Martin Morgan
2023-May-30 21:57 UTC
[Rd] Building R from source always fails on tools:::sysdata2LazyLoadDB
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
>
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>
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Prof Brian Ripley
2023-May-31 07:46 UTC
[Rd] Building R from source always fails on tools:::sysdata2LazyLoadDB
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.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-- Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford