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Is slicer 4.2 not compatible with windows7 OS? Crashes every time |
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@Christian: Regarding the "Crashed every time", do you mean that you can't start Slicer ? Or that it crashed while running EMSegment module ? |
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Whenever I start the EMSegment Task, Slicer stops during the preprocessing Task. The 32 Bit Version of slicer crashes with an error message.
I used the Hand Bone Segmentation from the Task library with the volume CT_Hand_Bone_Subject_1.nrrd from the task library. |
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Is this reproducible using Slicer on a 64-bit system ? If you monitor the memory usage, is Slicer running out of memory ?
Will know let the maintainer (Kilian) of EMSegment module helping you.
@Kilian: Any idea what could be wrong ? |
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I have 8GB Ram.
When the slicer EM segmenter crashes I have 3GB free memory.
It is also interesting that the sclicer when the EM Segmenter starts the window of slicer tells (not responding).
The CPU usage is also at a Maximum. |
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I have a Ubuntu machine - it works fine on that one with the newest build. Windows often has problems with memory allocation is too much memory is allocated at once. This has nothing to do with how much ram you have left but a "bug" in the OS. We previously have seen this problem . Sorry there is nothing I can do for you. By the way, how can I get access to CT_Hand_Bone_Subject_1.nrrd ? |
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You can find the file under the slicer installation path under EMSegmenter Tasks HandBone.
I can also send the file to you.
You may be right that under Windows the slicer consumes maximum CPU ressources so that the GUI is almost not interacting. |
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So finally Slicer is not working properly on Windows machines ?
It would be nice since in our University we are usin Windows in the laboratories |
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Yesterday I tested slicer to start in admin mode under Windows.
The Tasks now Ends in the preprocessing step of the EM segmenter (with Atlas) with an error message of slicer. |
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what is the error message ? |
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EMSegmenter Bug.docx (331,180 bytes)
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Starting slicer 4.3.1 in Windows 7 64Bit, 8GB Ram
- Start EMSegmenter with Atlas
- Select the CT Hand Bone Task
- Load CT -> CT_Hand_Bone_Subject_1.nrrd
- Press advanced
- next, next -> Preprocesing
- Preprocessing starts
2-3 seconds -> error message
Pre-processing did not execute correctly!!
I attached a word file with snapshots |
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@Christian: can you also past the error logs by going to the View Menu and selecting Error Log or by pressing Ctrl+0 ? It would greatly help |
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@Christian: can you also past the error logs by going to the View Menu and selecting Error Log or by pressing Ctrl+0 ? It would greatly help |
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I created a error log. Is there a way to Export the error log to a file ?
Snapshots of the log are attached to the issue |
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EMSegmenter Bug_ErrorLog.docx (460,354 bytes)
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It would help Kilian if you could provide the full error log - here's how:
- click on one of the rows at the top of the error log
- select all entries (Control-A) and all the text will show up in the lower panel
- click in the lower panel and copy-paste the text into a note in this bug report
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I uploaded the error.log file. |
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pohl
2014-04-08 08:08
developer
~0011554
Last edited: 2014-04-08 19:09
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very helpful - does not work bc of spaces in path
Sourcing task general file: C:/temp/Slicer/EMSegmentTaskCopy/GenericTask.tcl
couldn't read file "C:Program Files (x86)Slicer 4.3.1-2013-11-19inPythonslicer/tcl//Slicer3Adapters.tcl": no such file or directory
couldn't read file "C:Program Files (x86)Slicer 4.3.1-2013-11-19inPythonslicer/tcl//Slicer3Adapters.tcl": no such file or directory
while executing
"source $dir/Slicer3Adapters.tcl" |
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now the strange thing is that I cannot find in any file in the EMSegmenter directory that performs source $dir/Slicer3Adapters.tcl
(,i.e. grep Slicer3Adapters find . -name "*.*" does not return anything) .
JC, Steve: Any idea where this is coming from ? |
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The file "Slicer3Adapters.tcl" is currently located in Base/Python/Slicer/tcl (See [1]) and is sourced within the "tcl" function. See [2]
[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Base/Python/slicer/tcl/Slicer3Adapters.tcl?revision=21766&view=markup
[2] http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Base/Python/slicer/slicerqt-with-tcl.py?revision=23021&view=markup#l23 |
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tested on windows with:
t = tcl('puts hoot') and replicated the path issue.
