On 30/05/2023 22:57, Martin Morgan wrote:
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.
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
From: Tomas Kalibera <tomas.kalib...@gmail.com>
Date: Tuesday, May 30, 2023 at 4:54 PM
To: Martin Morgan <mtmorgan.b...@gmail.com>, R-devel <R-devel@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
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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