rstudio / reticulate

R Interface to Python
https://rstudio.github.io/reticulate
Apache License 2.0
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RStudio crashes when trying to import modules #723

Open pythiantech opened 4 years ago

pythiantech commented 4 years ago

This is my session info:

R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2   

And this is post loading reticulate

R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reticulate_1.14

loaded via a namespace (and not attached):
[1] compiler_3.6.2 tools_3.6.2    Rcpp_1.0.3     jsonlite_1.6.1

This is the output of py_config()

python:         /Users/dhirajkhanna/opt/anaconda3/bin/python
libpython:      /Users/dhirajkhanna/opt/anaconda3/lib/libpython3.7m.dylib
pythonhome:     /Users/dhirajkhanna/opt/anaconda3:/Users/dhirajkhanna/opt/anaconda3
version:        3.7.6 (default, Jan  8 2020, 13:42:34)  [Clang 4.0.1 (tags/RELEASE_401/final)]
numpy:          /Users/dhirajkhanna/opt/anaconda3/lib/python3.7/site-packages/numpy
numpy_version:  1.18.1

NOTE: Python version was forced by RETICULATE_PYTHON

Now when I try to open a REPL in the R session, it seems to work for operations like 2+2. However if I try to import a Python library, RStudio crashes. As soon as I start typing 'import' the crash occurs. It happens even when I am trying to type 'exit'.

I get the "Error Retrieving Help - Unable to establish connection with R session" popup. On clicking Ok, I get the "R Session Aborted" popup and RStudio crashes.

Doing the same thing in R gives me a segmentation fault. More details available here: https://stackoverflow.com/questions/59835609/trouble-loading-python-in-rstudio-with-reticulate

Heldera commented 4 years ago

Hi! I have the same problem! I have one Python file which I created from guide def add(x, y): return x + y And when I write in R: library(reticulate) source_python('add.py') I get "R Session Aborted. R encountered a fatal error. The session was terminated." without any additional info.

Heldera commented 4 years ago

I just tried to call the same combinations from RGui (64-bit) and got the message:

Error in sys$stdout$flush() attempt to apply non-function

I take a look into code and found double calling of this method (sys$stdout$flush()) at py_flush_output at R/python.R (line 1168). May it be related?

pythiantech commented 4 years ago

I am still stuck here. This is my current session info post upgrading R as well as my OS:

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.4

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3    packrat_0.5.0 

I am on reticulate version 1.15. However the crash persists.

Would appreciate some help here.

liuyigh commented 4 years ago

My workaround was to use VirtualBox to run a Linux machine for R and R Studio. Hope this can help you temporarily.

kevinushey commented 4 years ago

Ultimately, for us to be able to further diagnose we'd need a stack trace from the time when the process crashes. See https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/ for a guide on how you could get such a stack trace.

pythiantech commented 4 years ago

@kevinushey thanks for this. Went through your guide. The first thing I realized was that Anaconda had changed my path. Hence while launching R, it was launching R version 3.2 and not he one that I am using on RStudio. So I amended my path :

export PATH="/usr/local/bin:$PATH"

Now when I try to launch R with lldb attached, I am getting an error.

(lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"
Current executable set to '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).
(lldb) run
error: process exited with status -1 (Error 1)
(lldb)

I am now looking at how to fix this....

pythiantech commented 4 years ago

@kevinushey no joy on the above. Tried the vlagrind approach as explained in your article here. However, can't even install it on Catalina:

valgrind: This formula either does not compile or function as expected on macOS
versions newer than High Sierra due to an upstream incompatibility.
Error: An unsatisfied requirement failed this build.

Any suggestions?

kevinushey commented 4 years ago

Right, valgrind is unfortunately not supported on macOS anymore, as far as I can tell :-/

But lldb should work. Can you confirm that you have command line tools installed and up-to-date?

For what it's worth, it works for me:

kevinushey@Kevins-MBP:~/r/pkg/renv [master]
$ which lldb
/usr/bin/lldb
kevinushey@Kevins-MBP:~/r/pkg/renv [master]
$ R -d lldb
(lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"
Current executable set to '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64).
(lldb) run
Process 27613 launched: '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>
pythiantech commented 4 years ago

No joy whatsoever....Totally frustrated with this.

Anyway, for what its worth, on my terminal when I run which python, I get /Users/dhirajkhanna/opt/anaconda3/bin/python.

And when I run System.which('python') in R console, I get /usr/bin/python. Why should the locations of the executables be different?

@kevinushey this is the dump which is generated when I run repl_python() in R GUI and try to import any python module.

Process:               R [15248]
Path:                  /Applications/R.app/Contents/MacOS/R
Identifier:            org.R-project.R
Version:               R 3.6.3 GUI 1.70 El Capitan build (7735)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           R [15248]
User ID:               501

Date/Time:             2020-04-10 17:20:08.254 +0530
OS Version:            Mac OS X 10.15.4 (19E287)
Report Version:        12
Bridge OS Version:     3.0 (14Y908)
Anonymous UUID:        FF048770-90AF-1F29-F5AE-44C54595DD90

Sleep/Wake UUID:       902EDD78-9879-4398-85B2-1C46010A89C7

Time Awake Since Boot: 42000 seconds
Time Since Wake:       260 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       KERN_INVALID_ADDRESS at 0x0000000000000040
Exception Note:        EXC_CORPSE_NOTIFY

VM Regions Near 0x40:
--> 
    __TEXT                 0000000108dbc000-0000000108e49000 [  564K] r-x/rwx SM=COW  /Applications/R.app/Contents/MacOS/R

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libsystem_platform.dylib        0x00007fff69d5be52 _platform_strlen + 18
1   libR.dylib                      0x0000000108f7123e Rf_mkChar + 14 (envir.c:3803)
2   reticulate.so                   0x000000011a81056a SEXPREC* exception_to_condition_template<Rcpp::exception>(Rcpp::exception const&, bool) + 266
3   reticulate.so                   0x000000011a83666a _reticulate_py_call_impl.cold + 410

Thread 1:
0   libsystem_pthread.dylib         0x00007fff69d65b68 start_wqthread + 0

Thread 2:: JavaScriptCore bmalloc scavenger
0   libsystem_kernel.dylib          0x00007fff69ca9882 __psynch_cvwait + 10
1   libsystem_pthread.dylib         0x00007fff69d6a425 _pthread_cond_wait + 698
2   libc++.1.dylib                  0x00007fff66e39592 std::__1::condition_variable::wait(std::__1::unique_lock<std::__1::mutex>&) + 18
3   com.apple.JavaScriptCore        0x00007fff344140b4 void std::__1::condition_variable_any::wait<std::__1::unique_lock<bmalloc::Mutex> >(std::__1::unique_lock<bmalloc::Mutex>&) + 84
4   com.apple.JavaScriptCore        0x00007fff344188bb bmalloc::Scavenger::threadRunLoop() + 299
5   com.apple.JavaScriptCore        0x00007fff34418489 bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 9
6   com.apple.JavaScriptCore        0x00007fff3441ab67 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*) + 39
7   libsystem_pthread.dylib         0x00007fff69d6a109 _pthread_start + 148
8   libsystem_pthread.dylib         0x00007fff69d65b8b thread_start + 15

Thread 3:
0   libsystem_kernel.dylib          0x00007fff69caf0fe __select + 10
1   org.R-project.R                 0x0000000108dc0867 -[RController readThread:] + 647
2   com.apple.Foundation            0x00007fff322a9882 __NSThread__start__ + 1064
3   libsystem_pthread.dylib         0x00007fff69d6a109 _pthread_start + 148
4   libsystem_pthread.dylib         0x00007fff69d65b8b thread_start + 15

Thread 4:
0   libsystem_pthread.dylib         0x00007fff69d65b68 start_wqthread + 0

Thread 5:: com.apple.NSEventThread
0   libsystem_kernel.dylib          0x00007fff69ca6dfa mach_msg_trap + 10
1   libsystem_kernel.dylib          0x00007fff69ca7170 mach_msg + 60
2   com.apple.CoreFoundation        0x00007fff2fc1f0b5 __CFRunLoopServiceMachPort + 247
3   com.apple.CoreFoundation        0x00007fff2fc1db82 __CFRunLoopRun + 1319
4   com.apple.CoreFoundation        0x00007fff2fc1cffe CFRunLoopRunSpecific + 462
5   com.apple.AppKit                0x00007fff2d03d5b4 _NSEventThread + 132
6   libsystem_pthread.dylib         0x00007fff69d6a109 _pthread_start + 148
7   libsystem_pthread.dylib         0x00007fff69d65b8b thread_start + 15

Thread 6:
0   libsystem_pthread.dylib         0x00007fff69d65b68 start_wqthread + 0

Thread 7:
0   libsystem_pthread.dylib         0x00007fff69d65b68 start_wqthread + 0

