Re: [R-SIG-Mac] Running R with lldb

2020-08-05 Thread Duncan Murdoch 

Thanks, attaching to the process seemed simplest.

For others:  the manual talks about doing it with gdb, but the same 
syntax works with lldb.  Here's an example:  Start R, then open a new 
terminal window:


murdoch@djmair3 ~
$ ps
  PID TTY   TIME CMD
11293 ttys0000:00.08 -bash
13829 ttys0000:00.31 /Users/murdoch/R/R-devel/bin/exec/R
13804 ttys0010:00.03 -bash

murdoch@djmair3 ~
$ lldb -p 13829
(lldb) process attach --pid 13829
Process 13829 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGSTOP
frame #0: 0x7fff70eb10fe libsystem_kernel.dylib`__select + 10
libsystem_kernel.dylib`__select:
->  0x7fff70eb10fe <+10>: jae0x7fff70eb1108; <+20>
0x7fff70eb1100 <+12>: movq   %rax, %rdi
0x7fff70eb1103 <+15>: jmp0x7fff70eaa22d; cerror
0x7fff70eb1108 <+20>: retq
Target 0: (R) stopped.

Duncan Murdoch

On 05/08/2020 10:16 a.m., Prof Brian Ripley wrote:

One of the suggestions in

https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Debugging-on-macOS

should help.  Both worked for my build of R-devel yesterday 


On 05/08/2020 14:25, Duncan Murdoch wrote:

I'm now successfully building R-devel in /Users/murdoch/R/R-devel.  If I
run it from that directory using

   bin/R -d lldb

it starts, but "run" gives this error:

Process 11165 launched: '/Users/murdoch/R/R-devel/bin/exec/R' (x86_64)
dyld: Library not loaded: libRblas.dylib
    Referenced from: /Users/murdoch/R/R-devel/bin/exec/R
    Reason: image not found
Process 11165 stopped
* thread #1, stop reason = signal SIGABRT
      frame #0: 0x0001004c7ede dyld`__abort_with_payload + 10
dyld`__abort_with_payload:
->  0x1004c7ede <+10>: jae    0x1004c7ee8   ; <+20>
      0x1004c7ee0 <+12>: movq   %rax, %rdi
      0x1004c7ee3 <+15>: jmp    0x1004c6408   ; cerror_nocancel
      0x1004c7ee8 <+20>: retq
Target 0: (R) stopped.

I can start it from the /Users/murdoch/R/R-devel/lib directory where
libRblas.dylib lives.  Setting DYLD_LIBRARY_PATH or LD_LIBRARY_PATH to
point there doesn't help (either on the bin/R command line or exported).
   Is there some other way to run it from whatever directory I happen to
be in?

Duncan Murdoch

On 02/05/2020 11:26 p.m., Simon Urbanek wrote:

Vince,

Apple no longer allows debugging of distributed apps - see R for Mac
FAQ 10.17:
http://mac.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R


Another (not recommended) work-around is to disable SIP.

Cheers,
Simon




On 3/05/2020, at 10:42 AM, Vincent Carey 
wrote:

I'd like to make use of material in

https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/

But with R 4.0 I get

%vjcair> 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

error: process exited with status -1 (Error 1)

(lldb) quit

%vjcair> which lldb

/usr/bin/lldb

%vjcair> lldb --version

lldb-1100.0.30.12

Apple Swift version 5.1.3 (swiftlang-1100.0.282.1 clang-1100.0.33.15)


with gdb, there is a little more info -- and a peculiar warning that
mentions /Volumes/Builds/Simon/R4/h ...


%vjcair> R -d gdb

GNU gdb (GDB) 8.1

Copyright (C) 2018 Free Software Foundation, Inc.

License GPLv3+: GNU GPL version 3 or later
.

Find the GDB manual and other documentation resources online at:

.

For help, type "help".

Type "apropos word" to search for commands related to "word"...

Reading symbols from
/Library/Frameworks/R.framework/Resources/bin/exec/R...

warning:
`/Volumes/Builds/Simon/R4/high-sierra-x86_64/R-4.0-branch/src/main/Rmain.o':

can't open to read symbols: No such file or directory.

(no debugging symbols found)...done.

(gdb) run

Starting program:
/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/exec/R

Unable to find Mach task port for process-id 59032: (os/kern) failure
(0x5).

(please check gdb is codesigned - see taskgated(8))


sessionInfo()


R version 4.0.0 Patched (2020-04-27 r78309)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Mojave 10.14.6


Matrix products: default

BLAS:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib


LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib


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Re: [R-SIG-Mac] Running R with lldb

2020-08-05 Thread Prof Brian Ripley 

One of the suggestions in

https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Debugging-on-macOS

should help.  Both worked for my build of R-devel yesterday 


On 05/08/2020 14:25, Duncan Murdoch wrote:
I'm now successfully building R-devel in /Users/murdoch/R/R-devel.  If I 
run it from that directory using


  bin/R -d lldb

it starts, but "run" gives this error:

Process 11165 launched: '/Users/murdoch/R/R-devel/bin/exec/R' (x86_64)
dyld: Library not loaded: libRblas.dylib
   Referenced from: /Users/murdoch/R/R-devel/bin/exec/R
   Reason: image not found
Process 11165 stopped
* thread #1, stop reason = signal SIGABRT
     frame #0: 0x0001004c7ede dyld`__abort_with_payload + 10
dyld`__abort_with_payload:
->  0x1004c7ede <+10>: jae    0x1004c7ee8   ; <+20>
     0x1004c7ee0 <+12>: movq   %rax, %rdi
     0x1004c7ee3 <+15>: jmp    0x1004c6408   ; cerror_nocancel
     0x1004c7ee8 <+20>: retq
Target 0: (R) stopped.

