Re: [R-SIG-Mac] CRAN build of R linking to /usr/local/clang4/
Great, thanks much!
Gabor
On Sat, Dec 15, 2018 at 9:47 PM Simon Urbanek
wrote:
>
> Gabor,
>
> this appears to be a known issue with lldb[1] - it doesn’t pass DYLD_*
> variables to the executable anymore. You have to explicitly set it in lldb:
>
> process launch -v
> DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib
>
> or similar. Unfortunately, it means the wrapper can’t help here. You can get
> the full setting from R if the above is not sufficient:
>
> $ R --slave -e 'cat(Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH"))'
> /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server
>
> Cheers,
> Simon
>
> PS: I have fixed the path for the nightly builds so it should be fixed in
> tonight’s build, but the lesson is that the debugger does indeed have an
> environment that is different from the actual executable.
>
> [1] http://lists.llvm.org/pipermail/lldb-dev/2015-October/008691.html
>
>
> > On Dec 15, 2018, at 4:41 AM, Gábor Csárdi wrote:
> >
> > On Sat, Dec 15, 2018 at 2:29 AM Simon Urbanek
> > wrote:
> > [...]
> >> although the R binary itself was omitted. However it doesn’t actually
> >> matter, because it is always executed through the R shell wrapper which
> >> correctly prepends $R_HOME/lib which is why R works just fine.
> >
> > This does not seem to happen with
> >
> > ❯ R -d lldb
> > (lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"
> > [...]
> > (lldb) run
> > [...]
> > Process 52551 launched:
> > '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64)
> > dyld: Library not loaded: /usr/local/clang4/lib/libomp.dylib
> > Referenced from: /Library/Frameworks/R.framework/Resources/bin/exec/R
> > Reason: image not found
> > Process 52551 stopped
> > * thread #1, stop reason = signal SIGABRT
> >frame #0: 0x00010002c9ee dyld`__abort_with_payload + 10
> > dyld`__abort_with_payload:
> > -> 0x10002c9ee <+10>: jae0x10002c9f8 ; <+20>
> >0x10002c9f0 <+12>: movq %rax, %rdi
> >0x10002c9f3 <+15>: jmp0x10002c300 ; cerror_nocancel
> >0x10002c9f8 <+20>: retq
> > (lldb)
> >
> > So maybe this is a bug in the R shell wrapper then? I am not sure, but
> > it would be nice to make 'R -d lldb' work out of the box.
> >
> > Thanks,
> > G.
> >
> > [...]
> >
>
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Re: [R-SIG-Mac] CRAN build of R linking to /usr/local/clang4/
Gabor,
this appears to be a known issue with lldb[1] - it doesn’t pass DYLD_*
variables to the executable anymore. You have to explicitly set it in lldb:
process launch -v
DYLD_FALLBACK_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/lib
or similar. Unfortunately, it means the wrapper can’t help here. You can get
the full setting from R if the above is not sufficient:
$ R --slave -e 'cat(Sys.getenv("DYLD_FALLBACK_LIBRARY_PATH"))'
/Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server
Cheers,
Simon
PS: I have fixed the path for the nightly builds so it should be fixed in
tonight’s build, but the lesson is that the debugger does indeed have an
environment that is different from the actual executable.
[1] http://lists.llvm.org/pipermail/lldb-dev/2015-October/008691.html
> On Dec 15, 2018, at 4:41 AM, Gábor Csárdi wrote:
>
> On Sat, Dec 15, 2018 at 2:29 AM Simon Urbanek
> wrote:
> [...]
>> although the R binary itself was omitted. However it doesn’t actually
>> matter, because it is always executed through the R shell wrapper which
>> correctly prepends $R_HOME/lib which is why R works just fine.
>
> This does not seem to happen with
>
> ❯ R -d lldb
> (lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R"
> [...]
> (lldb) run
> [...]
