Re: [R-SIG-Mac] Can't open files in 4.0 or 4.01

Carl Witthoft Sun, 28 Jun 2020 14:21:41 -0700

Hi, here's my sample R 10 dump:

Sampling process 16681 for 10 seconds with 1 millisecond of run timebetween samples

Sampling completed, processing symbols...

Sample analysis of process 16681 written to file/tmp/R_2020-06-28_170339_imcz.sample.txt


Analysis of sampling R (pid 16681) every 1 millisecond
Process:         R [16681]
Path:            /Applications/R.app/Contents/MacOS/R
Load Address:    0x10e3dc000
Identifier:      org.R-project.R
Version:         R for R 4.0.1 GUI 1.72 Catalina build (7845)
Code Type:       X86-64
Parent Process:  ??? [1]

Date/Time:       2020-06-28 17:03:39.436 -0400
Launch Time:     2020-06-28 17:02:38.458 -0400
OS Version:      Mac OS X 10.15.5 (19F101)
Report Version:  7
Analysis Tool:   /usr/bin/sample

Physical footprint:         190.6M
Physical footprint (peak):  233.4M
----

Call graph:
    8617 Thread_2990078   DispatchQueue_1: com.apple.main-thread  (serial)
    + 8617 start  (in libdyld.dylib) + 1  [0x7fff735e3cc9]
    +   8617 main  (in R) + 792  [0x10e3ddfa8]
    +     8617 -[REngine runREPL]  (in R) + 177  [0x10e3ee441]
    +       8617 run_REngineRmainloop  (in R) + 263  [0x10e3f9837]

+ 8617 R_ReplDLLdo1 (in libR.dylib) + 148 [0x10e5ff1e4]main.c:371

    +           8617 Re_ReadConsole  (in R) + 184  [0x10e3ebd38]

