for thread: 0x0000000003362800 +R14=0x000000000335ee18 is pointing into the stack for thread: 0x0000000003362800 +R15=0x0000000003362800 is a thread + + +Stack: [0x0000000003260000,0x0000000003360000], sp=0x000000000335eba0, free space=1018k +Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code) +V [jvm.dll+0x14a6eb] +C [awt.dll+0x69df4] +C [awt.dll+0x6cb34] +C [awt.dll+0x6cbf2] +C 0x0000000003478c67 + +Java frames: (J=compiled Java code, j=interpreted, Vv=VM code) +j sun.awt.windows.ThemeReader.getThemeMargins(JIII)Ljava/awt/Insets;+0 +j sun.awt.windows.ThemeReader.getThemeMargins(Ljava/lang/String;III)Ljava/awt/Insets;+18 +j com.sun.java.swing.plaf.windows.XPStyle.getMargin(Ljava/awt/Component;Lcom/sun/java/swing/plaf/windows/TMSchema$Part;Lcom/sun/java/swing/plaf/windows/TMSchema$State;Lcom/sun/java/swing/plaf/windows/TMSchema$Prop;)Ljava/awt/Insets;+19 +j com.sun.java.swing.plaf.windows.WindowsInternalFrameTitlePane$WindowsTitlePaneLayout.(Lcom/sun/java/swing/plaf/windows/WindowsInternalFrameTitlePane;)V+49 +j com.sun.java.swing.plaf.windows.WindowsInternalFrameTitlePane.createLayout()Ljava/awt/LayoutManager;+5 +j javax.swing.plaf.basic.BasicInternalFrameTitlePane.installTitlePane()V+23 +j javax.swing.plaf.basic.BasicInternalFrameTitlePane.(Ljavax/swing/JInternalFrame;)V+10 +j com.sun.java.swing.plaf.windows.WindowsInternalFrameTitlePane.(Ljavax/swing/JInternalFrame;)V+2 +j com.sun.java.swing.plaf.windows.WindowsDesktopIconUI.installComponents()V+9 +j javax.swing.plaf.basic.BasicDesktopIconUI.installUI(Ljavax/swing/JComponent;)V+24 +j com.sun.java.swing.plaf.windows.WindowsDesktopIconUI.installUI(Ljavax/swing/JComponent;)V+2 +j javax.swing.JComponent.setUI(Ljavax/swing/plaf/ComponentUI;)V+39 +j javax.swing.JInternalFrame$JDesktopIcon.setUI(Ljavax/swing/plaf/DesktopIconUI;)V+2 +j javax.swing.JInternalFrame$JDesktopIcon.updateUI()V+21 +j javax.swing.JInternalFrame$JDesktopIcon.(Ljavax/swing/JInternalFrame;)V+15 +j javax.swing.JInternalFrame.(Ljava/lang/String;ZZZZ)V+101 +j javax.swing.JInternalFrame.()V+7 +j jalview.jbgui.GTreePanel.()V+1 +j jalview.gui.TreePanel.(Ljalview/gui/AlignmentPanel;Ljalview/io/NewickFile;Ljava/lang/String;Ljalview/datamodel/AlignmentView;)V+1 +j jalview.gui.AlignFrame.showNewickTree(Ljalview/io/NewickFile;Ljava/lang/String;Ljalview/datamodel/AlignmentView;IIII)Ljalview/gui/TreePanel;+25 +j jalview.gui.AlignFrame.showNewickTree(Ljalview/io/NewickFile;Ljava/lang/String;IIII)Ljalview/gui/TreePanel;+11 +j jalview.gui.AlignFrame.showNewickTree(Ljalview/io/NewickFile;Ljava/lang/String;)Ljalview/gui/TreePanel;+11 +j jalview.bin.Jalview.parseArguments(Ljalview/bin/ArgsParser;Z)Ljava/lang/Object;+1237 +j jalview.bin.Jalview.doMain([Ljava/lang/String;)V+999 +j jalview.bin.Jalview.main([Ljava/lang/String;)V+4 +v ~StubRoutines::call_stub + +--------------- P R O C E S S --------------- + +Java Threads: ( => current thread ) + 0x0000000019ec1800 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=12976, stack(0x000000001c450000,0x000000001c550000)] + 0x0000000019ec6800 JavaThread "AWT-Windows" daemon [_thread_in_native, id=6712, stack(0x000000001a5d0000,0x000000001a6d0000)] + 0x0000000019ec7800 JavaThread "AWT-Shutdown" [_thread_blocked, id=12756, stack(0x000000001a4d0000,0x000000001a5d0000)] + 0x0000000019ec5000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=20276, stack(0x000000001a3d0000,0x000000001a4d0000)] + 0x00000000194c8800 JavaThread "Service Thread" daemon [_thread_blocked, id=7928, stack(0x0000000019890000,0x0000000019990000)] + 0x0000000017b46800 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=17860, stack(0x0000000019390000,0x0000000019490000)] + 0x0000000017b35800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=9844, stack(0x0000000019290000,0x0000000019390000)] + 0x0000000017b30000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=14528, stack(0x0000000019190000,0x0000000019290000)] + 0x0000000017b2e000 JavaThread "Attach Listener" daemon [_thread_blocked, id=20176, stack(0x0000000019090000,0x0000000019190000)] + 0x0000000017b2c800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=13584, stack(0x0000000018f90000,0x0000000019090000)] + 0x000000000345c800 JavaThread "Finalizer" daemon [_thread_blocked, id=18536, stack(0x0000000018da0000,0x0000000018ea0000)] + 0x0000000003451800 JavaThread "Reference Handler" daemon [_thread_blocked, id=14488, stack(0x0000000018ca0000,0x0000000018da0000)] +=>0x0000000003362800 JavaThread "main" [_thread_in_vm, id=15352, stack(0x0000000003260000,0x0000000003360000)] + +Other Threads: + 0x0000000017af8800 VMThread [stack: 0x0000000018ba0000,0x0000000018ca0000] [id=16360] + 0x0000000017b8d800 WatcherThread [stack: 0x0000000019990000,0x0000000019a90000] [id=1872] + +VM state:not at safepoint (normal execution) + +VM Mutex/Monitor currently owned by a thread: None + +Heap: + PSYoungGen total 35840K, used 25054K [0x00000000d8600000, 0x00000000dae00000, 0x0000000100000000) + eden space 30720K, 81% used [0x00000000d8600000,0x00000000d9e77978,0x00000000da400000) + from space 5120K, 0% used [0x00000000da900000,0x00000000da900000,0x00000000dae00000) + to space 5120K, 0% used [0x00000000da400000,0x00000000da400000,0x00000000da900000) + ParOldGen total 81920K, used 0K [0x0000000089200000, 0x000000008e200000, 0x00000000d8600000) + object space 81920K, 0% used [0x0000000089200000,0x0000000089200000,0x000000008e200000) + Metaspace used 14483K, capacity 14664K, committed 14720K, reserved 1062912K + class space used 1820K, capacity 1900K, committed 1920K, reserved 1048576K + +Card table byte_map: [0x0000000012820000,0x0000000012be0000] byte_map_base: 0x00000000123d7000 + +Marking Bits: (ParMarkBitMap*) 0x000000005f9b3e30 + Begin Bits: [0x0000000013260000, 0x0000000015018000) + End Bits: [0x0000000015018000, 0x0000000016dd0000) + +Polling page: 0x00000000016a0000 + +CodeCache: size=245760Kb used=3539Kb max_used=3552Kb free=242220Kb + bounds [0x0000000003460000, 0x00000000037e0000, 0x0000000012460000] + total_blobs=1478 nmethods=1014 adapters=377 + compilation: enabled + +Compilation events (10 events): +Event: 1.334 Thread 0x0000000017b46800 nmethod 1009 0x00000000037d5290 code [0x00000000037d5420, 0x00000000037d58f8] +Event: 1.334 Thread 0x0000000017b46800 988 3 java.lang.StringBuffer:: (7 bytes) +Event: 1.334 Thread 0x0000000017b46800 nmethod 988 0x00000000037d1590 code [0x00000000037d1700, 0x00000000037d19b0] +Event: 1.334 Thread 