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Fixed by replacing backslashes with forward slashes in the tcl directory. Not sure when this became and issue, since earlier versions of the tpycl layer worked fine on windows. Probably this issue is a byproduct of the cmakeified python or some other change. |
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Fixed in rev 23066.
@Kilian, please close once you confirm. |
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@ChristianMenard, please close once you confirm. |
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what should i do now to get the slicer working. Can I Change the script by myself |
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It looks like the nightly build for windows is failing for an unrelated reason. Hopefully it will be available in the next couple days.
In the mean time, you could try applying this fix (add the one line replacing backslashes with slashes). You just need to find the corresponding file in your slicer installation. On windows you may need to change the access controls to make the file writable in order to make the changes.
http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Base/Python/slicer/slicerqt-with-tcl.py?r1=23066&r2=23065&pathrev=23066 |
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I tested it it works :)
Thx a lot
Christian |
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Dear all
I have downloaded a new nightly Version of slicer (4.3.1-2014-06-30 r23404)
and the Hand bone Segmentation reports an error. The error log is atteched to the issue
Kind regards Christian |
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Thanks for reporting this - the key info in the log file is: "fileDEBUGTransform_RegFilterOutput.mat"
This is due to a problem in brains that I know is being worked on:
https://github.com/BRAINSia/BRAINSTools/issues/120 |
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This issue is fixed in the latest origin/master of BRAINSTools, but other issues related to an incompatibility with the latest version of SlicerExecutionModel is being worked on.
Hopefully these issues can be resolved in the next few days. |
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I fixed the incompatibility issue. Now the fixed version of BRAINSTools has to be integrated into the slicer enviornment |
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Sweet! |
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@Hans: Let me know when you have an updated version of BRAINSTools and I will update the sha1 in Slicer. |
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@JC The problem with SlicerExecutionModel having a separate exposed "find_package(ITK COMPONENTS {MINIMUM_LIST})" that implicitly preceeds building of other packages and their use of "find_package(ITK COMPONENTS {LARGE_LIST})" has been a large distraction to getting these changes tested and implemented.
I think I've got a stable testing ground again.
I also found why it was taking so long. The default values were changed to insane values (convergence threshold of 0.0) and sampling strategy was defaulting to 100% of all pixels (instead of the previous 1%).
There should be something available by Monday afternoon. |
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@jcfr I have a tried, but there is a new llinker error now related to inclusion of ITKIODCMTK component of ITK.
Here is the current patch set:
https://github.com/hjmjohnson/Slicer/tree/20140715BRAINSToolsUpdate
Hans |
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For reference, as of r23468, the new version of BRAINS has been integrated.
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23468 |
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Most likely fixed by r23638 / r23640
Please, re-open if this is still an issue.