+ 8617 -[RController handleReadConsole:] (in R) + 158[0x10e3e29be]+ 8617 -[RController doProcessEvents:] (in R) + 190[0x10e3e836e]+ 8617 -[NSApplication(NSEvent)_nextEventMatchingEventMask:untilDate:inMode:dequeue:] (in AppKit) +1352 [0x7fff3685c070]+ 8617 _DPSNextEvent (in AppKit) + 883[0x7fff3685d829]+ 8617_BlockUntilNextEventMatchingListInModeWithFilter (in HIToolbox) + 64[0x7fff38215579]+ 8617 ReceiveNextEventCommon (in HIToolbox)+ 359 [0x7fff382156f4]+ 8617 RunCurrentEventLoopInMode (inHIToolbox) + 292 [0x7fff38215abd]+ 8617 CFRunLoopRunSpecific (inCoreFoundation) + 462 [0x7fff395e6ece]+ 8617 __CFRunLoopRun (inCoreFoundation) + 874 [0x7fff395e7895]+ 8617 __CFRunLoopDoObservers (inCoreFoundation) + 457 [0x7fff395e82f7]+ 8617__CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ (inCoreFoundation) + 23 [0x7fff395e83c5]+ 8617___NSRunLoopObserverCreateWithHandler_block_invoke (in AppKit) + 41[0x7fff3711c850]+ 8617__62+[CATransaction(NSCATransaction)NS_setFlushesWithDisplayLink]_block_invoke (in AppKit) + 266[0x7fff369fd591]+ 8617CA::Transaction::commit() (in QuartzCore) + 644 [0x7fff450ac0a0]+ 8617CA::Context::commit_transaction(CA::Transaction*, double) (inQuartzCore) + 334 [0x7fff450ad4b6]+ 8617CA::Layer::display_if_needed(CA::Transaction*) (in QuartzCore) + 757[0x7fff450cf1fd]+ 8617-[_NSViewBackingLayer display] (in AppKit) + 800 [0x7fff36948977]+ 8617-[_NSBackingLayer display] (in AppKit) + 537 [0x7fff369e6e8a]+ 8617 -[CALayer_display] (in QuartzCore) + 2103 [0x7fff450d0162]+ 8617 invocationfunction for block in CA::Layer::display_() (in QuartzCore) + 53[0x7fff451307d9]+ 8617CABackingStoreUpdate_ (in QuartzCore) + 595 [0x7fff450d0c5d]+ 8617-[NSView(NSLayerKitGlue)_drawViewBackingLayer:inContext:drawingHandler:] (in AppKit) + 1271[0x7fff369e749a]+ 8617-[NSView(NSInternal)_recursive:displayRectIgnoringOpacity:inContext:stopAtLayerBackedViews:](in AppKit) + 2170 [0x7fff369e809e]+ 8617_NSViewDrawRect (in AppKit) + 139 [0x7fff369e8d8f]+ 8617-[_NSRulerContentView drawRect:] (in AppKit) + 157 [0x7fff36f6bd67]+8617 -[NSRulerView _drawContentRect:] (in AppKit) + 233 [0x7fff36f6b02f]+8617 -[NoodleLineNumberView drawHashMarksAndLabelsInRect:] (in R) + 345[0x10e42e8e9]+8617 -[NSLayoutManager(NSPrivate)_glyphRangeForBoundingRect:inTextContainer:fast:okToFillHoles:] (inUIFoundation) + 857 [0x7fff6a63611b]+8617 -[NSLayoutManager(NSPrivate)_firstPassGlyphRangeForBoundingRect:inTextContainer:okToFillHoles:] (inUIFoundation) + 1441 [0x7fff6a63765a]+8617 _NSFastFillAllLayoutHolesForGlyphRange (in UIFoundation) +1863 [0x7fff6a615870]+8617 _resizeTextViewsIfNeeded (in UIFoundation) + 284[0x7fff6a64c405]+8617 -[NSLayoutManager(NSPrivate)_resizeTextViewForTextContainer:] (in UIFoundation) + 1103[0x7fff6a607338]+8617 -[NSTextView setConstrainedFrameSize:] (in AppKit) +591 [0x7fff36993ebb]+8617 -[NSTextView