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[Bioc-devel] Unable to use lldb debugger

5 messages · Shian Su, Dolors Pelegri, Hani Habra +1 more

Original
Hani Habra
# 
Hi All,
I'm trying to use the lldb debugger to debug some R code, but keep getting
the following error:

(base) 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' (arm64).
(lldb) run
error: process exited with status -1 (attach failed (Not allowed to attach
to process.  Look in the console messages (Console.app), near the
debugserver entries when the attached failed.  The subsystem that denied
the attach permission will likely have logged an informative message about
why it was denied.))

I tried looking at Console.app, but couldn't find anything informative
there. Only thing I found was "enabling developer mode" with "sudo
DevToolsSecurity -enable", but that solved nothing. Does anyone understand
what the issue is?

Thanks,
Hani Habra
Shian Su
# 
Hi Hani,

The command you showed works fine on my MacBook Pro. However I am on an Intel Mac. I see that your R is (arm64), so there?s probably some issues trying to attach across compatibility layers.

Does your debugging specifically require C level debugging, and also M1 Macs? I?d see how far you can get with the R debugger and consider using another machine to do lldb level debugging.

Kind regards,
Shian
Dolors Pelegri
# 
Hi Hani,

I?m working with an iMac and the debuger for R 4.1 doesn?t work, the command R -d lldb only works in R release 3.6.3 and previous

https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R <https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R>

in section 10.17 there is a possible solution but I have not tried it 


Kind regards,

Dolors

  
  


  


      

    

    

      
      

        


  

        

      Hani Habra
    

    

      
      #
    

  


  

      
Thank you Shian & Dolors for your replies.

Shian, the error is on the C level so it does require a C level debugger
(lldb being most useful). It does not require an M1 Mac though, so maybe I
could try with my older mac next time... unless what Dolors says is true
and I can no longer do the lldb command since my package requires R 4.0 or
later.

Thank you Dolors for finding that, that's the most information I've gotten
about this. I can try that out the next time I have a similar issue, though
hopefully by then Bioconductor or someone else can have updated
instructions for debugging on a Mac.

Kind regards,
Hani

        
On Fri, Jul 2, 2021 at 2:11 AM Dolors Pelegri <dpelegri at gmail.com> wrote:

        

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
      #
    

  


  

      
When I try to debug on my macOS, I need to do the following

```
R -d lldb
(lldb) process launch --environment DYLD_LIBRARY_PATH=/Users/ma38727/bin/R-devel/lib
```
where `/Users/ma38727/bin/` is the location on my system where R is installed.

Martin

?On 7/2/21, 11:32 AM, "Bioc-devel on behalf of Hani Habra" <bioc-devel-bounces at r-project.org on behalf of hhabra1 at gmail.com> wrote:

    Thank you Shian & Dolors for your replies.

    Shian, the error is on the C level so it does require a C level debugger
    (lldb being most useful). It does not require an M1 Mac though, so maybe I
    could try with my older mac next time... unless what Dolors says is true
    and I can no longer do the lldb command since my package requires R 4.0 or
    later.

    Thank you Dolors for finding that, that's the most information I've gotten
    about this. I can try that out the next time I have a similar issue, though
    hopefully by then Bioconductor or someone else can have updated
    instructions for debugging on a Mac.

    Kind regards,
    Hani

        
On Fri, Jul 2, 2021 at 2:11 AM Dolors Pelegri <dpelegri at gmail.com> wrote:

        
> Hi Hani,
    >
    > I?m working with an iMac and the debuger for R 4.1 doesn?t work, the
    > command R -d lldb only works in R release 3.6.3 and previous
    >
    >
    > https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R
    >
    > in section 10.17 there is a possible solution but I have not tried it
    >
    >
    > Kind regards,
    >
    > Dolors
    >
    >
    > El 2 jul 2021, a les 7:18, Shian Su <su.s at wehi.edu.au> va escriure:
    >
    > Hi Hani,
    >
    > The command you showed works fine on my MacBook Pro. However I am on an
    > Intel Mac. I see that your R is (arm64), so there?s probably some issues
    > trying to attach across compatibility layers.
    >
    > Does your debugging specifically require C level debugging, and also M1
    > Macs? I?d see how far you can get with the R debugger and consider using
    > another machine to do lldb level debugging.
    >
    > Kind regards,
    > Shian
    >

        
> On 2 Jul 2021, at 3:47 am, Hani Habra <hhabra1 at gmail.com> wrote:

        
>
    > Hi All,
    > I'm trying to use the lldb debugger to debug some R code, but keep getting
    > the following error:
    >
    > (base) 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' (arm64).
    > (lldb) run
    > error: process exited with status -1 (attach failed (Not allowed to attach
    > to process.  Look in the console messages (Console.app), near the
    > debugserver entries when the attached failed.  The subsystem that denied
    > the attach permission will likely have logged an informative message about
    > why it was denied.))
    >
    > I tried looking at Console.app, but couldn't find anything informative
    > there. Only thing I found was "enabling developer mode" with "sudo
    > DevToolsSecurity -enable", but that solved nothing. Does anyone understand
    > what the issue is?
    >
    > Thanks,
    > Hani Habra
    >
    > [[alternative HTML version deleted]]
    >
    > _______________________________________________
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    > https://stat.ethz.ch/mailman/listinfo/bioc-devel
    >
    >
    > _______________________________________________
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    > https://stat.ethz.ch/mailman/listinfo/bioc-devel
    >
    >
    >


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