Thread 8:
0   libsystem_kernel.dylib          0x00007fff69ca9756 __semwait_signal + 10
1   libsystem_c.dylib               0x00007fff69c2ceea nanosleep + 196
2   libsystem_c.dylib               0x00007fff69c2cde4 usleep + 53

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x00007fbfc8720d38  rbx: 0x0000000000000041  rcx: 0x0000000000000041  rdx: 0x0000000000000041
  rdi: 0x0000000000000040  rsi: 0x0000000000000016  rbp: 0x00007ffee6e36570  rsp: 0x00007ffee6e36570
   r8: 0x00000000000130a8   r9: 0x0000000000000000  r10: 0x000000011aa15a40  r11: 0x000000011aa15a38
  r12: 0x000000011a857a10  r13: 0x00007fbfc8720d38  r14: 0x00007ffee6e365e0  r15: 0x00007fbfc9811260
  rip: 0x00007fff69d5be52  rfl: 0x0000000000000202  cr2: 0x000000010919b730

Logical CPU:     0
Error Code:      0x020000b8
Trap Number:     133

Binary Images:
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       0x108ed0000 -        0x10919afff +libR.dylib (0) <CBB92189-79C4-312A-86CC-A2BC7A118EF1> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
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    0x7fff68e04000 -     0x7fff68e31ffb  libssl.46.dylib (47.100.4) <E051B5B3-F59C-30E2-BE70-6D70685F4E7C> /usr/lib/libssl.46.dylib
    0x7fff68f61000 -     0x7fff68f64ffb  libutil.dylib (57) <07ED7CF0-1744-3386-B8B2-0DDBD446999E> /usr/lib/libutil.dylib
    0x7fff68f65000 -     0x7fff68f72ff7  libxar.1.dylib (425.2) <625F24E1-1A0F-3301-9F99-F0F3DADE0287> /usr/lib/libxar.1.dylib
    0x7fff68f78000 -     0x7fff6905aff7  libxml2.2.dylib (33.3) <24147A90-E3EB-3926-BFB0-5F0FC9F706E2> /usr/lib/libxml2.2.dylib
    0x7fff6905e000 -     0x7fff69086fff  libxslt.1.dylib (16.9) <8C8648B1-F2CA-38EA-A409-D6F19715C6E6> /usr/lib/libxslt.1.dylib
    0x7fff69087000 -     0x7fff69099ff3  libz.1.dylib (76) <6A449C6A-DF88-36C1-8F2D-DB9A808263B5> /usr/lib/libz.1.dylib
    0x7fff69947000 -     0x7fff6994cff3  libcache.dylib (83) <5F90FFCE-403B-3724-991D-BA32401D99C5> /usr/lib/system/libcache.dylib
    0x7fff6994d000 -     0x7fff69958fff  libcommonCrypto.dylib (60165) <C7A5E3F7-1E5A-3785-875A-B6647082B614> /usr/lib/system/libcommonCrypto.dylib
    0x7fff69959000 -     0x7fff69960fff  libcompiler_rt.dylib (101.2) <A517E149-2D25-3C04-BCEF-F69149C85B18> /usr/lib/system/libcompiler_rt.dylib
    0x7fff69961000 -     0x7fff6996aff7  libcopyfile.dylib (166.40.1) <1A5270B5-0D97-35DA-9296-4F4A428BC6A2> /usr/lib/system/libcopyfile.dylib
    0x7fff6996b000 -     0x7fff699fdfe3  libcorecrypto.dylib (866.100.30) <FCDEC0D1-8C30-3989-BDD1-996BBC715C29> /usr/lib/system/libcorecrypto.dylib
    0x7fff69b0a000 -     0x7fff69b4aff0  libdispatch.dylib (1173.100.2) <EB592997-B11C-3AB3-85B1-F725F3D0B412> /usr/lib/system/libdispatch.dylib
    0x7fff69b4b000 -     0x7fff69b81fff  libdyld.dylib (750.5) <D2A07EF5-A64B-3692-BE13-89DAA2EC5E80> /usr/lib/system/libdyld.dylib
    0x7fff69b82000 -     0x7fff69b82ffb  libkeymgr.dylib (30) <CC5A2B43-770B-3C6C-BA10-AA3A6B4A142D> /usr/lib/system/libkeymgr.dylib
    0x7fff69b83000 -     0x7fff69b8fff3  libkxld.dylib (6153.101.6) <77282DCB-83D6-3199-874E-9A4A0FD7D4F3> /usr/lib/system/libkxld.dylib
    0x7fff69b90000 -     0x7fff69b90ff7  liblaunch.dylib (1738.100.39) <A7FF7357-600F-3014-8C28-A4F367717E8D> /usr/lib/system/liblaunch.dylib
    0x7fff69b91000 -     0x7fff69b96ff7  libmacho.dylib (959.0.1) <D8FED478-25A2-3844-AE4B-A5C9F9827615> /usr/lib/system/libmacho.dylib
    0x7fff69b97000 -     0x7fff69b99ff3  libquarantine.dylib (110.40.3) <51E0304F-AB11-3BF7-99DC-BB916CC9088B> /usr/lib/system/libquarantine.dylib
    0x7fff69b9a000 -     0x7fff69b9bff7  libremovefile.dylib (48) <078F29AB-26BA-3493-BCAA-E1E75A187521> /usr/lib/system/libremovefile.dylib
    0x7fff69b9c000 -     0x7fff69bb3ff3  libsystem_asl.dylib (377.60.2) <0F1BAC19-2AE0-3F8E-9B90-AACF819B2BF7> /usr/lib/system/libsystem_asl.dylib
    0x7fff69bb4000 -     0x7fff69bb4ff7  libsystem_blocks.dylib (74) <32224AFF-C06F-3279-B753-097194EDEF49> /usr/lib/system/libsystem_blocks.dylib
    0x7fff69bb5000 -     0x7fff69c3cfff  libsystem_c.dylib (1353.100.2) <4F5EED22-4D46-3F04-8C64-C492CDAD70EB> /usr/lib/system/libsystem_c.dylib
    0x7fff69c3d000 -     0x7fff69c40ffb  libsystem_configuration.dylib (1061.101.1) <2A2C778D-07EB-35C7-A954-8BF8FD74BD75> /usr/lib/system/libsystem_configuration.dylib
    0x7fff69c41000 -     0x7fff69c44fff  libsystem_coreservices.dylib (114) <FDA41CC4-170A-3D93-85BD-838A563B03C4> /usr/lib/system/libsystem_coreservices.dylib
    0x7fff69c45000 -     0x7fff69c4dfff  libsystem_darwin.dylib (1353.100.2) <B567B86D-8818-38A4-A861-03EB83B55867> /usr/lib/system/libsystem_darwin.dylib
    0x7fff69c4e000 -     0x7fff69c55fff  libsystem_dnssd.dylib (1096.100.3) <7C690DF5-E119-33FB-85CD-9EFC67A36E40> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff69c56000 -     0x7fff69c57ffb  libsystem_featureflags.dylib (17) <415D83EF-084C-3485-B757-53001870EA94> /usr/lib/system/libsystem_featureflags.dylib
    0x7fff69c58000 -     0x7fff69ca5ff7  libsystem_info.dylib (538) <17049D3F-C798-3651-B391-1551FC699D3E> /usr/lib/system/libsystem_info.dylib
    0x7fff69ca6000 -     0x7fff69cd2ff7  libsystem_kernel.dylib (6153.101.6) <E76440E1-D1E8-3D9A-8B47-D01F554FF1C4> /usr/lib/system/libsystem_kernel.dylib
    0x7fff69cd3000 -     0x7fff69d1afff  libsystem_m.dylib (3178) <74741FA8-5C29-3241-9046-4FC91C6A6D4A> /usr/lib/system/libsystem_m.dylib
    0x7fff69d1b000 -     0x7fff69d42fff  libsystem_malloc.dylib (283.100.5) <97833239-2F83-3AEB-A426-0593997C8A54> /usr/lib/system/libsystem_malloc.dylib
    0x7fff69d43000 -     0x7fff69d50ffb  libsystem_networkextension.dylib (1095.100.29) <C9E988B2-6A18-35C0-9577-63201E9D6018> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff69d51000 -     0x7fff69d5aff7  libsystem_notify.dylib (241.100.2) <E405F84B-BD4F-3874-9755-CB3EC86E18D5> /usr/lib/system/libsystem_notify.dylib
    0x7fff69d5b000 -     0x7fff69d63fef  libsystem_platform.dylib (220.100.1) <6EF12F34-C33F-36BF-9A9A-2A35EA19EFE0> /usr/lib/system/libsystem_platform.dylib
    0x7fff69d64000 -     0x7fff69d6efff  libsystem_pthread.dylib (416.100.3) <A8514582-E000-3854-911A-0A73D2C79600> /usr/lib/system/libsystem_pthread.dylib
    0x7fff69d6f000 -     0x7fff69d73ff3  libsystem_sandbox.dylib (1217.101.2) <E9D78CDE-FB67-32E7-BABC-9EFC23AA0DC6> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff69d74000 -     0x7fff69d76fff  libsystem_secinit.dylib (62.100.2) <AAC639E5-7103-3366-A602-8FC6944E2C13> /usr/lib/system/libsystem_secinit.dylib
    0x7fff69d77000 -     0x7fff69d7effb  libsystem_symptoms.dylib (1238.100.26) <487B92DE-45F9-39F9-A478-89BBD478157D> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff69d7f000 -     0x7fff69d95ff2  libsystem_trace.dylib (1147.100.8) <BB90B1FD-8C09-3DF4-BD8B-9E4AEADFEA2B> /usr/lib/system/libsystem_trace.dylib
    0x7fff69d97000 -     0x7fff69d9cff7  libunwind.dylib (35.4) <CC87C836-BE9D-334E-A0E6-0297D52E9D73> /usr/lib/system/libunwind.dylib
    0x7fff69d9d000 -     0x7fff69dd2ffe  libxpc.dylib (1738.100.39) <32B0E31E-9DA3-328B-A962-BC9591B93537> /usr/lib/system/libxpc.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 145511
    thread_create: 0
    thread_set_state: 33