setFrameSize:] (in AppKit) + 145[0x7fff36a22865]+8617 -[NSTextView(NSPrivate) _setFrameSize:forceScroll:](in AppKit) + 962 [0x7fff36a22d31]+8617 -[NSView setFrameSize:] (in AppKit) + 1800[0x7fff368968cc]+8617 -[NSView(NSInternal)_updateLayerGeometryFromView] (in AppKit) + 776 [0x7fff3687e504]+8617 -[NSView setNeedsDisplay:] (in AppKit) + 52[0x7fff3687c774]+8617 -[NSTextViewsetNeedsDisplayInRect:avoidAdditionalLayout:] (in AppKit) + 1040[0x7fff369931d5]+8617 -[NSLayoutManager(NSPrivate)_glyphRangeForBoundingRect:inTextContainer:fast:okToFillHoles:] (inUIFoundation) + 857 [0x7fff6a63611b]+8617 -[NSLayoutManager(NSPrivate)_firstPassGlyphRangeForBoundingRect:inTextContainer:okToFillHoles:] (inUIFoundation) + 1441 [0x7fff6a63765a]+8617 _NSFastFillAllLayoutHolesForGlyphRange(in UIFoundation) + 1596 [0x7fff6a615765]+8617 -[NSLayoutManager(NSPrivate)_fillLayoutHoleForCharacterRange:desiredNumberOfLines:isSoft:] (inUIFoundation) + 1106 [0x7fff6a643391]+8617 -[NSATSTypesetterlayoutCharactersInRange:forLayoutManager:maximumNumberOfLineFragments:](in UIFoundation) + 815 [0x7fff6a644d87]+8617 -[NSTypesetterlayoutCharactersInRange:forLayoutManager:maximumNumberOfLineFragments:](in UIFoundation) + 241 [0x7fff6a644f0f]+8617 -[NSTypesetter_layoutGlyphsInLayoutManager:startingAtGlyphIndex:maxNumberOfLineFragments:maxCharacterIndex:nextGlyphIndex:nextCharacterIndex:](in UIFoundation) + 3120 [0x7fff6a5fb0d9]+8617 -[NSATSTypesetterlayoutParagraphAtPoint:] (in UIFoundation) + 181 [0x7fff6a64573f]+8617 -[NSATSTypesetter_layoutLineFragmentStartingWithGlyphAtIndex:characterIndex:atPoint:renderingContext:](in UIFoundation) + 6960 [0x7fff6a629c1e]+8617-[NSLayoutManager(NSPrivate)setLineFragmentRect:forGlyphRange:usedRect:baselineOffset:] (inUIFoundation) + 85 [0x7fff6a649124]+8617 -[NSLayoutManagersetLineFragmentRect:forGlyphRange:usedRect:] (in UIFoundation) + 328[0x7fff6a649299]+8617-[NSLayoutManager(NSPrivate)_updateUsageForTextContainer:addingUsedRect:] (in UIFoundation) + 529[0x7fff6a602305]+8617-[NSLayoutManager(NSPrivate) _resizeTextViewForTextContainer:] (inUIFoundation) + 1103 [0x7fff6a607338]+8617 -[NSTextViewsetConstrainedFrameSize:] (in AppKit) + 591 [0x7fff36993ebb]+8617 -[NSTextViewsetFrameSize:] (in AppKit) + 145 [0x7fff36a22865]+8617-[NSTextView(NSPrivate) _setFrameSize:forceScroll:] (in AppKit) + 962[0x7fff36a22d31]+8617 -[NSViewsetFrameSize:] (in AppKit) + 3248 [0x7fff36896e74]+8617 -[NSView_postFrameChangeNotification] (in AppKit) + 82 [0x7fff3689e131]+8617-[NSClipView _reflectDocumentViewFrameChange] (in AppKit) + 634[0x7fff368e254a]+8617__45-[NSClipView _reflectDocumentViewFrameChange]_block_invoke (inAppKit) + 95 [0x7fff368e2752]+8617-[NSScrollView reflectScrolledClipView:] (in AppKit) + 774[0x7fff368f1ec7]+8617-[NSScrollView _tileWithoutRecursing] (in AppKit) + 35 [0x7fff369016bd]+