> Process 52551 launched:
> '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64)
> dyld: Library not loaded: /usr/local/clang4/lib/libomp.dylib
> Referenced from: /Library/Frameworks/R.framework/Resources/bin/exec/R
> Reason: image not found
> Process 52551 stopped
> * thread #1, stop reason = signal SIGABRT
>frame #0: 0x00010002c9ee dyld`__abort_with_payload + 10
> dyld`__abort_with_payload:
> -> 0x10002c9ee <+10>: jae0x10002c9f8 ; <+20>
>0x10002c9f0 <+12>: movq %rax, %rdi
>0x10002c9f3 <+15>: jmp0x10002c300 ; cerror_nocancel
>0x10002c9f8 <+20>: retq
> (lldb)
>
> So maybe this is a bug in the R shell wrapper then? I am not sure, but
> it would be nice to make 'R -d lldb' work out of the box.
>
> Thanks,
> G.
>
> [...]
>
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Re: [R-SIG-Mac] CRAN build of R linking to /usr/local/clang4/
On Sat, Dec 15, 2018 at 2:29 AM Simon Urbanek wrote: [...] > although the R binary itself was omitted. However it doesn’t actually matter, > because it is always executed through the R shell wrapper which correctly > prepends $R_HOME/lib which is why R works just fine. This does not seem to happen with ❯ R -d lldb (lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R" [...] (lldb) run [...] Process 52551 launched: '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64) dyld: Library not loaded: /usr/local/clang4/lib/libomp.dylib Referenced from: /Library/Frameworks/R.framework/Resources/bin/exec/R Reason: image not found Process 52551 stopped * thread #1, stop reason = signal SIGABRT frame #0: 0x00010002c9ee dyld`__abort_with_payload + 10 dyld`__abort_with_payload: -> 0x10002c9ee <+10>: jae0x10002c9f8 ; <+20> 0x10002c9f0 <+12>: movq %rax, %rdi 0x10002c9f3 <+15>: jmp0x10002c300 ; cerror_nocancel 0x10002c9f8 <+20>: retq (lldb) So maybe this is a bug in the R shell wrapper then? I am not sure, but it would be nice to make 'R -d lldb' work out of the box. Thanks, G. [...] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] CRAN build of R linking to /usr/local/clang4/
Gabor, unfortunately, I didn’t see your original e-mail. The paths are correct in libraries, e.g.: $ otool -L /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib | grep libomp /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libomp.dylib (compatibility version 5.0.0, current version 5.0.0) as well as packages: $ otool -L BNN/libs/BNN.so | grep libomp /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libomp.dylib (compatibility version 5.0.0, current version 5.0.0) although the R binary itself was omitted. However it doesn’t actually matter, because it is always executed through the R shell wrapper which correctly prepends $R_HOME/lib which is why R works just fine. This has nothing to do with clang4/clang6. We use clang6 to compile, it is only a matter of the location of Intel’s libomp. Cheers, Simon > On Dec 14, 2018, at 6:00 PM, Gábor Csárdi wrote: > > Would it be possible to fix this for the builds of the upcoming release? > > Thanks, > Gabor > On Wed, Oct 10, 2018 at 11:12 PM Gábor Csárdi wrote: >> >> https://cran.r-project.org/bin/macosx/tools/ suggests installing a >> special clang6 build. OTOH, the R binary links to a library that comes >> with CRAN's clang4 build: >> >> ❯ otool -L /Library/Frameworks/R.framework/Resources/bin/exec/R >> /Library/Frameworks/R.framework/Resources/bin/exec/R: >> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib >> (compatibility version 3.5.0, current version 3.5.1) >> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.dylib >> (compatibility version 0.0.0, current version 0.0.0) >> /usr/local/clang4/lib/libomp.dylib (compatibility version 5.0.0, >> current version 5.0.0) >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current >> version 1226.10.1) >> >> Notice '/usr/local/clang4/lib/libomp.dylib' above. R seems to run >> happily without this file, though, until you start it with lldb: >> >> ❯ R -d lldb >> (lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R" >> Current executable set to >> '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64). >> (lldb) run >> Process 74239 launched: >> '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64) >> dyld: Library not loaded: /usr/local/clang4/lib/libomp.dylib >> Referenced from: /Library/Frameworks/R.framework/Resources/bin/exec/R >> Reason: image not found >> Process 74239 stopped >> * thread #1, stop reason = signal SIGABRT >>frame #0: 0x00010002c9ee dyld`__abort_with_payload + 10 >> dyld`__abort_with_payload: >> -> 0x10002c9ee <+10>: jae0x10002c9f8 ; <+20> >>0x10002c9f0 <+12>: movq %rax, %rdi >>0x10002c9f3 <+15>: jmp0x10002c300 ; cerror_nocancel >>0x10002c9f8 <+20>: retq >> >> After clang4 is installed from http://r.research.att.com/libs/ >> everything is fine. >> >> Is linking to this library intentional? If yes, then maybe the web >> could be updated to suggest installing clang6 and clang4? >> >> Thanks, >> Gabor > > ___ > 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] CRAN build of R linking to /usr/local/clang4/
