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

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]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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:
> 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]]
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
	[[alternative HTML version deleted]]