8617 -[NSScrollView tile]  (in AppKit) + 680  [0x7fff36901982]

+8617 -[NSScrollView _setContentViewFrame:] (in AppKit) + 328[0x7fff36904d5f]+

8617 -[NSView setFrame:]  (in AppKit) + 423  [0x7fff368a882e]

+

  8617 -[NSClipView setFrameSize:]  (in AppKit) + 425  [0x7fff368e1d43]

+

    8617 -[NSView setFrameSize:]  (in AppKit) + 2045  [0x7fff368969c1]

+8617 -[NSView resizeSubviewsWithOldSize:] (in AppKit) + 525[0x7fff368bb49d]+8617 -[NSView resizeWithOldSuperviewSize:] (in AppKit) + 1178[0x7fff368bbd79]+

          8617 -[NSView setFrame:]  (in AppKit) + 423  [0x7fff368a882e]

+8617 -[NSTextView setFrameSize:] (in AppKit) + 145[0x7fff36a22865]+8617 -[NSTextView(NSPrivate) _setFrameSize:forceScroll:](in AppKit) + 1130 [0x7fff36a22dd9]+8617 -[NSLayoutManagerboundingRectForGlyphRange:inTextContainer:] (in UIFoundation) + 47[0x7fff6a65231c]+8617 -[NSLayoutManager(NSPrivate)_boundingRectForGlyphRange:inTextContainer:fast:fullLineRectsOnly:] (inUIFoundation) + 108 [0x7fff6a64d9e4]+8617 -[NSLayoutManager(NSPrivate)_rectArrayForRange:withinSelectionRange:rangeIsCharRange:singleRectOnly:fullLineRectsOnly:inTextContainer:rectCount:rangeWithinContainer:glyphsDrawOutsideLines:](in UIFoundation) + 58 [0x7fff6a7a0681]+8617 -[NSLayoutManager(NSPrivate)_rectArrayForRange:withinSelectionRange:rangeIsCharRange:singleRectOnly:fullLineRectsOnly:inTextContainer:rectCount:rangeWithinContainer:glyphsDrawOutsideLines:rectArray:rectArrayCapacity:](in UIFoundation) + 748 [0x7fff6a612fe6]+8617 _NSFastFillAllLayoutHolesForGlyphRange(in UIFoundation) + 1596 [0x7fff6a615765]+8617 -[NSLayoutManager(NSPrivate)_fillLayoutHoleForCharacterRange:desiredNumberOfLines:isSoft:] (inUIFoundation) + 1106 [0x7fff6a643391]+8617 -[NSATSTypesetterlayoutCharactersInRange:forLayoutManager:maximumNumberOfLineFragments:](in UIFoundation) + 283 [0x7fff6a644b73]+8617 -[NSATSTypesetterlayoutCharactersInRange:forLayoutManager:maximumNumberOfLineFragments:](in UIFoundation) + 815 [0x7fff6a644d87]+8617 -[NSTypesetterlayoutCharactersInRange:forLayoutManager:maximumNumberOfLineFragments:](in UIFoundation) + 241 [0x7fff6a644f0f]+8617 -[NSTypesetter_layoutGlyphsInLayoutManager:startingAtGlyphIndex:maxNumberOfLineFragments:maxCharacterIndex:nextGlyphIndex:nextCharacterIndex:](in UIFoundation) + 2950 [0x7fff6a5fb02f]+8617 -[NSTypesetter_getRemainingNominalParagraphRange:andParagraphSeparatorRange:charactarIndex:layoutManager:string:](in UIFoundation) + 1233 [0x7fff6a64543f]+

                                      8617 0x0

+8617 _sigtramp (inlibsystem_platform.dylib) + 29 [0x7fff737dc5fd]+8617 sigactionSegv (inlibR.dylib) + 675 [0x10e601673] main.c:623+8617 Re_ReadConsole (in R)+ 184 [0x10e3ebd38]+8617 -[RControllerhandleReadConsole:] (in R) + 158 [0x10e3e29be]+8617 -[RControllerdoProcessEvents:] (in R) + 190 [0x10e3e836e]+8617-[NSApplication(NSEvent)_nextEventMatchingEventMask:untilDate:inMode:dequeue:] (in AppKit) +1352 [0x7fff3685c070]+8617 _DPSNextEvent(in AppKit) + 883 [0x7fff3685d829]+8617_BlockUntilNextEventMatchingListInModeWithFilter (in HIToolbox) + 64[0x7fff38215579]+8617ReceiveNextEventCommon (in HIToolbox) + 584 [0x7fff382157d5]+8617RunCurrentEventLoopInMode (in HIToolbox) + 292 [0x7fff38215abd]+8617CFRunLoopRunSpecific (in CoreFoundation) + 462 [0x7fff395e6ece]+8617__CFRunLoopRun (in CoreFoundation) + 1871 [0x7fff395e7c7a]+8617__CFRunLoopDoTimers (in CoreFoundation) + 322 [0x7fff39602ed7]+8617__CFRunLoopDoTimer (in CoreFoundation) + 859 [0x7fff396033ef]+

8617 __CFRUNLOOP_IS_CALLING_OUT_TO_A_TIMER_CALLBACK_FUNCTION__ (inCoreFoundation) + 20 [0x7fff39603889]+


8617 __NSFireDelayedPerform  (in Foundation) + 415  [0x7fff3bcba6e2]

+

8617 _NSFastFillAllLayoutHolesForGlyphRange (in UIFoundation) + 1596[0x7fff6a615765]+

8617 -[NSLayoutManager(NSPrivate)_fillLayoutHoleForCharacterRange:desiredNumberOfLines:isSoft:] (inUIFoundation) + 1106 [0x7fff6a643391]+

8617 -[NSATSTypesetterlayoutCharactersInRange:forLayoutManager:maximumNumberOfLineFragments:](in UIFoundation) + 283 [0x7fff6a644b73]+