VM Region Summary:
ReadOnly portion of Libraries: Total=805.0M resident=0K(0%) swapped_out_or_unallocated=805.0M(100%)
Writable regions: Total=2.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.1G(100%)

                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               256K        2 
Activity Tracing                   256K        1 
CG backing stores                 35.0M        3 
CG image                          1432K       16 
CoreAnimation                     66.8M       42 
CoreGraphics                         8K        1 
CoreImage                          612K       21 
CoreUI image data                 1376K       14 
Foundation                          24K        2 
Image IO                           368K       13 
JS JIT generated code              1.0G        3 
JS VM Isolated Heap                 40K        2 
Kernel Alloc Once                    8K        1 
MALLOC                           476.0M      189 
MALLOC guard page                   32K        7 
MALLOC_LARGE (reserved)            356K        2         reserved VM address space (unallocated)
MALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)
Memory Tag 242                      12K        1 
SQLite page cache                   64K        1 
STACK GUARD                       56.0M        9 
Stack                             12.1M        9 
VM_ALLOCATE                       8592K       52 
VM_ALLOCATE (reserved)            96.0M        1         reserved VM address space (unallocated)
WebKit Malloc                     7272K        9 
__DATA                            45.5M      466 
__DATA_CONST                        45K        4 
__FONT_DATA                          4K        1 
__LINKEDIT                       397.2M       60 
__OBJC_RO                         32.2M        1 
__OBJC_RW                         1892K        2 
__TEXT                           407.7M      437 
__UNICODE                          564K        1 
mapped file                      284.3M       51 
shared memory                      636K       14 
===========                     =======  ======= 
TOTAL                              3.3G     1439 
TOTAL, minus reserved VM space     2.8G     1439 

Model: MacBookPro14,3, BootROM 205.0.0.0.0, 4 processors, Quad-Core Intel Core i7, 2.8 GHz, 16 GB, SMC 2.45f3
Graphics: kHW_IntelHDGraphics630Item, Intel HD Graphics 630, spdisplays_builtin
Graphics: kHW_AMDRadeonPro555Item, Radeon Pro 555, spdisplays_pcie_device, 2 GB
Memory Module: BANK 0/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320
Memory Module: BANK 1/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x173), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1600.4)
Bluetooth: Version 7.0.4f6, 3 services, 18 devices, 1 incoming serial ports
Network Service: Apple USB Ethernet Adapter, Ethernet, en5
Network Service: USB 10/100/1000 LAN, Ethernet, en8
Network Service: Wi-Fi, AirPort, en0
Network Service: Thunderbolt Bridge, Ethernet, bridge0
USB Device: USB 3.0 Bus
USB Device: Apple T1 Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 41.4
Thunderbolt Bus: MacBook Pro, Apple Inc., 41.4

Does this help?

kevinushey commented 4 years ago

It does -- the error seems to indicate the crash is coming from the Rcpp bits included in reticulate:

0   libsystem_platform.dylib        0x00007fff69d5be52 _platform_strlen + 18
1   libR.dylib                      0x0000000108f7123e Rf_mkChar + 14 (envir.c:3803)
2   reticulate.so                   0x000000011a81056a SEXPREC* exception_to_condition_template<Rcpp::exception>(Rcpp::exception const&, bool) + 266
3   reticulate.so                   0x000000011a83666a _reticulate_py_call_impl.cold + 410

I'll see if I can learn more about what's going on...

kevinushey commented 4 years ago

Are you able to reproduce with a clean re-install of both Rcpp and reticulate? E.g.

install.packages("Rcpp")
install.packages("reticulate")
reticulate::import("sys")
kevinushey commented 4 years ago

It would also help if you installed reticulate with debug symbols enabled so we could get a better backtrace.

pythiantech commented 4 years ago

@kevinushey thanks for this! A clean install of Rcpp and reticulate seems to have worked. No crashes so far!

In case I run into problems, how do I install reticulate with debug symbols enabled?

pythiantech commented 4 years ago

And I am back, with yet another crash :(. Did all the steps as mentioned above, but again getting the same crash. Here's the crash report. Looks like something to do with libstd++6.dylib

Process:               R [16693]
Path:                  /Applications/R.app/Contents/MacOS/R
Identifier:            org.R-project.R
Version:               R 3.6.3 GUI 1.70 El Capitan build (7735)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           R [16693]
User ID:               501

Date/Time:             2020-06-14 08:16:11.495 +0530
OS Version:            Mac OS X 10.15.5 (19F101)
Report Version:        12
Bridge OS Version:     3.0 (14Y908)
Anonymous UUID:        FF048770-90AF-1F29-F5AE-44C54595DD90

Sleep/Wake UUID:       D06B7CE2-83E4-435A-A965-1053760A3227

Time Awake Since Boot: 9900 seconds
Time Since Wake:       1600 seconds

System Integrity Protection: enabled

Crashed Thread:        0  Dispatch queue: com.apple.main-thread

Exception Type:        EXC_BAD_ACCESS (SIGSEGV)
Exception Codes:       EXC_I386_GPFLT
Exception Note:        EXC_CORPSE_NOTIFY

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0   libstdc++.6.dylib               0x000000011aaf0a3a d_demangle_callback.constprop.0 + 26

Thread 1:
0   libsystem_pthread.dylib         0x00007fff704d3b68 start_wqthread + 0

Thread 2:: JavaScriptCore bmalloc scavenger
0   libsystem_kernel.dylib          0x00007fff70417882 __psynch_cvwait + 10
1   libsystem_pthread.dylib         0x00007fff704d8425 _pthread_cond_wait + 698
2   libc++.1.dylib                  0x00007fff6d5a7592 std::__1::condition_variable::wait(std::__1::unique_lock<std::__1::mutex>&) + 18
3   com.apple.JavaScriptCore        0x00007fff3aad3224 void std::__1::condition_variable_any::wait<std::__1::unique_lock<bmalloc::Mutex> >(std::__1::unique_lock<bmalloc::Mutex>&) + 84
4   com.apple.JavaScriptCore        0x00007fff3aad7a2b bmalloc::Scavenger::threadRunLoop() + 299
5   com.apple.JavaScriptCore        0x00007fff3aad75f9 bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 9
6   com.apple.JavaScriptCore        0x00007fff3aad9cd7 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*) + 39
7   libsystem_pthread.dylib         0x00007fff704d8109 _pthread_start + 148
8   libsystem_pthread.dylib         0x00007fff704d3b8b thread_start + 15

Thread 3:
0   libsystem_kernel.dylib          0x00007fff7041d0fe __select + 10
1   org.R-project.R                 0x000000010e5fb867 -[RController readThread:] + 647
2   com.apple.Foundation            0x00007fff389677a2 __NSThread__start__ + 1064
3   libsystem_pthread.dylib         0x00007fff704d8109 _pthread_start + 148
4   libsystem_pthread.dylib         0x00007fff704d3b8b thread_start + 15

Thread 4:: com.apple.NSEventThread
0   libsystem_kernel.dylib          0x00007fff70414dfa mach_msg_trap + 10
1   libsystem_kernel.dylib          0x00007fff70415170 mach_msg + 60
2   com.apple.CoreFoundation        0x00007fff362d8f85 __CFRunLoopServiceMachPort + 247
3   com.apple.CoreFoundation        0x00007fff362d7a52 __CFRunLoopRun + 1319
4   com.apple.CoreFoundation        0x00007fff362d6ece CFRunLoopRunSpecific + 462
5   com.apple.AppKit                0x00007fff336ef144 _NSEventThread + 132
6   libsystem_pthread.dylib         0x00007fff704d8109 _pthread_start + 148
7   libsystem_pthread.dylib         0x00007fff704d3b8b thread_start + 15