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23638
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23640 |
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I tested the latest nightly build again for the Hand bone Segmentation
The Operation stopt with the message
Preprocessing did not execute correctly. I uploaded the error log
regards Christian |
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I tested the latest nightly build again for the Hand bone Segmentation
the Operation stopt with the message
-> Preprocessing did not execute correctly. I uploaded the error log
regards Christian |
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I was able to replicate the issue on Ubuntu - will dig deeper |
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Slicer4 r23738
Tcl file as not updated to VTK 6 |
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@Christian: Can you check that the bug is resolved in the few days to have it closed before the Slicer 4.4 release, which will be in a couple of days ? |
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I have tested the task again with
Version: nightly 2014-10-14 r23738
The Task by using the Default Parameters ended without error now and with the correct results. Good work
But when i press Show plot (plot distribution) just after the preprocessing step slicer () slicerapp-real) crashes
Problemsignatur:
Problemereignisname: BEX64
Anwendungsname: SlicerApp-real.exe
Anwendungsversion: 0.0.0.0
Anwendungszeitstempel: 543cde96
Fehlermodulname: MSVCR90.dll
Fehlermodulversion: 9.0.30729.6161
Fehlermodulzeitstempel: 4dace4e7
Ausnahmeoffset: 00000000000552d4
Ausnahmecode: c0000417
Ausnahmedaten: 0000000000000000
Betriebsystemversion: 6.1.7601.2.1.0.256.4
Gebietsschema-ID: 1031
Zusatzinformation 1: c321
Zusatzinformation 2: c32141485647a5e147b98e15e67eb468
Zusatzinformation 3: 57fe
Zusatzinformation 4: 57fea4f48145a44535e886e56f13a125
Lesen Sie unsere Datenschutzbestimmungen online:
http://go.microsoft.com/fwlink/?linkid=104288&clcid=0x0407
Wenn die Onlinedatenschutzbestimmungen nicht verfügbar sind, lesen Sie unsere Datenschutzbestimmungen offline:
C:\Windows\system32\de-DE\erofflps.txt
Closing Slicer (press x) the following message occurs
ignisname: APPCRASH
Anwendungsname: SlicerApp-real.exe
Anwendungsversion: 0.0.0.0
Anwendungszeitstempel: 543cde96
Fehlermodulname: QtCore4.dll
Fehlermodulversion: 4.8.6.0
Fehlermodulzeitstempel: 53d99eb0
Ausnahmecode: c0000005
Ausnahmeoffset: 0000000000029787
Betriebsystemversion: 6.1.7601.2.1.0.256.4
Gebietsschema-ID: 1031
Zusatzinformation 1: 8e2b
Zusatzinformation 2: 8e2b14e21a3ea97943e2a146f8cb922c
Zusatzinformation 3: ef06
Zusatzinformation 4: ef0631e90db695b7f2862d65354338ad
Lesen Sie unsere Datenschutzbestimmungen online:
http://go.microsoft.com/fwlink/?linkid=104288&clcid=0x0407
Wenn die Onlinedatenschutzbestimmungen nicht verfügbar sind, lesen Sie unsere Datenschutzbestimmungen offline:
C:\Windows\system32\de-DE\erofflps.txt |
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I cannot reproduce the bug on Ubuntu. Here is fast way to get to it
- Select EMSegmenter -> Select CT Hand Bone Task -> Press Advance
- Step 2: Atlas -> Next
- Press Next until Step 6
- Step 6 : deselect "register the atlas to the input scan" -> press next
- Step 7: Select "plot distribution
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I will try your workaround on another newly installed machine and will Report the result immediately |
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I was able to reproduce this in a debug windows build. Here's the stack trace. It is using -1 as an index into a vector.