8617 -[NSATSTypesetterlayoutCharactersInRange:forLayoutManager:maximumNumberOfLineFragments:](in UIFoundation) + 815 [0x7fff6a644d87]+

8617 -[NSTypesetterlayoutCharactersInRange:forLayoutManager:maximumNumberOfLineFragments:](in UIFoundation) + 241 [0x7fff6a644f0f]+

8617 -[NSTypesetter_layoutGlyphsInLayoutManager:startingAtGlyphIndex:maxNumberOfLineFragments:maxCharacterIndex:nextGlyphIndex:nextCharacterIndex:](in UIFoundation) + 2950 [0x7fff6a5fb02f]+

8617 -[NSTypesetter_getRemainingNominalParagraphRange:andParagraphSeparatorRange:charactarIndex:layoutManager:string:](in UIFoundation) + 1233 [0x7fff6a64543f]+

8617 -[RScriptEditorTypeSetteractionForControlCharacterAtIndex:] (in R) + 47 [0x10e43b59f]+


                8617 0x0 + 0  [0x0]
    8617 Thread_2990146: JavaScriptCore bmalloc scavenger

+ 8617 thread_start (in libsystem_pthread.dylib) + 15[0x7fff737e3b8b]+ 8617 _pthread_start (in libsystem_pthread.dylib) + 148[0x7fff737e8109]+ 8617 void*std::__1::__thread_proxy<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct,std::__1::default_delete<std::__1::__thread_struct> >, void(*)(bmalloc::Scavenger*), bmalloc::Scavenger*> >(void*) (inJavaScriptCore) + 39 [0x7fff3dde9cd7]+ 8617bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) (inJavaScriptCore) + 9 [0x7fff3dde75f9]+ 8617 bmalloc::Scavenger::threadRunLoop() (inJavaScriptCore) + 299 [0x7fff3dde7a2b]+ 8617 voidstd::__1::condition_variable_any::wait<std::__1::unique_lock<bmalloc::Mutex>>(std::__1::unique_lock<bmalloc::Mutex>&) (in JavaScriptCore) + 84[0x7fff3dde3224]+ 8617std::__1::condition_variable::wait(std::__1::unique_lock<std::__1::mutex>&)(in libc++.1.dylib) + 18 [0x7fff708b7592]+ 8617 _pthread_cond_wait (inlibsystem_pthread.dylib) + 698 [0x7fff737e8425]+ 8617 __psynch_cvwait (in libsystem_kernel.dylib)+ 10 [0x7fff73727882]

    8617 Thread_2990223

+ 8617 thread_start (in libsystem_pthread.dylib) + 15[0x7fff737e3b8b]+ 8617 _pthread_start (in libsystem_pthread.dylib) + 148[0x7fff737e8109]+ 8617 __NSThread__start__ (in Foundation) + 1064[0x7fff3bc777a2]

    +       8617 -[RController readThread:]  (in R) + 512  [0x10e3e0950]

+ 8617 __select (in libsystem_kernel.dylib) + 10[0x7fff7372d0fe]

    8617 Thread_2990341: com.apple.NSEventThread

+ 8617 thread_start (in libsystem_pthread.dylib) + 15[0x7fff737e3b8b]+ 8617 _pthread_start (in libsystem_pthread.dylib) + 148[0x7fff737e8109]

    +     8617 _NSEventThread  (in AppKit) + 132  [0x7fff369ff144]

+ 8617 CFRunLoopRunSpecific (in CoreFoundation) + 462[0x7fff395e6ece]+ 8617 __CFRunLoopRun (in CoreFoundation) + 1319[0x7fff395e7a52]+ 8617 __CFRunLoopServiceMachPort (in CoreFoundation) +247 [0x7fff395e8f85]+ 8617 mach_msg (in libsystem_kernel.dylib) + 60[0x7fff73725170]+ 8617 mach_msg_trap (in libsystem_kernel.dylib) +10 [0x7fff73724dfa]