Thread 5:
0   libsystem_pthread.dylib         0x00007fff704d3b68 start_wqthread + 0

Thread 6:
0   libsystem_kernel.dylib          0x00007fff70417756 __semwait_signal + 10
1   libsystem_c.dylib               0x00007fff7039aeea nanosleep + 196
2   libsystem_c.dylib               0x00007fff7039ade4 usleep + 53
3   reticulate.so                   0x000000011ae66062 eventPollingWorker + 66 (event_loop.cpp:106)
4   reticulate.so                   0x000000011ae66301 tthread::thread::wrapper_function(void*) + 17 (tinythread.h:874)
5   libsystem_pthread.dylib         0x00007fff704d8109 _pthread_start + 148
6   libsystem_pthread.dylib         0x00007fff704d3b8b thread_start + 15

Thread 7:
0   libsystem_pthread.dylib         0x00007fff704d3b68 start_wqthread + 0

Thread 8:
0   libsystem_pthread.dylib         0x00007fff704d3b68 start_wqthread + 0

Thread 0 crashed with X86 Thread State (64-bit):
  rax: 0x000000011ae8e640  rbx: 0x00007ffee15f78cc  rcx: 0x00007ffee15f78cc  rdx: 0x00007ffee15f7870
  rdi: 0x3970706352344e22  rsi: 0x000000011aae72c0  rbp: 0x00007ffee15f7860  rsp: 0x00007ffee15f7630
   r8: 0x0000000000024951   r9: 0xffffffff00000000  r10: 0x00007fff965a6c00  r11: 0x00007ffdc6773b81
  r12: 0x3970706352344e22  r13: 0x00007ffee15f7870  r14: 0x0000000000000001  r15: 0x00007ff05fc7c0f0
  rip: 0x000000011aaf0a3a  rfl: 0x0000000000000206  cr2: 0x000000010e9d3730

Logical CPU:     0
Error Code:      0x020000b8
Trap Number:     133

Binary Images:
       0x10e5f7000 -        0x10e683ff3 +org.R-project.R (R 3.6.3 GUI 1.70 El Capitan build - 7735) <8EFEC130-9D72-3B6C-9C52-901B712071C5> /Applications/R.app/Contents/MacOS/R
       0x10e708000 -        0x10e9d2fff +libR.dylib (0) <CBB92189-79C4-312A-86CC-A2BC7A118EF1> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
       0x10eb96000 -        0x10ebc0ff7 +libRblas.dylib (0) <CEB0747F-EC57-3430-A81F-E229A6C8B7BC> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.dylib
       0x10ebca000 -        0x10ece9fff +libgfortran.3.dylib (0) <53830B74-39EA-3EA7-8673-3CC9F041F6B7> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib
       0x10ed56000 -        0x10ed8dfe7 +libquadmath.0.dylib (0) <F6B458A7-8193-3831-B86E-DD832A5A19BE> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib
       0x10eda3000 -        0x10edcdfd9 +libreadline.5.2.dylib (5.2) /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib
       0x10ede1000 -        0x10ee49fff +libomp.dylib (0) <5F2A02FB-2D20-3D6C-BEEE-40CA5EE3618C> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libomp.dylib
       0x10ee77000 -        0x10ee8cfef +libgcc_s.1.dylib (0) <20CA2D94-AB72-312A-ADD8-7912FE2574A0> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib
       0x1114ef000 -        0x1114f2047  libobjc-trampolines.dylib (787.1) <8212B354-A106-3806-A022-A60F2B2FA5C9> /usr/lib/libobjc-trampolines.dylib
       0x117aaf000 -        0x117aafffb +_move.cpython-37m-darwin.so (0) <9F92A2B0-79E4-3647-901D-37ECBF8387FE> /Users/USER/*/_move.cpython-37m-darwin.so
       0x117b85000 -        0x117b8afff +methods.so (0) <9AB137EF-2749-336A-9FF8-CE4B6C2BDEF8> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/methods/libs/methods.so
       0x117b90000 -        0x117b98ff3 +utils.so (0) <7F0723F4-14BF-3D15-9671-FE4D95E6703B> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/utils/libs/utils.so
       0x117b9f000 -        0x117bd3ff3 +grDevices.so (0) <7D3907E3-3D6C-3B80-AC07-8F4FA66C1454> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/grDevices/libs/grDevices.so
       0x117bee000 -        0x117c27ff7 +graphics.so (0) <5E8E9899-C97B-3E86-90D3-84D0460F50E1> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/graphics/libs/graphics.so
       0x1199c5000 -        0x119a6ffff +stats.so (0) <AB5F99E8-5777-3707-9D66-6C5C9419309A> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/stats/libs/stats.so
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    0x7fff6f7f5000 -     0x7fff6f807ff3  libz.1.dylib (76) <DB120508-3BED-37A8-B439-5235EAB4618A> /usr/lib/libz.1.dylib
    0x7fff700b5000 -     0x7fff700baff3  libcache.dylib (83) <A5ECC751-A681-30D8-B33C-D192C15D25C8> /usr/lib/system/libcache.dylib
    0x7fff700bb000 -     0x7fff700c6fff  libcommonCrypto.dylib (60165.120.1) <C321A74A-AA91-3785-BEBF-BEDC6975026C> /usr/lib/system/libcommonCrypto.dylib
    0x7fff700c7000 -     0x7fff700cefff  libcompiler_rt.dylib (101.2) <652A6012-7E5C-3F4F-9438-86BC094526F3> /usr/lib/system/libcompiler_rt.dylib
    0x7fff700cf000 -     0x7fff700d8ff7  libcopyfile.dylib (166.40.1) <40113A69-A81C-3397-ADC6-1D16B9A22C3E> /usr/lib/system/libcopyfile.dylib
    0x7fff700d9000 -     0x7fff7016bfe3  libcorecrypto.dylib (866.120.3) <5E4B0E50-24DD-3E04-9374-EDA9FFD6257B> /usr/lib/system/libcorecrypto.dylib
    0x7fff70278000 -     0x7fff702b8ff0  libdispatch.dylib (1173.100.2) <201EDBF3-0B36-31BA-A7CB-443CE35C05D4> /usr/lib/system/libdispatch.dylib
    0x7fff702b9000 -     0x7fff702effff  libdyld.dylib (750.5) <7E711A46-5E4D-393C-AEA6-440E2A5CCD0C> /usr/lib/system/libdyld.dylib
    0x7fff702f0000 -     0x7fff702f0ffb  libkeymgr.dylib (30) <52662CAA-DB1F-30A3-BE13-D6274B1A6D7B> /usr/lib/system/libkeymgr.dylib
    0x7fff702f1000 -     0x7fff702fdff3  libkxld.dylib (6153.121.2) <5EBB4886-C7B6-31D6-AA63-D861B2D58FCE> /usr/lib/system/libkxld.dylib
    0x7fff702fe000 -     0x7fff702feff7  liblaunch.dylib (1738.120.8) <07CF647B-F9DC-3907-AD98-2F85FCB34A72> /usr/lib/system/liblaunch.dylib
    0x7fff702ff000 -     0x7fff70304ff7  libmacho.dylib (959.0.1) <D91DFF00-E22F-3796-8A1C-4C1F5F8FA03C> /usr/lib/system/libmacho.dylib
    0x7fff70305000 -     0x7fff70307ff3  libquarantine.dylib (110.40.3) <D3B7D02C-7646-3FB4-8529-B36DCC2419EA> /usr/lib/system/libquarantine.dylib
    0x7fff70308000 -     0x7fff70309ff7  libremovefile.dylib (48) <B5E88D9B-C2BE-3496-BBB2-C996317E18A3> /usr/lib/system/libremovefile.dylib
    0x7fff7030a000 -     0x7fff70321ff3  libsystem_asl.dylib (377.60.2) <1170348D-2491-33F1-AA79-E2A05B4A287C> /usr/lib/system/libsystem_asl.dylib
    0x7fff70322000 -     0x7fff70322ff7  libsystem_blocks.dylib (74) <7AFBCAA6-81BE-36C3-8DB0-AAE0A4ACE4C5> /usr/lib/system/libsystem_blocks.dylib
    0x7fff70323000 -     0x7fff703aafff  libsystem_c.dylib (1353.100.2) <935DDCE9-4ED0-3F79-A05A-A123DDE399CC> /usr/lib/system/libsystem_c.dylib
    0x7fff703ab000 -     0x7fff703aeffb  libsystem_configuration.dylib (1061.120.2) <EA9BC2B1-5001-3463-9FAF-39FF61CAC87C> /usr/lib/system/libsystem_configuration.dylib
    0x7fff703af000 -     0x7fff703b2fff  libsystem_coreservices.dylib (114) <3D0A3AA8-8415-37B2-AAE3-66C03BCE8B55> /usr/lib/system/libsystem_coreservices.dylib
    0x7fff703b3000 -     0x7fff703bbfff  libsystem_darwin.dylib (1353.100.2) <6EEC9975-EE3B-3C95-AA5B-030FD10587BC> /usr/lib/system/libsystem_darwin.dylib
    0x7fff703bc000 -     0x7fff703c3fff  libsystem_dnssd.dylib (1096.100.3) <0115092A-E61B-317D-8670-41C7C34B1A82> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff703c4000 -     0x7fff703c5ffb  libsystem_featureflags.dylib (17) <AFDB5095-0472-34AC-BA7E-497921BF030A> /usr/lib/system/libsystem_featureflags.dylib
    0x7fff703c6000 -     0x7fff70413ff7  libsystem_info.dylib (538) <851693E9-C079-3547-AD41-353F8C248BE8> /usr/lib/system/libsystem_info.dylib
    0x7fff70414000 -     0x7fff70440ff7  libsystem_kernel.dylib (6153.121.2) <9F9902C9-A46F-3CA9-B7F9-5CCFE98FBF75> /usr/lib/system/libsystem_kernel.dylib
    0x7fff70441000 -     0x7fff70488fff  libsystem_m.dylib (3178) <436CFF76-6A99-36F2-A3B6-8D017396A050> /usr/lib/system/libsystem_m.dylib
    0x7fff70489000 -     0x7fff704b0fff  libsystem_malloc.dylib (283.100.6) <D4BA7DF2-57AC-33B0-B948-A688EE43C799> /usr/lib/system/libsystem_malloc.dylib
    0x7fff704b1000 -     0x7fff704beffb  libsystem_networkextension.dylib (1095.120.6) <6DE86DB0-8CD2-361E-BD6A-A34282B47847> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff704bf000 -     0x7fff704c8ff7  libsystem_notify.dylib (241.100.2) <7E9E2FC8-DF26-340C-B196-B81B11850C46> /usr/lib/system/libsystem_notify.dylib
    0x7fff704c9000 -     0x7fff704d1fef  libsystem_platform.dylib (220.100.1) <736920EA-6AE0-3B1B-BBDA-7DCDF0C229DF> /usr/lib/system/libsystem_platform.dylib
    0x7fff704d2000 -     0x7fff704dcfff  libsystem_pthread.dylib (416.100.3) <77488669-19A3-3993-AD65-CA5377E2475A> /usr/lib/system/libsystem_pthread.dylib
    0x7fff704dd000 -     0x7fff704e1ff3  libsystem_sandbox.dylib (1217.120.7) <20C93D69-6452-3C82-9521-8AE54345C66F> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff704e2000 -     0x7fff704e4fff  libsystem_secinit.dylib (62.100.2) <E851113D-D5B1-3FB0-9D29-9C7647A71961> /usr/lib/system/libsystem_secinit.dylib
    0x7fff704e5000 -     0x7fff704ecffb  libsystem_symptoms.dylib (1238.120.1) <25C3866B-004E-3621-9CD3-B1E9C4D887EB> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff704ed000 -     0x7fff70503ff2  libsystem_trace.dylib (1147.120) <A1ED1D3A-5FAD-3559-A1D6-1BE4E1C5756A> /usr/lib/system/libsystem_trace.dylib
    0x7fff70505000 -     0x7fff7050aff7  libunwind.dylib (35.4) <253A12E2-F88F-3838-A666-C5306F833CB8> /usr/lib/system/libunwind.dylib
    0x7fff7050b000 -     0x7fff70540ffe  libxpc.dylib (1738.120.8) <68D433B6-DCFF-385D-8620-F847FB7D4A5A> /usr/lib/system/libxpc.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 37546
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=973.6M resident=0K(0%) swapped_out_or_unallocated=973.6M(100%)
Writable regions: Total=1.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.9G(100%)

                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               384K        3 
Activity Tracing                   256K        1 
CG backing stores                 35.0M        3 
CG image                          1380K       11 
CoreAnimation                     70.2M       31 
CoreGraphics                         8K        1 
CoreImage                          320K       13 
CoreUI image data                 1076K       11 
Foundation                          28K        2 
Image IO                           384K       15 
JS JIT generated code              1.0G        3 
JS VM Isolated Heap                 40K        2 
Kernel Alloc Once                    8K        1 
MALLOC                           458.9M      290 
MALLOC guard page                   32K        7 
MALLOC_LARGE (reserved)            356K        2         reserved VM address space (unallocated)
MALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)
Memory Tag 242                      12K        1 
Memory Tag 251                      24K        2 
SQLite page cache                   64K        1 
STACK GUARD                       56.0M        9 
Stack                             12.1M        9 
VM_ALLOCATE                        144K       19 
WebKit Malloc                     7272K        9 
__DATA                            50.4M      581 
__DATA_CONST                        85K        5 
__FONT_DATA                          4K        1 
__LINKEDIT                       417.7M      136 
__OBJC_RO                         32.2M        1 
__OBJC_RW                         1892K        2 
__TEXT                           555.9M      513 
__UNICODE                          564K        1 
mapped file                      284.7M       51 
shared memory                      636K       14 
===========                     =======  ======= 
TOTAL                              3.3G     1752 
TOTAL, minus reserved VM space     2.9G     1752 

Model: MacBookPro14,3, BootROM 207.0.0.0.0, 4 processors, Quad-Core Intel Core i7, 2.8 GHz, 16 GB, SMC 2.45f4
Graphics: kHW_IntelHDGraphics630Item, Intel HD Graphics 630, spdisplays_builtin
Graphics: kHW_AMDRadeonPro555Item, Radeon Pro 555, spdisplays_pcie_device, 2 GB
Memory Module: BANK 0/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320
Memory Module: BANK 1/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x173), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1610.1)
Bluetooth: Version 7.0.5f6, 3 services, 18 devices, 1 incoming serial ports
Network Service: Apple USB Ethernet Adapter, Ethernet, en5
Network Service: USB 10/100/1000 LAN, Ethernet, en8
Network Service: Wi-Fi, AirPort, en0
Network Service: Thunderbolt Bridge, Ethernet, bridge0
USB Device: USB 3.0 Bus
USB Device: Apple T1 Controller
Thunderbolt Bus: MacBook Pro, Apple Inc., 41.4
Thunderbolt Bus: MacBook Pro, Apple Inc., 41.4
pythiantech commented 4 years ago

I have tried reinstalling reticulate both from CRAN as well as the dev version. No joy.

kevinushey commented 4 years ago

The fact that the crash is occurring in libstdc++.6.dylib is weird, since R on macOS typically uses libc++ (since things are compiled by clang instead of gcc).

Any idea what might be going on there?

pythiantech commented 4 years ago

Drawing a complete blank here. Open to suggestions.

systats commented 4 years ago

Somehow putting the code as Rstudio Job fixes this issue for me: rstudioapi::jobRunScript("job_keras.R", workingDir = ".")

pythiantech commented 3 years ago

After hearing so many good things about how people are using Python and R together, I tried giving this another shot. No joy again :(

Here's my latest session info:

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5      digest_0.6.27   later_1.1.0.1   mime_0.9        R6_2.5.0        xtable_1.8-4    magrittr_2.0.1 
 [8] evaluate_0.14   rlang_0.4.9     promises_1.1.1  rmarkdown_2.5   tools_4.0.2     shiny_1.5.0     fastmap_1.0.1  
[15] httpuv_1.5.4    xfun_0.19       yaml_2.2.1      compiler_4.0.2  htmltools_0.5.0 knitr_1.30     

And here's the latest crash report:

Process:               R [9133]
Path:                  /Applications/R.app/Contents/MacOS/R
Identifier:            org.R-project.R
Version:               R for R 4.0.2 GUI 1.72 Catalina build (7847)
Code Type:             X86-64 (Native)
Parent Process:        ??? [1]
Responsible:           R [9133]
User ID:               501

Date/Time:             2020-12-12 17:50:12.725 +0530
OS Version:            Mac OS X 10.15.7 (19H15)
Report Version:        12
Bridge OS Version:     3.0 (14Y908)
Anonymous UUID:        FF048770-90AF-1F29-F5AE-44C54595DD90

Sleep/Wake UUID:       17203DA1-788D-4E33-9C01-483ED7E11FC6

Time Awake Since Boot: 28000 seconds
Time Since Wake:       9200 seconds

System Integrity Protection: enabled

Crashed Thread:        Unknown

Exception Type:        EXC_BAD_ACCESS (Code Signature Invalid)
Exception Codes:       0x0000000000000032, 0x000000010c5ff000
Exception Note:        EXC_CORPSE_NOTIFY

Termination Reason:    Namespace CODESIGNING, Code 0x2

kernel messages:

VM Regions Near 0x10c5ff000:
    VM_ALLOCATE            000000010c5fe000-000000010c5ff000 [    4K] rwx/rwx SM=PRV  
--> mapped file            000000010c5ff000-000000010c600000 [    4K] r--/r-x SM=PRV  
    CoreAnimation          000000010c600000-000000010c646000 [  280K] rw-/rwx SM=PRV  

Application Specific Information:
dyld: in dlopen()
/Users/dhirajkhanna/opt/anaconda3/lib/libmkl_intel_thread.dylib

Thread 0:
0   libsystem_pthread.dylib         0x00007fff71b8cb68 start_wqthread + 0

Thread 1:: JavaScriptCore bmalloc scavenger
0   libsystem_kernel.dylib          0x00007fff71ad0882 __psynch_cvwait + 10
1   libsystem_pthread.dylib         0x00007fff71b91425 _pthread_cond_wait + 698
2   libc++.1.dylib                  0x00007fff6ec5f592 std::__1::condition_variable::wait(std::__1::unique_lock<std::__1::mutex>&) + 18
3   com.apple.JavaScriptCore        0x00007fff3c11a274 void std::__1::condition_variable_any::wait<std::__1::unique_lock<bmalloc::Mutex> >(std::__1::unique_lock<bmalloc::Mutex>&) + 84
4   com.apple.JavaScriptCore        0x00007fff3c11ea7b bmalloc::Scavenger::threadRunLoop() + 299
5   com.apple.JavaScriptCore        0x00007fff3c11e649 bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 9
6   com.apple.JavaScriptCore        0x00007fff3c120d27 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*) + 39
7   libsystem_pthread.dylib         0x00007fff71b91109 _pthread_start + 148
8   libsystem_pthread.dylib         0x00007fff71b8cb8b thread_start + 15

Thread 2:
0   libsystem_kernel.dylib          0x00007fff71ad60fe __select + 10
1   org.R-project.R                 0x00000001078e3960 -[RController readThread:] + 512
2   com.apple.Foundation            0x00007fff39fae7a2 __NSThread__start__ + 1064
3   libsystem_pthread.dylib         0x00007fff71b91109 _pthread_start + 148
4   libsystem_pthread.dylib         0x00007fff71b8cb8b thread_start + 15

Thread 3:: Dispatch queue: com.apple.root.default-qos.overcommit
0   libdispatch.dylib               0x00007fff7194e51f _dispatch_kq_drain + 116
1   libdispatch.dylib               0x00007fff7194e455 _dispatch_event_loop_drain + 297
2   libdispatch.dylib               0x00007fff71945460 _dispatch_source_invoke + 1990
3   libdispatch.dylib               0x00007fff71942c09 _dispatch_workloop_worker_thread + 596
4   libsystem_pthread.dylib         0x00007fff71b8da3d _pthread_wqthread + 290
5   libsystem_pthread.dylib         0x00007fff71b8cb77 start_wqthread + 15

Thread 4:: com.apple.NSEventThread
0   libsystem_kernel.dylib          0x00007fff71acddfa mach_msg_trap + 10
1   libsystem_kernel.dylib          0x00007fff71ace170 mach_msg + 60
2   com.apple.CoreFoundation        0x00007fff3791cef5 __CFRunLoopServiceMachPort + 247
3   com.apple.CoreFoundation        0x00007fff3791b9c2 __CFRunLoopRun + 1319
4   com.apple.CoreFoundation        0x00007fff3791ae3e CFRunLoopRunSpecific + 462
5   com.apple.AppKit                0x00007fff34d2e954 _NSEventThread + 132
6   libsystem_pthread.dylib         0x00007fff71b91109 _pthread_start + 148
7   libsystem_pthread.dylib         0x00007fff71b8cb8b thread_start + 15

Thread 5:
0   libsystem_pthread.dylib         0x00007fff71b8cb68 start_wqthread + 0

Unknown thread crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000000  rbx: 0x000000010c5ff000  rcx: 0x0000000000000000  rdx: 0x0000000000000818
  rdi: 0x000000010c5ff000  rsi: 0x00007ffee8308630  rbp: 0x00007ffee8308010  rsp: 0x00007ffee8308010
   r8: 0x000000000000000f   r9: 0x0000000000000000  r10: 0x0000000000000001  r11: 0x0000000000000202
  r12: 0x0000000000000000  r13: 0x000000000000000f  r14: 0x0000000000000818  r15: 0x00006000036ad5c0
  rip: 0x00000001178be450  rfl: 0x0000000000010246  cr2: 0x000000010c5ff000

Logical CPU:     0
Error Code:      0x00000004 (no mapping for user data read)
Trap Number:     14

