Re: [R-SIG-Mac] Advise on building R on OSX without optimization for debugging
On 13/07/2020 11:14, Simon Urbanek wrote: On Jul 13, 2020, at 7:59 PM, Prof Brian Ripley wrote: On 08/07/2020 21:38, Simon Urbanek wrote: Dmitriy, due to permissions and the various limitations on passing environment variables across processes it is often easier to simply run R and attach the debugger to it: $ R [...] Sys.getpid() [1] 89955 $ sudo lldb Password: (lldb) attach 89955 [...] (lldb) c Process 89955 resuming On Catalina I can do that for a version of R I compiled, but not for a notarized binary distribution (which also refuses to be run under a debugger). The lldb error message is maximally uninformative: (lldb) attach 16682 error: attach failed: Error 1 or (lldb) run error: process exited with status -1 (Error 1) I presume that is intentional on Apple's part and there is no way round it other than weakening security (e.g. disable SIP)? Correct. It is annoying enough that it made to to the FAQ: https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R So the recommended way is to use the non-notarised builds (you can also disable SIP but that is not recommended). And, yes, it would be nice if lldb provided a more useful error... I suspect that it would be actually sufficient to provide just a exec/R binary that doesn't use hardened run-time, but it couldn't be distributed in the Apple Installer ... unless we create it with the post install script ... something to test I suppose... Thanks. My issues have been when my own build works but yours does not but while I am still checking on High Sierra I have workarounds. AFAIR the issues have all been array overruns which only sometimes cause segfaults. Best, Simon My memory was that it did work on High Sierra (I sometimes use it to investigate packages which segfault under your distribution but not with my builds) and I have just re-checked there with the CRAN distribution of 4.0.2. Brian Ripley -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Advise on building R on OSX without optimization for debugging
> On Jul 13, 2020, at 7:59 PM, Prof Brian Ripley wrote: > > On 08/07/2020 21:38, Simon Urbanek wrote: >> Dmitriy, >> due to permissions and the various limitations on passing environment >> variables across processes it is often easier to simply run R and attach the >> debugger to it: >> $ R >> [...] >>> Sys.getpid() >> [1] 89955 >>> >> $ sudo lldb >> Password: >> (lldb) attach 89955 >> [...] >> (lldb) c >> Process 89955 resuming > > On Catalina I can do that for a version of R I compiled, but not for a > notarized binary distribution (which also refuses to be run under a > debugger). The lldb error message is maximally uninformative: > > (lldb) attach 16682 > error: attach failed: Error 1 > > or > > (lldb) run > error: process exited with status -1 (Error 1) > > I presume that is intentional on Apple's part and there is no way round it > other than weakening security (e.g. disable SIP)? > Correct. It is annoying enough that it made to to the FAQ: https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#I-cannot-attach-debugger-to-R So the recommended way is to use the non-notarised builds (you can also disable SIP but that is not recommended). And, yes, it would be nice if lldb provided a more useful error... I suspect that it would be actually sufficient to provide just a exec/R binary that doesn't use hardened run-time, but it couldn't be distributed in the Apple Installer ... unless we create it with the post install script ... something to test I suppose... Best, Simon > My memory was that it did work on High Sierra (I sometimes use it to > investigate packages which segfault under your distribution but not with my > builds) and I have just re-checked there with the CRAN distribution of 4.0.2. > > Brian Ripley > > -- > Brian D. Ripley, rip...@stats.ox.ac.uk > Emeritus Professor of Applied Statistics, University of Oxford > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Advise on building R on OSX without optimization for debugging
On 08/07/2020 21:38, Simon Urbanek wrote: Dmitriy, due to permissions and the various limitations on passing environment variables across processes it is often easier to simply run R and attach the debugger to it: $ R [...] Sys.getpid() [1] 89955 $ sudo lldb Password: (lldb) attach 89955 [...] (lldb) c Process 89955 resuming On Catalina I can do that for a version of R I compiled, but not for a notarized binary distribution (which also refuses to be run under a debugger). The lldb error message is maximally uninformative: (lldb) attach 16682 error: attach failed: Error 1 or (lldb) run error: process exited with status -1 (Error 1) I presume that is intentional on Apple's part and there is no way round it other than weakening security (e.g. disable SIP)? My memory was that it did work on High Sierra (I sometimes use it to investigate packages which segfault under your distribution but not with my builds) and I have just re-checked there with the CRAN distribution of 4.0.2. Brian Ripley -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Advise on building R on OSX without optimization for debugging
Thanks, Simon, That helped a lot and I was able to debug the error. Also I got another advice in a private email from Rodney Sparapani where he suggested making symlinks to libRblas.dylib, libR.dylib in the workdir. That worked as well. On Thu, Jul 9, 2020 at 1:16 AM Simon Urbanek wrote: > Dmitriy, > > due to permissions and the various limitations on passing environment > variables across processes it is often easier to simply run R and attach > the debugger to it: > > $ R > [...] > > Sys.getpid() > [1] 89955 > > > > $ sudo lldb > Password: > (lldb) attach 89955 > [...] > (lldb) c > Process 89955 resuming > > Also note that you shouldn't change Makeconf by hand, simply supply any > CFLAGS you need to configure, e.g.: > > ../R-devel/configure --enable-R-shlib 'CFLAGS=-Wall -g -O0' > 'CXXFLAGS=-Wall -g -O0' > > Cheers, > Simon > > > > On Jul 8, 2020, at 11:08 PM, Dmitriy Selivanov < > selivanov.dmit...@gmail.com> wrote: > > > > Dear all, > > > > I'm trying to debug a segfault reported here > > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17850 (thanks Kevin > for > > the nice article > > https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/ about > > debugging with lldb) > > > > I need to compile R without optimization (with the O0 flag) instead of > > using binaries provided by Simon. > > > > Here I have difficulties. What I've tried: > > > > 1. Downloaded latest R-devel from > > https://stat.ethz.ch/R/daily/R-devel.tar.gz > > 2. Downloaded xz and pcre2 as suggested here > > https://mac.r-project.org/tools/ > > 3. run ./confilgure > > 4. replaced O2 with O0 in Makeconf > > 5. make > > > > Now R is compiled and I can launch it with ./bin/R. However when I run it > > with lldb > > > > 1. ./bin/R -d lldb > > 2. run > > > > I'm, getting: > > > > Process 74482 launched: > > '/Users/dmitry.selivanov/Downloads/R-devel/bin/exec/R' (x86_64) > > > > dyld: Library not loaded: libRblas.dylib > > > > Referenced from: /Users/dmitry.selivanov/Downloads/R-devel/bin/exec/R > > > > Reason: image not found > > > > Process 74482 stopped > > > > * thread #1, stop reason = signal SIGABRT > > > >frame #0: 0x000100574ebe dyld`__abort_with_payload + 10 > > > > dyld`__abort_with_payload: > > > > -> 0x100574ebe <+10>: jae0x100574ec8 ; <+20> > > > >0x100574ec0 <+12>: movq %rax, %rdi > > > >0x100574ec3 <+15>: jmp0x1005733e8 ; cerror_nocancel > > > >0x100574ec8 <+20>: retq > > > > Target 0: (R) stopped. > > > > > > Any suggestions? Things are much easier on linux-based docker images, > but I > > can't reproduce the reported bug there... > > > > > > Regards > > Dmitriy Selivanov > > > > [[alternative HTML version deleted]] > > > > ___ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > -- Regards Dmitriy Selivanov [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Advise on building R on OSX without optimization for debugging
