R devel - May 2023 - Building R from source always fails on tools:::sysdata2LazyLoadDB

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
>
tools:::sysdata2LazyLoadDB("/Users/ma38727/src/R-devel/src/library/utils/R/sysdata.rda","../../../library/utils/R")
zsh: killed     R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla

or simply
> tools:::sysdata2LazyLoadDB
zsh: killed     R_DEFAULT_PACKAGES=NULL LC_ALL=C R_ENABLE_JIT=0 TZ=UTC
../../../bin/R

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On Tue, 30 May 2023 20:09:53 +0000
Martin Morgan <mtmorgan.bioc at gmail.com> wrote:
> ~/bin/R-devel/src/library/utils $   R_DEFAULT_PACKAGES=NULL
> ../../../bin/R --vanilla
> >
tools:::sysdata2LazyLoadDB("/Users/ma38727/src/R-devel/src/library/utils/R/sysdata.rda","../../../library/utils/R")
> >  
> zsh: killed     R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla
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?)

-- 
Best regards,
Ivan

On 5/30/23 22:09, Martin Morgan wrote:
> 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
>>
tools:::sysdata2LazyLoadDB("/Users/ma38727/src/R-devel/src/library/utils/R/sysdata.rda","../../../library/utils/R")
> zsh: killed     R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla
>
> or simply
>
>> tools:::sysdata2LazyLoadDB
> zsh: killed     R_DEFAULT_PACKAGES=NULL LC_ALL=C R_ENABLE_JIT=0 TZ=UTC
../../../bin/R
If it is macOS, it might be worth checking the system logs (Console 
app). It may be some system security feature.

Tomas
>
> 	[[alternative HTML version deleted]]
>
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