Binary Images:
       0x1078df000 -        0x107966ffb +org.R-project.R (R for R 4.0.2 GUI 1.72 Catalina build - 7847) <0A358543-3A28-3D0C-AF38-A3820070A210> /Applications/R.app/Contents/MacOS/R
       0x1079f1000 -        0x107cf8ff7 +libR.dylib (0) <583EA0D6-DFEF-39EC-A783-AB5362181407> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib
       0x107ee2000 -        0x107f0afff +libRblas.dylib (0) <FE8F45A3-8DD0-37AB-B105-2945C1CB87E7> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
       0x107f15000 -        0x108146fef +libgfortran.5.dylib (0) <5B0F7278-9D16-3B60-A413-59EEF538E568> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib
       0x1081cf000 -        0x108207fff +libquadmath.0.dylib (0) <856F3E97-EECB-3DDE-AF45-56AEA7758A1E> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib
       0x10821c000 -        0x108231fef +libgcc_s.1.dylib (1) <C1F47CA1-564E-36B8-BE6F-7A5FDD88E2C6> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib
       0x10a8c6000 -        0x10a8c9047  libobjc-trampolines.dylib (787.1) <88F9B648-C455-36F8-BBB9-7D1A9F57D073> /usr/lib/libobjc-trampolines.dylib
       0x10c5c6000 -        0x10c5e1ff7 +grid.so (0) <133E3D50-426F-38FC-ACB9-30823F047879> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/grid/libs/grid.so
       0x10c5f4000 -        0x10c5f6ff3 +lattice.so (0) <0995EB7B-B1EC-3944-9717-9D164DDBC55E> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/lattice/libs/lattice.so
       0x10c6c5000 -        0x10c6d0ff7 +jsonlite.so (0) <86EE68B7-CD49-3740-8F5F-FD3E2D846019> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/jsonlite/libs/jsonlite.so
       0x10e949000 -        0x10e94afff +_heapq.cpython-37m-darwin.so (0) <40FDE5CF-54CD-3798-AEA2-2C6BF3F554B6> /Users/USER/*/_heapq.cpython-37m-darwin.so
       0x10e94e000 -        0x10e953fff +libffi.6.dylib (0) <0E5DEF5D-B75C-3B8F-9D37-FA945A5D9035> /Users/USER/*/libffi.6.dylib
       0x10e957000 -        0x10e958ff3 +_mklinit.cpython-37m-darwin.so (0) <7A2282D1-662D-3389-BC70-CADE31B8FBA8> /Users/USER/*/_mklinit.cpython-37m-darwin.so
       0x10e95b000 -        0x10e95cfff +_posixsubprocess.cpython-37m-darwin.so (0) <FBD34B39-CCE7-36A1-82EA-1B6C1324C94B> /Users/USER/*/_posixsubprocess.cpython-37m-darwin.so
       0x10ea1c000 -        0x10ea21ff7 +methods.so (0) <0F3E383F-C576-3189-AA08-B332F2BFCE45> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/methods/libs/methods.so
       0x10ea2c000 -        0x10ea34ff3 +utils.so (0) <B7190B64-F372-3A53-8C1D-53277C0A54AA> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/utils/libs/utils.so
       0x10ea3f000 -        0x10ea73ff7 +grDevices.so (0) <69152EF8-73F3-399C-9412-4E328387FE64> /Library/Frameworks/R.framework/Versions/4.0/Resources/library/grDevices/libs/grDevices.so
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    0x7fff6f599000 -     0x7fff6f5f8ff7  libcups.2.dylib (483.6) <C88D78FE-D238-376C-B16A-39270E39A79D> /usr/lib/libcups.2.dylib
    0x7fff6f5fa000 -     0x7fff6f65fff7  libcurl.4.dylib (118.120.2) <28809E22-6EF2-3AC7-9501-D77FB6FC5FBD> /usr/lib/libcurl.4.dylib
    0x7fff6f702000 -     0x7fff6f702fff  libenergytrace.dylib (21) <162DFCC0-8F48-3DD0-914F-FA8653E27B26> /usr/lib/libenergytrace.dylib
    0x7fff6f703000 -     0x7fff6f71bfff  libexpat.1.dylib (19.60.2) <FED7C38B-92D8-342D-AED7-871B12D1F7E7> /usr/lib/libexpat.1.dylib
    0x7fff6f729000 -     0x7fff6f72bfff  libfakelink.dylib (149.1) <36146CB2-E6A5-37BB-9EE8-1B4034D8F3AD> /usr/lib/libfakelink.dylib
    0x7fff6f73a000 -     0x7fff6f73ffff  libgermantok.dylib (24) <D2AE5AC0-EDCE-3216-B8C9-CF59292A545F> /usr/lib/libgermantok.dylib
    0x7fff6f740000 -     0x7fff6f749ff7  libheimdal-asn1.dylib (564.140.1) <0AC6FB62-2B0F-3E93-A931-E4DC4B1D757A> /usr/lib/libheimdal-asn1.dylib
    0x7fff6f74a000 -     0x7fff6f83afff  libiconv.2.dylib (59) <18311A67-E4EF-3CC7-95B3-C0EDEE3A282F> /usr/lib/libiconv.2.dylib
    0x7fff6f83b000 -     0x7fff6fa92fff  libicucore.A.dylib (64260.0.1) <8AC2CB07-E7E0-340D-A849-186FA1F27251> /usr/lib/libicucore.A.dylib
    0x7fff6faac000 -     0x7fff6faadfff  liblangid.dylib (133) <30CFC08C-EF36-3CF5-8AEA-C1CB070306B7> /usr/lib/liblangid.dylib
    0x7fff6faae000 -     0x7fff6fac6ff3  liblzma.5.dylib (16) <C131EF18-2CDD-3271-8A30-A8760D4FE166> /usr/lib/liblzma.5.dylib
    0x7fff6fade000 -     0x7fff6fb85ff7  libmecab.dylib (883.11) <0D5BFD01-D4A7-3C8D-AA69-C329C1A69792> /usr/lib/libmecab.dylib
    0x7fff6fb86000 -     0x7fff6fde8ff1  libmecabra.dylib (883.11) <E31DE74D-1B88-377F-ACD3-D789D29C3AE7> /usr/lib/libmecabra.dylib
    0x7fff70155000 -     0x7fff70184fff  libncurses.5.4.dylib (57) <995DFEEA-40F3-377F-B73D-D02AC59D591F> /usr/lib/libncurses.5.4.dylib
    0x7fff702b4000 -     0x7fff70730ff5  libnetwork.dylib (1880.120.4) <BA294A54-F309-398D-B308-F97032AFF555> /usr/lib/libnetwork.dylib
    0x7fff70731000 -     0x7fff70748fff  libnetworkextension.dylib (1095.140.2) <D0E8454C-33A9-3F96-B3A0-EDB12C32283A> /usr/lib/libnetworkextension.dylib
    0x7fff707d1000 -     0x7fff70804fde  libobjc.A.dylib (787.1) <6DF81160-5E7F-3E31-AA1E-C875E3B98AF6> /usr/lib/libobjc.A.dylib
    0x7fff70805000 -     0x7fff70806ff7  libodfde.dylib (26) <33F49412-5106-35B8-AA60-5A497C3967E6> /usr/lib/libodfde.dylib
    0x7fff70817000 -     0x7fff7081bfff  libpam.2.dylib (25.100.1) <0502F395-8EE6-3D2A-9239-06FD5622E19E> /usr/lib/libpam.2.dylib
    0x7fff7081e000 -     0x7fff70854ff7  libpcap.A.dylib (89.120.1) <A76EC076-A8EA-354C-B95F-7AB1EAFBCC65> /usr/lib/libpcap.A.dylib
    0x7fff70894000 -     0x7fff708a2ff9  libperfcheck.dylib (37.100.2) <9D9C4879-8A80-34C4-B0D2-BE341FD6D321> /usr/lib/libperfcheck.dylib
    0x7fff708d8000 -     0x7fff708f0fff  libresolv.9.dylib (67.40.1) <C57EDFEF-D36A-310B-8D14-8C68A625B1E8> /usr/lib/libresolv.9.dylib
    0x7fff708f2000 -     0x7fff70936ff7  libsandbox.1.dylib (1217.141.2) <E8BA5E84-66AF-3995-8F8E-DDC93B0A88E1> /usr/lib/libsandbox.1.dylib
    0x7fff70937000 -     0x7fff70949ff7  libsasl2.2.dylib (213.120.1) <E7573AC1-83FD-305A-8FB8-03145BDA286B> /usr/lib/libsasl2.2.dylib
    0x7fff7094a000 -     0x7fff7094bff7  libspindump.dylib (281.3) <AE8C1AE9-5CBC-332F-BBE8-370A2A19FED6> /usr/lib/libspindump.dylib
    0x7fff7094c000 -     0x7fff70b36ff7  libsqlite3.dylib (308.5) <35A2BD9F-4E33-30DE-A994-4AB585AC3AFE> /usr/lib/libsqlite3.dylib
    0x7fff70c2a000 -     0x7fff70c57ffb  libssl.46.dylib (47.140.1) <06932872-13DA-33E3-8C28-7B49FC582039> /usr/lib/libssl.46.dylib
    0x7fff70d87000 -     0x7fff70d8affb  libutil.dylib (57) <F01467F6-23A7-37EE-A170-33CE1577B41D> /usr/lib/libutil.dylib
    0x7fff70d8b000 -     0x7fff70d98ff7  libxar.1.dylib (425.2) <EE964412-9E25-30B3-BCC0-CCEFBCC8094B> /usr/lib/libxar.1.dylib
    0x7fff70d9e000 -     0x7fff70e80fff  libxml2.2.dylib (33.5) <A579D158-2E09-316C-872E-DD9D93401B2F> /usr/lib/libxml2.2.dylib
    0x7fff70e84000 -     0x7fff70eacfff  libxslt.1.dylib (16.9) <34A45627-DA5B-37D2-9609-65B425E0010A> /usr/lib/libxslt.1.dylib
    0x7fff70ead000 -     0x7fff70ebfff3  libz.1.dylib (76) <793D9643-CD83-3AAC-8B96-88D548FAB620> /usr/lib/libz.1.dylib
    0x7fff7176e000 -     0x7fff71773ff3  libcache.dylib (83) <AF488D13-9E89-35E0-B078-BE37CC5B8586> /usr/lib/system/libcache.dylib
    0x7fff71774000 -     0x7fff7177ffff  libcommonCrypto.dylib (60165.120.1) <C7912BE5-993E-3581-B2A0-6AABDC8C5562> /usr/lib/system/libcommonCrypto.dylib
    0x7fff71780000 -     0x7fff71787fff  libcompiler_rt.dylib (101.2) <49B8F644-5705-3F16-BBE0-6FFF9B17C36E> /usr/lib/system/libcompiler_rt.dylib
    0x7fff71788000 -     0x7fff71791ff7  libcopyfile.dylib (166.40.1) <3C481225-21E7-370A-A30E-0CCFDD64A92C> /usr/lib/system/libcopyfile.dylib
    0x7fff71792000 -     0x7fff71824fdb  libcorecrypto.dylib (866.140.1) <60567BF8-80FA-359A-B2F3-A3BAEFB288FD> /usr/lib/system/libcorecrypto.dylib
    0x7fff71931000 -     0x7fff71971ff0  libdispatch.dylib (1173.100.2) <CD9C059C-91D9-30E8-8926-5B9CD0D5D4F5> /usr/lib/system/libdispatch.dylib
    0x7fff71972000 -     0x7fff719a8fff  libdyld.dylib (750.6) <789A18C2-8AC7-3C88-813D-CD674376585D> /usr/lib/system/libdyld.dylib
    0x7fff719a9000 -     0x7fff719a9ffb  libkeymgr.dylib (30) <DB3337BE-01CA-3425-BD0C-87774FC0CDC0> /usr/lib/system/libkeymgr.dylib
    0x7fff719aa000 -     0x7fff719b6ff3  libkxld.dylib (6153.141.2.2) <30AACC57-2314-3863-94B2-64AB3E002B35> /usr/lib/system/libkxld.dylib
    0x7fff719b7000 -     0x7fff719b7ff7  liblaunch.dylib (1738.140.1) <AFBCBDD3-0B55-3ECD-8E04-A73A3A57356B> /usr/lib/system/liblaunch.dylib
    0x7fff719b8000 -     0x7fff719bdff7  libmacho.dylib (959.0.1) <AA613A9C-961A-3B67-B696-4622FA59FC4E> /usr/lib/system/libmacho.dylib
    0x7fff719be000 -     0x7fff719c0ff3  libquarantine.dylib (110.40.3) <F234E51D-FD0B-3EE4-B679-AE3EE9C536C3> /usr/lib/system/libquarantine.dylib
    0x7fff719c1000 -     0x7fff719c2ff7  libremovefile.dylib (48) <7C7EFC79-BD24-33EF-B073-06AED234593E> /usr/lib/system/libremovefile.dylib
    0x7fff719c3000 -     0x7fff719daff3  libsystem_asl.dylib (377.60.2) <1563EE02-0657-3B78-99BE-A947C24122EF> /usr/lib/system/libsystem_asl.dylib
    0x7fff719db000 -     0x7fff719dbff7  libsystem_blocks.dylib (74) <0D53847E-AF5F-3ACF-B51F-A15DEA4DEC58> /usr/lib/system/libsystem_blocks.dylib
    0x7fff719dc000 -     0x7fff71a63fff  libsystem_c.dylib (1353.100.2) <BBDED5E6-A646-3EED-B33A-91E4331EA063> /usr/lib/system/libsystem_c.dylib
    0x7fff71a64000 -     0x7fff71a67ffb  libsystem_configuration.dylib (1061.141.1) <0EE84C33-64FD-372B-974A-AF7A136F2068> /usr/lib/system/libsystem_configuration.dylib
    0x7fff71a68000 -     0x7fff71a6bfff  libsystem_coreservices.dylib (114) <A199156E-058D-3ABB-BCE9-4B9F20DCED0F> /usr/lib/system/libsystem_coreservices.dylib
    0x7fff71a6c000 -     0x7fff71a74fff  libsystem_darwin.dylib (1353.100.2) <5B12B5DB-3F30-37C1-8ECC-49A66B1F2864> /usr/lib/system/libsystem_darwin.dylib
    0x7fff71a75000 -     0x7fff71a7cfff  libsystem_dnssd.dylib (1096.100.3) <EBB4C2C2-E031-3094-B40A-E67BF261D295> /usr/lib/system/libsystem_dnssd.dylib
    0x7fff71a7d000 -     0x7fff71a7effb  libsystem_featureflags.dylib (17) <29FD922A-EC2C-3F25-BCCC-B58D716E60EC> /usr/lib/system/libsystem_featureflags.dylib
    0x7fff71a7f000 -     0x7fff71accff7  libsystem_info.dylib (538) <8A321605-5480-330B-AF9E-64E65DE61747> /usr/lib/system/libsystem_info.dylib
    0x7fff71acd000 -     0x7fff71af9ff7  libsystem_kernel.dylib (6153.141.2.2) <5CDBBC06-6CA6-3432-9FDA-681047866F3E> /usr/lib/system/libsystem_kernel.dylib
    0x7fff71afa000 -     0x7fff71b41fff  libsystem_m.dylib (3178) <00F331F1-0D09-39B3-8736-1FE90E64E903> /usr/lib/system/libsystem_m.dylib
    0x7fff71b42000 -     0x7fff71b69fff  libsystem_malloc.dylib (283.100.6) <8549294E-4C53-36EB-99F3-584A7393D8D5> /usr/lib/system/libsystem_malloc.dylib
    0x7fff71b6a000 -     0x7fff71b77ffb  libsystem_networkextension.dylib (1095.140.2) <F06C65C5-2CBE-313C-96E1-A09240F9FE57> /usr/lib/system/libsystem_networkextension.dylib
    0x7fff71b78000 -     0x7fff71b81ff7  libsystem_notify.dylib (241.100.2) <FA22F928-D91B-3AA5-96BB-3186AC0FB264> /usr/lib/system/libsystem_notify.dylib
    0x7fff71b82000 -     0x7fff71b8afef  libsystem_platform.dylib (220.100.1) <009A7C1F-313A-318E-B9F2-30F4C06FEA5C> /usr/lib/system/libsystem_platform.dylib
    0x7fff71b8b000 -     0x7fff71b95fff  libsystem_pthread.dylib (416.100.3) <62CB1A98-0B8F-31E7-A02B-A1139927F61D> /usr/lib/system/libsystem_pthread.dylib
    0x7fff71b96000 -     0x7fff71b9aff3  libsystem_sandbox.dylib (1217.141.2) <051C4018-4345-3034-AC98-6DE42FB8273B> /usr/lib/system/libsystem_sandbox.dylib
    0x7fff71b9b000 -     0x7fff71b9dfff  libsystem_secinit.dylib (62.100.2) <F80872AA-E1FD-3D7E-8729-467656EC6561> /usr/lib/system/libsystem_secinit.dylib
    0x7fff71b9e000 -     0x7fff71ba5ffb  libsystem_symptoms.dylib (1238.120.1) <5820A2AF-CE72-3AB3-ABCC-273A3419FB55> /usr/lib/system/libsystem_symptoms.dylib
    0x7fff71ba6000 -     0x7fff71bbcff2  libsystem_trace.dylib (1147.120) <04B47629-847B-3D74-8ABE-C05EF9DEEFE4> /usr/lib/system/libsystem_trace.dylib
    0x7fff71bbe000 -     0x7fff71bc3ff7  libunwind.dylib (35.4) <42B7B509-BAFE-365B-893A-72414C92F5BF> /usr/lib/system/libunwind.dylib
    0x7fff71bc4000 -     0x7fff71bf9ffe  libxpc.dylib (1738.140.1) <3E243A41-030F-38E3-9FD2-7B38C66C35B1> /usr/lib/system/libxpc.dylib