Would it be possible to fix this for the builds of the upcoming release? Thanks, Gabor On Wed, Oct 10, 2018 at 11:12 PM Gábor Csárdi wrote: > > https://cran.r-project.org/bin/macosx/tools/ suggests installing a > special clang6 build. OTOH, the R binary links to a library that comes > with CRAN's clang4 build: > > ❯ otool -L /Library/Frameworks/R.framework/Resources/bin/exec/R > /Library/Frameworks/R.framework/Resources/bin/exec/R: > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib > (compatibility version 3.5.0, current version 3.5.1) > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.dylib > (compatibility version 0.0.0, current version 0.0.0) > /usr/local/clang4/lib/libomp.dylib (compatibility version 5.0.0, > current version 5.0.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > version 1226.10.1) > > Notice '/usr/local/clang4/lib/libomp.dylib' above. R seems to run > happily without this file, though, until you start it with lldb: > > ❯ R -d lldb > (lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R" > Current executable set to > '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64). > (lldb) run > Process 74239 launched: > '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64) > dyld: Library not loaded: /usr/local/clang4/lib/libomp.dylib > Referenced from: /Library/Frameworks/R.framework/Resources/bin/exec/R > Reason: image not found > Process 74239 stopped > * thread #1, stop reason = signal SIGABRT > frame #0: 0x00010002c9ee dyld`__abort_with_payload + 10 > dyld`__abort_with_payload: > -> 0x10002c9ee <+10>: jae0x10002c9f8 ; <+20> > 0x10002c9f0 <+12>: movq %rax, %rdi > 0x10002c9f3 <+15>: jmp0x10002c300 ; cerror_nocancel > 0x10002c9f8 <+20>: retq > > After clang4 is installed from http://r.research.att.com/libs/ > everything is fine. > > Is linking to this library intentional? If yes, then maybe the web > could be updated to suggest installing clang6 and clang4? > > Thanks, > Gabor ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] CRAN build of R linking to /usr/local/clang4/
https://cran.r-project.org/bin/macosx/tools/ suggests installing a special clang6 build. OTOH, the R binary links to a library that comes with CRAN's clang4 build: ❯ otool -L /Library/Frameworks/R.framework/Resources/bin/exec/R /Library/Frameworks/R.framework/Resources/bin/exec/R: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib (compatibility version 3.5.0, current version 3.5.1) /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /usr/local/clang4/lib/libomp.dylib (compatibility version 5.0.0, current version 5.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1226.10.1) Notice '/usr/local/clang4/lib/libomp.dylib' above. R seems to run happily without this file, though, until you start it with lldb: ❯ R -d lldb (lldb) target create "/Library/Frameworks/R.framework/Resources/bin/exec/R" Current executable set to '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64). (lldb) run Process 74239 launched: '/Library/Frameworks/R.framework/Resources/bin/exec/R' (x86_64) dyld: Library not loaded: /usr/local/clang4/lib/libomp.dylib Referenced from: /Library/Frameworks/R.framework/Resources/bin/exec/R Reason: image not found Process 74239 stopped * thread #1, stop reason = signal SIGABRT frame #0: 0x00010002c9ee dyld`__abort_with_payload + 10 dyld`__abort_with_payload: -> 0x10002c9ee <+10>: jae0x10002c9f8 ; <+20> 0x10002c9f0 <+12>: movq %rax, %rdi 0x10002c9f3 <+15>: jmp0x10002c300 ; cerror_nocancel 0x10002c9f8 <+20>: retq After clang4 is installed from http://r.research.att.com/libs/ everything is fine. Is linking to this library intentional? If yes, then maybe the web could be updated to suggest installing clang6 and clang4? Thanks, Gabor ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