msvcp90d.dll!std::_Debug_message(const wchar_t * message=0x000007fec6b05238, const wchar_t * file=0x000007fec6b05280, unsigned int line=779) Line 24 C++
vtkSlicerEMSegmentModuleLogic.dll!std::vector<double,std::allocator<double> >::operator[](unsigned __int64 _Pos=18446744073709551615) Line 780 C++
vtkSlicerEMSegmentModuleLogic.dll!vtkMRMLEMSTreeParametersLeafNode::GetLogMean(int index=-1) Line 499 + 0x1c bytes C++
vtkSlicerEMSegmentModuleLogic.dll!vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogMean(__int64 nodeID=1001, int volumeNumber=-1) Line 614 C++
vtkSlicerEMSegmentModuleLogic.dll!vtkEMSegmentMRMLManager::GetTreeNodeDistributionLogMeanWithCorrection(__int64 nodeID=1001, int volumeNumber=-1) Line 4520 + 0x29 bytes C++
qSlicerEMSegmentModuleWidgets.dll!qSlicerEMSegmentGraphWidgetPrivate::updateClass(int64 classID=1001, int input=1) Line 196 + 0x2f bytes C++
qSlicerEMSegmentModuleWidgets.dll!qSlicerEMSegmentGraphWidgetPrivate::addClass(int64 classID=1001) Line 187 + 0x1b bytes C++
qSlicerEMSegmentModuleWidgets.dll!qSlicerEMSegmentGraphWidget::updateFromMRMLManager() Line 297 + 0x12 bytes C++
qSlicerEMSegmentModuleWidgets.dll!qSlicerEMSegmentGraphWidget::setMRMLManager(vtkEMSegmentMRMLManager newMRMLManager=0x000000001148b040) Line 248 C++
qSlicerEMSegmentModuleWidgets.dll!qSlicerEMSegmentGraphWidget::qt_static_metacall(QObject _o=0x000000004749a540, QMetaObject::Call _c=InvokeMetaMethod, int _id=0, void _a=0x00000000002d8990) Line 57 + 0x1f bytes C++
qSlicerEMSegmentModuleWidgets.dll!qSlicerEMSegmentGraphWidget::qt_metacall(QMetaObject::Call _c=InvokeMetaMethod, int _id=0, void _a=0x00000000002d8990) Line 101 C++
PythonQt.dll!PythonQtCallSlot(PythonQtClassInfo classInfo=0x0000000004240c10, QObject objectToCall=0x000000004749a540, _object args=0x000000000dc751d0, bool strict=true, PythonQtSlotInfo info=0x000000004749cd00, void firstArgument=0x0000000000000000, _object pythonReturnValue=0x00000000002d8d68, void directReturnValuePointer=0x0000000000000000) Line 171 + 0x3c bytes C++
PythonQt.dll!PythonQtSlotFunction_CallImpl(PythonQtClassInfo classInfo=0x0000000004240c10, QObject objectToCall=0x000000004749a540, PythonQtSlotInfo info=0x000000004749cd00, _object args=0x000000000dc751d0, _object __formal=0x0000000000000000, void firstArg=0x0000000000000000, void directReturnValuePointer=0x0000000000000000) Line 312 + 0x51 bytes C++
PythonQt.dll!PythonQtMemberFunction_Call(PythonQtSlotInfo info=0x000000004749cd00, _object m_self=0x000000000dda4bf8, _object args=0x000000000dc751d0, _object kw=0x0000000000000000) Line 250 + 0x5a bytes C++
PythonQt.dll!PythonQtSlotFunction_Call(_object func=0x000000000de60bc8, _object args=0x000000000dc751d0, _object kw=0x0000000000000000) Line 239 C++
python27.dll!000007fed9e62f25()
[Frames below may be incorrect and/or missing, no symbols loaded for python27.dll]
python27.dll!000007fed9ede4ab()
python27.dll!000007fed9eded5a()
python27.dll!000007fed9ee2464()
python27.dll!000007fed9ee3c69()
python27.dll!000007fed9e89db3()
python27.dll!000007fed9e62f25()
python27.dll!000007fed9e70d54()
python27.dll!000007fed9e62f25()
python27.dll!000007fed9edd168()
PythonQt.dll!PythonQtSignalTarget::call(_object callable=0x000000000df2eca8, const PythonQtMethodInfo methodInfos=0x00000000037a6350, void arguments=0x00000000002d9db0, bool skipFirstArgumentOfMethodInfo=false) Line 124 + 0x13 bytes C++
PythonQt.dll!PythonQtSignalTarget::call(void arguments=0x00000000002d9db0) Line 55 + 0x2e bytes C++
PythonQt.dll!PythonQtSignalReceiver::qt_metacall(QMetaObject::Call c=InvokeMetaMethod, int id=4, void arguments=0x00000000002d9db0) Line 261 C++
QtCored4.dll!QMetaObject::metacall(QObject object=0x00000000474953c0, QMetaObject::Call cl=InvokeMetaMethod, int idx=4, void argv=0x00000000002d9db0) Line 246 C++