    1 Thread_2990687
    + 1 start_wqthread  (in libsystem_pthread.dylib) + 0  [0x7fff737e3b68]
    1 Thread_2990704
      1 start_wqthread  (in libsystem_pthread.dylib) + 15  [0x7fff737e3b77]

1 _pthread_wqthread (in libsystem_pthread.dylib) + 390[0x7fff737e4aa1]1 __workq_kernreturn (in libsystem_kernel.dylib) + 10[0x7fff737264ce]


Total number in stack (recursive counted multiple, when >=5):

Sort by top of stack, same collapsed (when >= 5):
        0x0        8617
        __psynch_cvwait  (in libsystem_kernel.dylib)        8617
        __select  (in libsystem_kernel.dylib)        8617
        mach_msg_trap  (in libsystem_kernel.dylib)        8617

Binary Images:

0x10e3dc000 - 0x10e463ffb +org.R-project.R (R for R 4.0.1GUI 1.72 Catalina build - 7845) <DD6D28C9-4E80-37C7-91D2-73B758DB9A25>/Applications/R.app/Contents/MacOS/R0x10e4f1000 - 0x10e7f8ff7 +libR.dylib (0)<F7DAB29B-61CA-3D6E-BF10-0957D511C65B>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib0x10e9e4000 - 0x10ea0cfff +libRblas.dylib (0)<FE8F45A3-8DD0-37AB-B105-2945C1CB87E7>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib0x10ea1a000 - 0x10ec4bfef +libgfortran.5.dylib (0)<5B0F7278-9D16-3B60-A413-59EEF538E568>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib0x10ecd9000 - 0x10ed11fff +libquadmath.0.dylib (0)<856F3E97-EECB-3DDE-AF45-56AEA7758A1E>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib0x10ed2b000 - 0x10ed40fef +libgcc_s.1.dylib (1)<C1F47CA1-564E-36B8-BE6F-7A5FDD88E2C6>/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib0x1111b5000 - 0x1111b8047 libobjc-trampolines.dylib(787.1) <8212B354-A106-3806-A022-A60F2B2FA5C9>/usr/lib/libobjc-trampolines.dylib0x112b1f000 - 0x112b24ff7 +methods.so (0)<A17330DB-52B5-39D0-989D-10EC781251DA>/Library/Frameworks/R.framework/Versions/4.0/Resources/library/methods/libs/methods.so0x112b3a000 - 0x112bcbeff dyld (750.5)<E4698FBD-806A-3396-B279-E685BA37430B> /usr/lib/dyld0x112d1f000 - 0x112d27ff3 +utils.so (0)<23D016BF-E8AA-311B-A427-407AB8087B24>/Library/Frameworks/R.framework/Versions/4.0/Resources/library/utils/libs/utils.so0x1153ce000 - 0x1153d0ff3com.apple.CloudDocsFileProvider (1.0 - 698.14)<96DFA9EF-1BA8-3A50-B30B-72773341B00B>/System/Library/Frameworks/FileProvider.framework/OverrideBundles/CloudDocsFileProvider.bundle/Contents/MacOS/CloudDocsFileProvider0x115584000 - 0x115587fff com.apple.FileProviderOverride(304.1 - 304.1) <198EE5E5-B1B9-3223-8E23-1DFF89A553FA>/System/Library/Frameworks/FileProvider.framework/OverrideBundles/FileProviderOverride.bundle/Contents/MacOS/FileProviderOverride0x116bfc000 - 0x116c13ffbcom.apple.findersync.fileprovideroverride.FinderSyncCollaborationFileProviderOverride(1.0 - 1298.5.10) <CF308A32-9994-3092-81F4-DE59438CD142>/System/Library/Frameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride0x1182dc000 - 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On 6/28/20 12:25 PM, Brandon Hurr wrote:

Thanks Ben.
I fired up R did a 20 second sample as I loaded files and it went into ahang.
https://gist.github.com/bhive01/77ccd888da1ee74da12a5c91cfc3d727

Seems to have the symbols you describe. Is that more helpful?

Brandon


--
Carl Witthoft
c...@witthoft.com
resume: https://app.box.com/file/498153801347

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