0x0000000017b46800 997 1 com.stevesoft.pat.wrap.StringWrap::unwrap (5 bytes) +Event: 1.334 Thread 0x0000000017b46800 nmethod 997 0x00000000037d12d0 code [0x00000000037d1420, 0x00000000037d1530] +Event: 1.334 Thread 0x0000000017b46800 1001 1 java.lang.reflect.Constructor::getModifiers (5 bytes) +Event: 1.334 Thread 0x0000000017b46800 nmethod 1001 0x00000000037d1010 code [0x00000000037d1160, 0x00000000037d1270] +Event: 1.356 Thread 0x0000000017b46800 1013 3 java.lang.Class::arrayContentsEq (70 bytes) +Event: 1.356 Thread 0x0000000017b46800 nmethod 1013 0x00000000037d0550 code [0x00000000037d06e0, 0x00000000037d0b10] +Event: 1.358 Thread 0x0000000017b35800 1015 4 java.util.regex.Matcher::search (109 bytes) + +GC Heap History (0 events): +No events + +Deoptimization events (10 events): +Event: 0.546 Thread 0x0000000003362800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x000000000368f07c method=java.util.HashMap.putVal(ILjava/lang/Object;Ljava/lang/Object;ZZ)Ljava/lang/Object; @ 91 +Event: 0.546 Thread 0x0000000003362800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x000000000368f07c method=java.util.HashMap.putVal(ILjava/lang/Object;Ljava/lang/Object;ZZ)Ljava/lang/Object; @ 91 +Event: 0.546 Thread 0x0000000003362800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x000000000368f07c method=java.util.HashMap.putVal(ILjava/lang/Object;Ljava/lang/Object;ZZ)Ljava/lang/Object; @ 91 +Event: 0.546 Thread 0x0000000003362800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x000000000368f07c method=java.util.HashMap.putVal(ILjava/lang/Object;Ljava/lang/Object;ZZ)Ljava/lang/Object; @ 91 +Event: 0.652 Thread 0x0000000003362800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000003697464 method=java.util.HashMap.putVal(ILjava/lang/Object;Ljava/lang/Object;ZZ)Ljava/lang/Object; @ 181 +Event: 0.670 Thread 0x0000000003362800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000000036b3680 method=java.lang.StringCoding$StringDecoder.decode([BII)[C @ 33 +Event: 0.676 Thread 0x0000000003362800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000000036a39b0 method=java.util.HashMap.putVal(ILjava/lang/Object;Ljava/lang/Object;ZZ)Ljava/lang/Object; @ 181 +Event: 0.682 Thread 0x0000000003362800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000000369d1e4 method=java.util.HashMap.hash(Ljava/lang/Object;)I @ 1 +Event: 0.739 Thread 0x0000000003362800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000000361c754 method=java.lang.String.replace(CC)Ljava/lang/String; @ 2 +Event: 1.358 Thread 0x0000000003362800 Uncommon trap: reason=predicate action=maybe_recompile pc=0x00000000037b440c method=java.util.regex.Pattern$Start.match(Ljava/util/regex/Matcher;ILjava/lang/CharSequence;)Z @ 37 + +Classes redefined (0 events): +No events + +Internal exceptions (10 events): +Event: 0.217 Thread 0x0000000003362800 Exception (0x00000000d887dd90) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\jvm.cpp, line 1435] +Event: 0.218 Thread 0x0000000003362800 Exception (0x00000000d8881dd0) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\jvm.cpp, line 1435] +Event: 0.218 Thread 0x0000000003362800 Exception (0x00000000d88821c8) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\jvm.cpp, line 