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Building R from source always fails on tools:::sysdata2LazyLoadDB

6 messages · Martin Morgan, Ivan Krylov, Tomas Kalibera +1 more

Original
Martin Morgan
# 
I build my own R from source on an M1 mac. I have a clean svn checkout in one directory ~/src/R-devel. I switch to ~/bin/R-devel and the first time run

cd ~/bin/R-devel
~/src/R-devel/configure --enable-R-shlib 'CFLAGS=-g -O0' CPPFLAGS=-I/opt/R/arm64/include 'CXXFLAGS=-g -O0'
make -j

At some point in the future I svn update src/R-devel, then

cd ~/bin/R-devel
make -j

This always ends with

installing 'sysdata.rda'
/bin/sh: line 1: 99497 Done                    echo "tools:::sysdata2LazyLoadDB(\"/Users/XXX/src/R-devel/src/library/utils/R/sysdata.rda\",\"../../../library/utils/R\")"
     99498 Killed: 9               | R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../../bin/R --vanilla --no-echo
make[4]: *** [sysdata] Error 137
make[3]: *** [all] Error 2
make[2]: *** [R] Error 1
make[1]: *** [R] Error 1
make: *** [R] Error 1

what am I doing wrong? Is there a graceful way to fix this (my current solution is basically to start over, with `make distclean`)? If I cd into ~/bin/R-devel/src/library/utils I can start an interactive session and reproduce the error

~/bin/R-devel/src/library/utils $   R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla
zsh: killed     R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla

or simply
zsh: killed     R_DEFAULT_PACKAGES=NULL LC_ALL=C R_ENABLE_JIT=0 TZ=UTC ../../../bin/R
Ivan Krylov
# 
On Tue, 30 May 2023 20:09:53 +0000
Martin Morgan <mtmorgan.bioc at gmail.com> wrote:

            

      
      
      
    

        
Can you add the -d lldb flag to the command line (substitute lldb for a
different debugger if that's what you prefer) and get a backtrace at
the moment where R gets killed?

That signal 9 is suspicious. On Linux, I would expect a SIGKILL sent by
the OOM-Killer to a runaway process. On a Mac, I'm not sure at all, but
could it be related to some of the security features? (Does the system
save a crash report somewhere?)

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Tomas Kalibera
    

    

      
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On 5/30/23 22:09, Martin Morgan wrote:

            

      
      
      
    

        
If it is macOS, it might be worth checking the system logs (Console 
app). It may be some system security feature.

Tomas

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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Thanks Ivan & Tomas

A simpler way to trigger the problem is library(tools) or library.dynam("tools", "tools", ".") so I guess it is loading src/tools.so

Ivan, adding -d lldb I need to tell lldb where to find the R library

(lldb) process launch --environment DYLD_LIBRARY_PATH=/Users/ma38727/bin/R-devel/lib

And then `library(tools)` works. To run lldb I needed to grant Xcode permissions using my local administrator account.

@Thomas I can't see anything in the Console app logs, but this might be partly my ineptitude.

Martin

From: Tomas Kalibera <tomas.kalibera at gmail.com>
Date: Tuesday, May 30, 2023 at 4:54 PM
To: Martin Morgan <mtmorgan.bioc at gmail.com>, R-devel <R-devel at r-project.org>
Subject: Re: [Rd] Building R from source always fails on tools:::sysdata2LazyLoadDB

        
On 5/30/23 22:09, Martin Morgan wrote:

            

      
      
      
    

        
If it is macOS, it might be worth checking the system logs (Console
app). It may be some system security feature.

Tomas

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
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On 30/05/2023 22:57, Martin Morgan wrote:

            

      
      
      
    

        
Which version of macOS is this?

- Prior to Ventura it is the known behaviour.

- With Ventura the same happens if any R process from the current build 
is in use, even a crashed one. (The latter happened to me this morning: 
there were reports under Crash Reports in the Console App.)

As the R-admin manual says

"Updating an ?arm64? build may fail because of the bug described at 
https://openradar.appspot.com/FB8914243 but ab initio builds work. This 
has been far rarer since macOS 13."

Once it happens, you need to rebuild (make clean;make all should suffice).

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Martin Morgan
    

    

      
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Thank you, especially for the R-admin link and link to the underlying issue.

This is macOS Monterey version 12.6.5, so I am stuck with rebuilding -- empirically it seems like make distclean && <reconfigure> && make all is needed. This doesn't seem to make sense (shouldn't `make clean` remove all the compiled libraries?) so I'll investigate a bit more; maybe it is because I do not `make install`? I know there is no value in papering over upstream issues, but wonder if I were to unlink all (or some?) *so / *dylib before `make all` would be effective?

After the fact I realized that the R-SIG-mac mailing list might have been more appropriate, but I did not see the issue discussed there.

Martin

From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
Date: Wednesday, May 31, 2023 at 3:46 AM
To: Martin Morgan <mtmorgan.bioc at gmail.com>
Cc: Tomas Kalibera <tomas.kalibera at gmail.com>, R-devel <R-devel at r-project.org>
Subject: Re: [Rd] Building R from source always fails on tools:::sysdata2LazyLoadDB

        
On 30/05/2023 22:57, Martin Morgan wrote:

            

      
      
      
    

        
Which version of macOS is this?

- Prior to Ventura it is the known behaviour.

- With Ventura the same happens if any R process from the current build
is in use, even a crashed one. (The latter happened to me this morning:
there were reports under Crash Reports in the Console App.)

As the R-admin manual says

"Updating an ?arm64? build may fail because of the bug described at
https://openradar.appspot.com/FB8914243 but ab initio builds work. This
has been far rarer since macOS 13."

Once it happens, you need to rebuild (make clean;make all should suffice).

            

      
      
      
    

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