I can start it from the /Users/murdoch/R/R-devel/lib directory where 
libRblas.dylib lives.  Setting DYLD_LIBRARY_PATH or LD_LIBRARY_PATH to 
point there doesn't help (either on the bin/R command line or exported). 
  Is there some other way to run it from whatever directory I happen to 
be in?


Duncan Murdoch

On 02/05/2020 11:26 p.m., Simon Urbanek wrote:

Vince,

Apple no longer allows debugging of distributed apps - see R for Mac 
FAQ 10.17:
http://mac.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R 



Another (not recommended) work-around is to disable SIP.

Cheers,
Simon



On 3/05/2020, at 10:42 AM, Vincent Carey  
wrote:


I'd like to make use of material in

https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/

But with R 4.0 I get

%vjcair> 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

error: process exited with status -1 (Error 1)

(lldb) quit

%vjcair> which lldb

/usr/bin/lldb

%vjcair> lldb --version

lldb-1100.0.30.12

Apple Swift version 5.1.3 (swiftlang-1100.0.282.1 clang-1100.0.33.15)


with gdb, there is a little more info -- and a peculiar warning that
mentions /Volumes/Builds/Simon/R4/h ...


%vjcair> R -d gdb

GNU gdb (GDB) 8.1

Copyright (C) 2018 Free Software Foundation, Inc.

License GPLv3+: GNU GPL version 3 or later 
.

Find the GDB manual and other documentation resources online at:

.

For help, type "help".

Type "apropos word" to search for commands related to "word"...

Reading symbols from 
/Library/Frameworks/R.framework/Resources/bin/exec/R...


warning:
`/Volumes/Builds/Simon/R4/high-sierra-x86_64/R-4.0-branch/src/main/Rmain.o': 


can't open to read symbols: No such file or directory.

(no debugging symbols found)...done.

(gdb) run

Starting program:
/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/exec/R

Unable to find Mach task port for process-id 59032: (os/kern) failure 
(0x5).


(please check gdb is codesigned - see taskgated(8))


sessionInfo()


R version 4.0.0 Patched (2020-04-27 r78309)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Mojave 10.14.6


Matrix products: default

BLAS:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib 



LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib 



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--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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[R-SIG-Mac] Running R with lldb

2020-08-05 Thread Duncan Murdoch 
I'm now successfully building R-devel in /Users/murdoch/R/R-devel.  If I 
run it from that directory using


 bin/R -d lldb

it starts, but "run" gives this error:

Process 11165 launched: '/Users/murdoch/R/R-devel/bin/exec/R' (x86_64)
dyld: Library not loaded: libRblas.dylib
  Referenced from: /Users/murdoch/R/R-devel/bin/exec/R
  Reason: image not found
Process 11165 stopped
* thread #1, stop reason = signal SIGABRT
frame #0: 0x0001004c7ede dyld`__abort_with_payload + 10
dyld`__abort_with_payload:
->  0x1004c7ede <+10>: jae0x1004c7ee8   ; <+20>
0x1004c7ee0 <+12>: movq   %rax, %rdi
0x1004c7ee3 <+15>: jmp0x1004c6408   ; cerror_nocancel
0x1004c7ee8 <+20>: retq
Target 0: (R) stopped.

I can start it from the /Users/murdoch/R/R-devel/lib directory where 
libRblas.dylib lives.  Setting DYLD_LIBRARY_PATH or LD_LIBRARY_PATH to 
point there doesn't help (either on the bin/R command line or exported). 
 Is there some other way to run it from whatever directory I happen to 
be in?


Duncan Murdoch

On 02/05/2020 11:26 p.m., Simon Urbanek wrote:

Vince,

Apple no longer allows debugging of distributed apps - see R for Mac FAQ 10.17:
http://mac.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R

Another (not recommended) work-around is to disable SIP.

Cheers,
Simon




On 3/05/2020, at 10:42 AM, Vincent Carey  wrote:

I'd like to make use of material in

https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/

But with R 4.0 I get

%vjcair> 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

error: process exited with status -1 (Error 1)

(lldb) quit

%vjcair> which lldb

/usr/bin/lldb

%vjcair> lldb --version

lldb-1100.0.30.12

Apple Swift version 5.1.3 (swiftlang-1100.0.282.1 clang-1100.0.33.15)


with gdb, there is a little more info -- and a peculiar warning that
mentions /Volumes/Builds/Simon/R4/h ...


%vjcair> R -d gdb

GNU gdb (GDB) 8.1

Copyright (C) 2018 Free Software Foundation, Inc.

License GPLv3+: GNU GPL version 3 or later .

Find the GDB manual and other documentation resources online at:

.

For help, type "help".

Type "apropos word" to search for commands related to "word"...

Reading symbols from /Library/Frameworks/R.framework/Resources/bin/exec/R...

warning:
`/Volumes/Builds/Simon/R4/high-sierra-x86_64/R-4.0-branch/src/main/Rmain.o':
can't open to read symbols: No such file or directory.

(no debugging symbols found)...done.

(gdb) run

Starting program:
/Library/Frameworks/R.framework/Versions/4.0/Resources/bin/exec/R

Unable to find Mach task port for process-id 59032: (os/kern) failure (0x5).

(please check gdb is codesigned - see taskgated(8))


sessionInfo()


R version 4.0.0 Patched (2020-04-27 r78309)

Platform: x86_64-apple-darwin17.0 (64-bit)

Running under: macOS Mojave 10.14.6


Matrix products: default

BLAS:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib

LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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