1435] +Event: 0.234 Thread 0x0000000003362800 Exception (0x00000000d88a4d18) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\jni.cpp, line 709] +Event: 0.234 Thread 0x0000000003362800 Exception (0x00000000d88a6760) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\jni.cpp, line 709] +Event: 0.315 Thread 0x0000000003362800 Exception (0x00000000d8a7a650) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\jni.cpp, line 709] +Event: 0.358 Thread 0x0000000003362800 Exception (0x00000000d8b4a9a0) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\methodHandles.cpp, line 1167] +Event: 0.360 Thread 0x0000000003362800 Exception (0x00000000d8b57cc0) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\methodHandles.cpp, line 1167] +Event: 0.423 Thread 0x0000000003362800 Exception (0x00000000d8c04a48) thrown at [C:\re\workspace\8-2-build-windows-amd64-cygwin\jdk8u191\11896\hotspot\src\share\vm\prims\jni.cpp, line 709] +Event: 0.682 Thread 0x0000000003362800 Implicit null exception at 0x000000000369cf95 to 0x000000000369d1d5 + +Events (10 events): +Event: 1.359 loading class javax/swing/plaf/basic/BasicInternalFrameTitlePane$MoveAction +Event: 1.359 loading class javax/swing/plaf/basic/BasicInternalFrameTitlePane$MoveAction done +Event: 1.359 loading class javax/swing/plaf/basic/BasicInternalFrameTitlePane$SizeAction +Event: 1.359 loading class javax/swing/plaf/basic/BasicInternalFrameTitlePane$SizeAction done +Event: 1.359 loading class javax/swing/plaf/basic/BasicInternalFrameTitlePane$ShowSystemMenuAction +Event: 1.359 loading class javax/swing/plaf/basic/BasicInternalFrameTitlePane$ShowSystemMenuAction done +Event: 1.359 loading class com/sun/java/swing/plaf/windows/WindowsInternalFrameTitlePane$WindowsTitlePaneLayout +Event: 1.359 loading class javax/swing/plaf/basic/BasicInternalFrameTitlePane$TitlePaneLayout +Event: 1.359 loading class javax/swing/plaf/basic/BasicInternalFrameTitlePane$TitlePaneLayout done +Event: 1.359 loading class com/sun/java/swing/plaf/windows/WindowsInternalFrameTitlePane$WindowsTitlePaneLayout done + + +Dynamic libraries: +0x00007ff732450000 - 0x00007ff732487000 C:\Program Files\Java\jre1.8.0_191\bin\java.exe +0x00007ff8881a0000 - 0x00007ff888381000 C:\WINDOWS\SYSTEM32\ntdll.dll +0x00007ff887fc0000 - 0x00007ff888071000 C:\WINDOWS\System32\KERNEL32.DLL +0x00007ff884c00000 - 0x00007ff884e73000 C:\WINDOWS\System32\KERNELBASE.dll +0x00007ff886e80000 - 0x00007ff886f21000 C:\WINDOWS\System32\ADVAPI32.dll +0x00007ff8879c0000 - 0x00007ff887a5e000 C:\WINDOWS\System32\msvcrt.dll +0x00007ff887da0000 - 0x00007ff887dfb000 C:\WINDOWS\System32\sechost.dll +0x00007ff885630000 - 0x00007ff885754000 C:\WINDOWS\System32\RPCRT4.dll +0x00007ff885760000 - 0x00007ff8858f0000 C:\WINDOWS\System32\USER32.dll +0x00007ff884b30000 - 0x00007ff884b50000 C:\WINDOWS\System32\win32u.dll +0x00007ff887920000 - 0x00007ff887948000 C:\WINDOWS\System32\GDI32.dll +0x00007ff884910000 - 0x00007ff884aa1000 C:\WINDOWS\System32\gdi32full.dll +0x00007ff885590000 - 0x00007ff88562f000 C:\WINDOWS\System32\msvcp_win.dll +0x00007ff884570000 - 0x00007ff884668000 C:\WINDOWS\System32\ucrtbase.dll +0x00007ff86d030000 - 0x00007ff86d299000 