QtCored4.dll!QMetaObject::activate(QObject sender=0x00000000474945c0, const QMetaObject m=0x00000000534e05e8, int local_signal_index=2, void argv=0x00000000002d9db0) Line 3577 + 0x49 bytes C++
QtGuid4.dll!QAbstractButton::clicked(bool _t1=false) Line 220 C++
QtGuid4.dll!QAbstractButtonPrivate::emitClicked() Line 550 C++
QtGuid4.dll!QAbstractButtonPrivate::click() Line 541 + 0xa bytes C++
QtGuid4.dll!QAbstractButton::mouseReleaseEvent(QMouseEvent e=0x00000000002db128) Line 1124 C++
PythonQt.dll!PythonQtShell_QPushButton::mouseReleaseEvent(QMouseEvent e=0x00000000002db128) Line 10330 C++
QtGuid4.dll!QWidget::event(QEvent event=0x00000000002db128) Line 8377 C++
QtGuid4.dll!QAbstractButton::event(QEvent e=0x00000000002db128) Line 1083 C++
QtGuid4.dll!QPushButton::event(QEvent e=0x00000000002db128) Line 684 C++
PythonQt.dll!PythonQtShell_QPushButton::event(QEvent e=0x00000000002db128) Line 9958 C++
QtGuid4.dll!QApplicationPrivate::notify_helper(QObject receiver=0x00000000474945c0, QEvent e=0x00000000002db128) Line 4562 + 0x15 bytes C++
QtGuid4.dll!QApplication::notify(QObject receiver=0x00000000474945c0, QEvent e=0x00000000002db128) Line 4105 + 0x51 bytes C++
qSlicerBaseQTGUI.dll!qSlicerApplication::notify(QObject receiver=0x00000000474945c0, QEvent event=0x00000000002db128) Line 330 + 0x1e bytes C++
QtCored4.dll!QCoreApplication::notifyInternal(QObject receiver=0x00000000474945c0, QEvent event=0x00000000002db128) Line 949 + 0x26 bytes C++
QtCored4.dll!QCoreApplication::sendSpontaneousEvent(QObject receiver=0x00000000474945c0, QEvent event=0x00000000002db128) Line 234 + 0x4c bytes C++
QtGuid4.dll!QApplicationPrivate::sendMouseEvent(QWidget receiver=0x00000000474945c0, QMouseEvent event=0x00000000002db128, QWidget alienWidget=0x00000000474945c0, QWidget nativeWidget=0x000000000ef3e780, QWidget buttonDown=0x000000005381d340, QPointer<QWidget> & lastMouseReceiver={...}, bool spontaneous=true) Line 3171 + 0x16 bytes C++
QtGuid4.dll!QETWidget::translateMouseEvent(const tagMSG & msg={...}) Line 3382 + 0x3f bytes C++
QtGuid4.dll!QtWndProc(HWND__ hwnd=0x000000000001097a, unsigned int message=514, unsigned int64 wParam=0, int64 lParam=50528568) Line 1709 + 0x15 bytes C++
user32.dll!0000000076f79bd1()
user32.dll!0000000076f798da()
QtCored4.dll!QEventDispatcherWin32::processEvents(QFlags<enum QEventLoop::ProcessEventsFlag> flags=0x00000000002df3f0) Line 814 C++
QtGuid4.dll!QGuiEventDispatcherWin32::processEvents(QFlags<enum QEventLoop::ProcessEventsFlag> flags=0x00000000002df43c) Line 1212 + 0x27 bytes C++
QtCored4.dll!QEventLoop::processEvents(QFlags<enum QEventLoop::ProcessEventsFlag> flags=0x00000000002df4b8) Line 150 C++
QtCored4.dll!QEventLoop::exec(QFlags<enum QEventLoop::ProcessEventsFlag> flags=0x00000000002df540) Line 204 + 0x59 bytes C++
QtCored4.dll!QCoreApplication::exec() Line 1221 + 0x23 bytes C++
QtGuid4.dll!QApplication::exec() Line 3824 C++
SlicerApp-real.exe!`anonymous namespace'::SlicerAppMain(int argc=1, char argv=0x000000000360a0b0) Line 209 + 0x6 bytes C++
SlicerApp-real.exe!WinMain(HINSTANCE * hInstance=0x000000013f6a0000, HINSTANCE hPrevInstance=0x0000000000000000, char lpCmdLine=0x00000000003c7e5b, int nShowCmd=1) Line 228 + 0xe bytes C++
SlicerApp-real.exe!__tmainCRTStartup() Line 578 + 0x42 bytes C
SlicerApp-real.exe!WinMainCRTStartup() Line 403 C
kernel32.dll!0000000076e559ed()
ntdll.dll!000000007708c541()
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Steve : I believe I fixed it with r23748. Please check |
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This works for me. |
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I checked the new build and it worked now.
Thabnks a lot for the good work
regards Christian |
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