Dmitriy, due to permissions and the various limitations on passing environment variables across processes it is often easier to simply run R and attach the debugger to it: $ R [...] > Sys.getpid() [1] 89955 > $ sudo lldb Password: (lldb) attach 89955 [...] (lldb) c Process 89955 resuming Also note that you shouldn't change Makeconf by hand, simply supply any CFLAGS you need to configure, e.g.: ../R-devel/configure --enable-R-shlib 'CFLAGS=-Wall -g -O0' 'CXXFLAGS=-Wall -g -O0' Cheers, Simon > On Jul 8, 2020, at 11:08 PM, Dmitriy Selivanov > wrote: > > Dear all, > > I'm trying to debug a segfault reported here > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17850 (thanks Kevin for > the nice article > https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/ about > debugging with lldb) > > I need to compile R without optimization (with the O0 flag) instead of > using binaries provided by Simon. > > Here I have difficulties. What I've tried: > > 1. Downloaded latest R-devel from > https://stat.ethz.ch/R/daily/R-devel.tar.gz > 2. Downloaded xz and pcre2 as suggested here > https://mac.r-project.org/tools/ > 3. run ./confilgure > 4. replaced O2 with O0 in Makeconf > 5. make > > Now R is compiled and I can launch it with ./bin/R. However when I run it > with lldb > > 1. ./bin/R -d lldb > 2. run > > I'm, getting: > > Process 74482 launched: > '/Users/dmitry.selivanov/Downloads/R-devel/bin/exec/R' (x86_64) > > dyld: Library not loaded: libRblas.dylib > > Referenced from: /Users/dmitry.selivanov/Downloads/R-devel/bin/exec/R > > Reason: image not found > > Process 74482 stopped > > * thread #1, stop reason = signal SIGABRT > >frame #0: 0x000100574ebe dyld`__abort_with_payload + 10 > > dyld`__abort_with_payload: > > -> 0x100574ebe <+10>: jae0x100574ec8 ; <+20> > >0x100574ec0 <+12>: movq %rax, %rdi > >0x100574ec3 <+15>: jmp0x1005733e8 ; cerror_nocancel > >0x100574ec8 <+20>: retq > > Target 0: (R) stopped. > > > Any suggestions? Things are much easier on linux-based docker images, but I > can't reproduce the reported bug there... > > > Regards > Dmitriy Selivanov > > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Advise on building R on OSX without optimization for debugging
Dear all, I'm trying to debug a segfault reported here https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17850 (thanks Kevin for the nice article https://kevinushey.github.io/blog/2015/04/13/debugging-with-lldb/ about debugging with lldb) I need to compile R without optimization (with the O0 flag) instead of using binaries provided by Simon. Here I have difficulties. What I've tried: 1. Downloaded latest R-devel from https://stat.ethz.ch/R/daily/R-devel.tar.gz 2. Downloaded xz and pcre2 as suggested here https://mac.r-project.org/tools/ 3. run ./confilgure 4. replaced O2 with O0 in Makeconf 5. make Now R is compiled and I can launch it with ./bin/R. However when I run it with lldb 1. ./bin/R -d lldb 2. run I'm, getting: Process 74482 launched: '/Users/dmitry.selivanov/Downloads/R-devel/bin/exec/R' (x86_64) dyld: Library not loaded: libRblas.dylib Referenced from: /Users/dmitry.selivanov/Downloads/R-devel/bin/exec/R Reason: image not found Process 74482 stopped * thread #1, stop reason = signal SIGABRT frame #0: 0x000100574ebe dyld`__abort_with_payload + 10 dyld`__abort_with_payload: -> 0x100574ebe <+10>: jae0x100574ec8 ; <+20> 0x100574ec0 <+12>: movq %rax, %rdi 0x100574ec3 <+15>: jmp0x1005733e8 ; cerror_nocancel 0x100574ec8 <+20>: retq Target 0: (R) stopped. Any suggestions? Things are much easier on linux-based docker images, but I can't reproduce the reported bug there... Regards Dmitriy Selivanov [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