C:\WINDOWS\WinSxS\amd64_microsoft.windows.common-controls_6595b64144ccf1df_6.0.17134.885_none_fb42a3473065565f\COMCTL32.dll +0x00007ff887a60000 - 0x00007ff887d82000 C:\WINDOWS\System32\combase.dll +0x00007ff884ab0000 - 0x00007ff884b29000 C:\WINDOWS\System32\bcryptPrimitives.dll +0x00007ff887750000 - 0x00007ff88777d000 C:\WINDOWS\System32\IMM32.DLL +0x00007ff8814e0000 - 0x00007ff8814ec000 C:\WINDOWS\KATRK64.DLL +0x00007ff881450000 - 0x00007ff881463000 C:\WINDOWS\SYSTEM32\WTSAPI32.dll +0x0000000060d10000 - 0x0000000060de2000 C:\Program Files\Java\jre1.8.0_191\bin\msvcr100.dll +0x000000005f190000 - 0x000000005fa34000 C:\Program Files\Java\jre1.8.0_191\bin\server\jvm.dll +0x00007ff887d90000 - 0x00007ff887d98000 C:\WINDOWS\System32\PSAPI.DLL +0x00007ff880870000 - 0x00007ff880879000 C:\WINDOWS\SYSTEM32\WSOCK32.dll +0x00007ff886db0000 - 0x00007ff886e1c000 C:\WINDOWS\System32\WS2_32.dll +0x00007ff87e5b0000 - 0x00007ff87e5ba000 C:\WINDOWS\SYSTEM32\VERSION.dll +0x00007ff87af00000 - 0x00007ff87af23000 C:\WINDOWS\SYSTEM32\WINMM.dll +0x00007ff87aed0000 - 0x00007ff87aefa000 C:\WINDOWS\SYSTEM32\WINMMBASE.dll +0x00007ff8848c0000 - 0x00007ff884909000 C:\WINDOWS\System32\cfgmgr32.dll +0x0000000060d00000 - 0x0000000060d0f000 C:\Program Files\Java\jre1.8.0_191\bin\verify.dll +0x0000000060cd0000 - 0x0000000060cf9000 C:\Program Files\Java\jre1.8.0_191\bin\java.dll +0x0000000060c60000 - 0x0000000060c76000 C:\Program Files\Java\jre1.8.0_191\bin\zip.dll +0x00007ff8858f0000 - 0x00007ff886d30000 C:\WINDOWS\System32\SHELL32.dll +0x00007ff887f10000 - 0x00007ff887fb9000 C:\WINDOWS\System32\shcore.dll +0x00007ff884e80000 - 0x00007ff88558d000 C:\WINDOWS\System32\windows.storage.dll +0x00007ff886e20000 - 0x00007ff886e71000 C:\WINDOWS\System32\shlwapi.dll +0x00007ff884500000 - 0x00007ff884511000 C:\WINDOWS\System32\kernel.appcore.dll +0x00007ff8844e0000 - 0x00007ff8844ff000 C:\WINDOWS\System32\profapi.dll +0x00007ff884520000 - 0x00007ff88456c000 C:\WINDOWS\System32\powrprof.dll +0x00007ff8844d0000 - 0x00007ff8844da000 C:\WINDOWS\System32\FLTLIB.DLL +0x000000005fdd0000 - 0x000000005ff69000 C:\Program Files\Java\jre1.8.0_191\bin\awt.dll +0x00007ff888080000 - 0x00007ff888142000 C:\WINDOWS\System32\OLEAUT32.dll +0x00007ff87ae40000 - 0x00007ff87aecb000 C:\WINDOWS\SYSTEM32\apphelp.dll +0x00007ff8826a0000 - 0x00007ff882738000 C:\WINDOWS\system32\uxtheme.dll +0x00007ff886f30000 - 0x00007ff8870a3000 C:\WINDOWS\System32\MSCTF.dll +0x00007ff882b50000 - 0x00007ff882b79000 C:\WINDOWS\system32\dwmapi.dll +0x00007ff8875f0000 - 0x00007ff887741000 C:\WINDOWS\System32\ole32.dll +0x0000000060bc0000 - 0x0000000060c07000 C:\Program Files\Java\jre1.8.0_191\bin\fontmanager.dll +0x0000000060c30000 - 0x0000000060c4a000 C:\Program Files\Java\jre1.8.0_191\bin\net.dll +0x00007ff883d30000 - 0x00007ff883d96000 C:\WINDOWS\system32\mswsock.dll +0x0000000060c10000 - 0x0000000060c21000 C:\Program Files\Java\jre1.8.0_191\bin\nio.dll +0x0000000060c80000 - 0x0000000060cc2000 C:\Program Files\Java\jre1.8.0_191\bin\t2k.dll +0x00007ff87fd50000 - 0x00007ff87ff19000 C:\WINDOWS\SYSTEM32\dbghelp.dll + +VM Arguments: +jvm_args: -Djava.awt.headless=true +java_command: jalview.bin.Jalview nodisplay -open examples/uniref50.fa -sortbytree -props test/jalview/io/testProps.jvprops -colour zappo -jabaws http://www.compbio.dundee.ac.uk/jabaws -nosortbytree -features examples/testdata/plantfdx.features -annotations examples/testdata/plantfdx.annotations -tree examples/testdata/uniref50_test_tree +java_class_path (initial): C:\Users\hansonr\eclipse\configuration\org.eclipse.osgi\1009\0\.cp\lib\testng-remote.jar;C:\Users\hansonr\git\jalview1\classes;C:\Users\hansonr\git\jalview1\lib\activation.jar;C:\Users\hansonr\git\jalview1\lib\axis.jar;C:\Users\hansonr\git\jalview1\lib\commons-discovery.jar;C:\Users\hansonr\git\jalview1\lib\jaxrpc.jar;C:\Users\hansonr\git\jalview1\lib\jhall.jar;C:\Users\hansonr\git\jalview1\lib\mail.jar;C:\Users\hansonr\git\jalview1\lib\regex.jar;C:\Users\hansonr\git\jalview1\lib\saaj.jar;C:\Users\hansonr\git\jalview1\lib\wsdl4j.jar;C:\Users\hansonr\git\jalview1\lib\xercesImpl.jar;C:\Users\hansonr\git\jalview1\lib\JGoogleAnalytics_0.3.jar;C:\Users\hansonr\git\jalview1\lib\vamsas-client.jar;C:\Users\hansonr\git\jalview1\lib\commons-logging-1.1.1.jar;C:\Users\hansonr\git\jalview1\lib\apache-mime4j-0.6.jar;C:\Users\hansonr\git\jalview1\lib\httpclient-4.0.3.jar;C:\Users\hansonr\git\jalview1\lib\httpcore-4.0.1.jar;C:\Users\hansonr\git\jalview1\lib\httpmime-4.0.3.jar;C:\Users\hansonr\git\jalview1\lib\miglayout-4.0-swing.jar;C:\Users\hansonr\git\jalview1\lib\jswingreader-0.3.jar;C:\Users\hansonr\git\jalview1\lib\commons-codec-1.3.jar;C:\Users\hansonr\git\jalview1\lib;C:\Users\hansonr\git\jalview1\lib\jabaws-min-client-2.2.0.jar;C:\Users\hansonr\git\jalview1\lib;C:\Users\hansonr\git\jalview1\lib\json_simple-1.1.jar;C:\Users\hansonr\git\jalview1\lib\slf4j-api-1.7.7.jar;C:\Users\hansonr\git\jalview1\lib\jsoup-1.8.1.jar;C:\Users\hansonr\git\jalview1\lib\log4j-to-slf4j-2.0-rc2.jar;C:\Users\hansonr\git\jalview1\lib\slf4j-log4j12-1.7.7.jar;C:\Users\hansonr\git\jalview1\lib\VARNAv3-93.jar;C:\Users\hansonr\git\jalview1\lib\jfreesvg-2.1.jar;C:\Users\hansonr\git\jalview1\lib\quaqua-filechooser-only-8.0.jar;C:\Users\hansonr\git\jalview1\lib\VAqua5-patch.jar;C:\Users\hansonr\git\jalview1\utils\classgraph-4.1.6.jar;C:\Users\hansonr\git\jalview1\lib\xml-apis.jar;C:\Users\hansonr\eclipse\plugins\org.junit_4.12.0.v201504281640\junit.jar;C:\Users\hansonr\eclipse +Launcher Type: SUN_STANDARD + +Environment Variables: +JAVA_HOME=c:\program files\java\jdk1.8.0_191 +PATH=C:\Program Files\PerkinElmerInformatics\ChemOffice2018\ChemScript\Lib;c:\program files\java\jdk1.8.0_191;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;c:\d_drive\work;C:\Program Files\TortoiseHg\;C:\WINDOWS\System32\OpenSSH\;C:\Program Files\nodejs\;C:\Users\hansonr\AppData\Local\Microsoft\WindowsApps;C:\Users\hansonr\AppData\Roaming\npm +USERNAME=hansonr +OS=Windows_NT +PROCESSOR_IDENTIFIER=Intel64 Family 6 Model 78 Stepping 3, GenuineIntel + + + +--------------- S Y S T E M --------------- + +OS: Windows 10.0 , 64 bit Build 17134 (10.0.17134.753) + +CPU:total 4 (initial active 4) (2 cores per cpu, 2 threads per core) family 6 model 78 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, rtm, 3dnowpref, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2, adx + +Memory: 4k page, physical 7785760k(1566968k free), swap 15718136k(2288064k