External Modification Summary:
  Calls made by other processes targeting this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by this process:
    task_for_pid: 0
    thread_create: 0
    thread_set_state: 0
  Calls made by all processes on this machine:
    task_for_pid: 77392
    thread_create: 0
    thread_set_state: 0

VM Region Summary:
ReadOnly portion of Libraries: Total=822.1M resident=0K(0%) swapped_out_or_unallocated=822.1M(100%)
Writable regions: Total=852.7M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=852.7M(100%)

                                VIRTUAL   REGION 
REGION TYPE                        SIZE    COUNT (non-coalesced) 
===========                     =======  ======= 
Accelerate framework               256K        2 
Activity Tracing                   256K        1 
CG backing stores                 1160K        2 
CG image                          1420K       13 
CoreAnimation                     51.4M       42 
CoreGraphics                         8K        1 
CoreImage                          320K       13 
CoreUI image data                 1152K       11 
Foundation                          28K        2 
Image IO                           376K       14 
JS VM Isolated Heap                 40K        2 
Kernel Alloc Once                    8K        1 
MALLOC                           393.1M      197 
MALLOC guard page                   32K        7 
MALLOC_LARGE (reserved)            612K        3         reserved VM address space (unallocated)
MALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)
SQLite page cache                   64K        1 
STACK GUARD                       56.0M        7 
Stack                             11.0M        7 
VM_ALLOCATE                        240K       23 
WebKit Malloc                     7272K        9 
__DATA                            46.0M      475 
__DATA_CONST                        97K        5 
__FONT_DATA                          4K        1 
__LINKEDIT                       401.7M       68 
__OBJC_RO                         32.3M        1 
__OBJC_RW                         1908K        2 
__TEXT                           420.3M      444 
__UNICODE                          564K        1 
mapped file                      281.7M       51 
shared memory                      644K       17 
===========                     =======  ======= 
TOTAL                              2.0G     1424 
TOTAL, minus reserved VM space     1.7G     1424 

Model: MacBookPro14,3, BootROM 428.0.0.0.0, 4 processors, Quad-Core Intel Core i7, 2.8 GHz, 16 GB, SMC 2.45f4
Graphics: kHW_IntelHDGraphics630Item, Intel HD Graphics 630, spdisplays_builtin
Graphics: kHW_AMDRadeonPro555Item, Radeon Pro 555, spdisplays_pcie_device, 2 GB
Memory Module: BANK 0/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320
Memory Module: BANK 1/DIMM0, 8 GB, LPDDR3, 2133 MHz, 0x802C, 0x4D5435324C31473332443450472D30393320
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x173), Broadcom BCM43xx 1.0 (7.77.111.1 AirPortDriverBrcmNIC-1615.2)
Bluetooth: Version 7.0.6f7, 3 services, 18 devices, 1 incoming serial ports
Network Service: Apple USB Ethernet Adapter, Ethernet, en5
Network Service: USB 10/100/1000 LAN, Ethernet, en8
Network Service: Wi-Fi, AirPort, en0
Network Service: Thunderbolt Bridge, Ethernet, bridge0
USB Device: USB3.0 Hub
USB Device: USB 10/100/1000 LAN
USB Device: USB 3.0 Bus
USB Device: Apple T1 Controller
USB Device: USB2.0 Hub
Thunderbolt Bus: MacBook Pro, Apple Inc., 41.4
Thunderbolt Bus: MacBook Pro, Apple Inc., 41.4

Would really appreciate if someone can figure this out.

kevinushey commented 3 years ago
Application Specific Information:
dyld: in dlopen()
/Users/dhirajkhanna/opt/anaconda3/lib/libmkl_intel_thread.dylib

This looks like a problem in your Anaconda installation. I'd recommend either updating, or using a different copy of Python (e.g. a system installation of Python with a virtual environment derived from that install)