free) + +vm_info: Java HotSpot(TM) 64-Bit Server VM (25.191-b12) for windows-amd64 JRE (1.8.0_191-b12), built on Oct 6 2018 09:29:03 by "java_re" with MS VC++ 10.0 (VS2010) + +time: Tue Aug 27 16:43:20 2019 +elapsed time: 1 seconds (0d 0h 0m 1s) + diff --git a/nousagestats b/nousagestats new file mode 100644 index 0000000..98e89f2 --- /dev/null +++ b/nousagestats @@ -0,0 +1,60 @@ +>FER_CAPAA/1-97 Ferredoxin +-----------------------------------------------------------ASYKVKLITPDGP +IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG- +>FER_CAPAN/1-144 Ferredoxin, chloroplast precursor +MA------SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALFGLKS-A--NGGKVTCMASYKVKLITPDGP +IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV +TIETHKEAELVG- +>FER1_SOLLC/1-144 Ferredoxin-1, chloroplast precursor +MA------SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPEGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV +TIETHKEEELTA- +>Q93XJ9_SOLTU/1-144 Ferredoxin I precursor +MA------SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALFGLKS-G--RNGRITCMASYKVKLITPDGP +IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV +TIETHKEEELTA- +>FER1_PEA/1-149 Ferredoxin-1, chloroplast precursor +MATT---PALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFLGLKT-SLKRGDLAVAMASYKVKLVTPDGT +QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV +VIETHKEEDLTA- +>Q7XA98_TRIPR/1-152 Ferredoxin I +MATT---PALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP +QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV +TIETHKEEELTA- +>FER1_MESCR/1-148 Ferredoxin-1, chloroplast precursor +MAAT--TAALSGATMSTAFAPK--TPPMTAALPTNVGR--ALFGLKS-SASR-GRVTAMAAYKVTLVTPEGK +QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV +TIETHKEEELTA- +>FER1_SPIOL/1-147 Ferredoxin-1, chloroplast precursor +MAAT--TTTMMG--MATTFVPKPQAPPMMAALPSNTGR--SLFGLKT-GSR--GGRMTMAAYKVTLVTPTGN +VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV +TIETHKEEELTA- +>FER3_RAPSA/1-96 Ferredoxin, leaf L-A +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDDQIAEGFVLTCAAYPTSDV +TIETHREEDMV-- +>FER2_ARATH/1-148 Ferredoxin-2, chloroplast precursor +MAST----ALSSAIVGTSFIRRSPAPISLRSLPSANTQ--SLFGLKS-GTARGGRVTAMATYKVKFITPEGE +LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV +TIETHKEEDIV-- +>FER_BRANA/1-96 Ferredoxin +-----------------------------------------------------------ATYKVKFITPEGE +QEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGFVDQSDESFLDDDQIAEGFVLTCAAYPTSDV +TIETHKEEELV-- +>FER1_ARATH/1-148 Ferredoxin-1, chloroplast precursor +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV +VIETHKEEAIM-- +>Q93Z60_ARATH/1-118 At1g10960/T19D16_12 +MAST----ALSSAIVSTSFLRRQQTPISLRSLPFANTQ--SLFGLKS-STARGGRVTAMATYKVKFITPEGE +QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD------------------- +------------- +>FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor +MATVLGSPRAPAFFFSSSSLRAAPAPTAV--ALPAAKV--GIMGRSA-SSRR--RLRAQATYNVKLITPEGE +VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV +VIETHKEEELTGA +>O80429_MAIZE/1-140 Ferredoxin +MAAT---------ALSMSILR---APPPCFSSPLRLRV--AVAKPLA-APMRRQLLRAQATYNVKLITPEGE +VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV +VIETHKEDDLL--