[R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical'

Mon May 1 03:34:27 CEST 2023

Rodney,

I don't know much about OpenMP and macOS, but note that these days
  https://mac.r-project.org/tools/
says
  "Additional information on the OpenMP page is available for those
interested in OpenMP support which is not supported by Apple, but still
possible with additional libraries."
and links to
  https://mac.r-project.org/openmp/

I _believe_ that this requires the _user_ (or the check/build system) of
the package on macOS to install one of the custom clang compilers listed on
the page. For this reason, I don't think it is trivial to get the
package through CRAN or distribute the package if it links / uses OpenMP. I
could be wrong of course, since it is not something I follow. I am guessing
the best solution (which could be complicated) is to have a configure
script which checks at build time whether the system supports OpenMP. This
feels like something someone has thought about.

Best,
Kasper

On Sat, Apr 29, 2023 at 6:32 PM Sparapani, Rodney via R-SIG-Mac <
r-sig-mac using r-project.org> wrote:

> Oh, that was totally self-inflicted.
> I had commented out PKG_LIBS in Makevars.in
> That does work on Linux with OpenMP somehow.
> However, it does NOT with macOS.  Thanks
>
> --
> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
> Director, Wisconsin Chapter of the American Statistical Association
> Institute for Health and Equity, Division of Biostatistics
> Medical College of Wisconsin, Milwaukee Campus
>
>
> From: R-SIG-Mac <r-sig-mac-bounces using r-project.org> on behalf of Sparapani,
> Rodney via R-SIG-Mac <r-sig-mac using r-project.org>
> Date: Saturday, April 29, 2023 at 4:18 PM
> To: r-sig-mac using r-project.org <r-sig-mac using r-project.org>
> Subject: [R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical'
> ATTENTION: This email originated from a sender outside of MCW. Use caution
> when clicking on links or opening attachments.
> ________________________________
>
> Hi Gang:
>
> After hours of debugging, I�m stuck and hoping that someone has an
> idea of what the issue is here.  Any hints/tips/etc. are greatly
> appreciated!
>
> I�m getting this error from my CRAN package, nftbart.  Right now, I�m
> preparing for a new release: v1.6.  However, I�m stumped by this error
> message that I get when installing with OpenMP.  Without OpenMP,
> everything is fine; however, the package benefits greatly from OpenMP.
>
> I am getting the same results for R 4.2.3 and 4.3.0 RC.  The source code is
> on github at
> https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$
> <
> https://urldefense.com/v3/__https:/github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$
> >
>
> So, to demonstrate, you just need to do something like this�
>
>
> $ git clone
> https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$
> <
> https://urldefense.com/v3/__https:/github.com/rsparapa/bnptools.git__;!!H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$>
> DIR
>
> $ cd DIR
>
> $ R CMD build nftbart
>
> $ R CMD INSTALL nftbart_1.6.tar.gz
>
> * installing to library
> �/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library�
>
> * installing *source* package �nftbart� ...
>
> ** using staged installation
>
> checking whether the C++ compiler works... yes
>
> checking for C++ compiler default output file name... a.out
>
> checking for suffix of executables...
>
> checking whether we are cross compiling... no
>
> checking for suffix of object files... o
>
> checking whether we are using the GNU C++ compiler... yes
>
> checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
>
> checking for clang++ -arch x86_64 -std=gnu++17 option to support OpenMP...
> -lomp -Xclang -fopenmp
>
> configure: creating ./config.status
>
> config.status: creating src/Makevars
>
> ** libs
>
> using C compiler: �Apple clang version 14.0.3 (clang-1403.0.22.14.1)�
>
> using C++ compiler: �Apple clang version 14.0.3 (clang-1403.0.22.14.1)�
>
> using SDK: ��
>
> clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -lomp -Xclang -fopenmp
> -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include'
> -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c
> init.c -o init.o
>
> clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -lomp
> -Xclang -fopenmp
> -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include'
> -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c
> nftbart.cpp -o nftbart.o
>
> clang++ -arch x86_64 -std=gnu++17 -dynamiclib
> -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
> -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib
> -L/opt/R/x86_64/lib -o nftbart.so init.o nftbart.o
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
>
> installing to
> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs
>
> ** R
>
> ** data
>
> ** demo
>
> ** byte-compile and prepare package for lazy loading
>
> ** help
>
> *** installing help indices
>
> ** building package indices
>
> ** testing if installed package can be loaded from temporary location
>
> Error: package or namespace load failed for �nftbart� in dyn.load(file,
> DLLpath = DLLpath, ...):
>
>  unable to load shared object
> '/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so':
>
>
> dlopen(/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-nftbart/00new/nftbart/libs/nftbart.so,
> 0x0006): symbol not found in flat namespace '___kmpc_critical'
>
> Error: loading failed
>
> Execution halted
>
> ERROR: loading failed
>
> * removing
> �/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart�
>
> * restoring previous
> �/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/nftbart�
>
> > sessionInfo()
> R version 4.3.0 Patched (2023-04-27 r84338)
> Platform: x86_64-apple-darwin20 (64-bit)
> Running under: macOS Ventura 13.2.1
>
> Matrix products: default
> BLAS:
>  /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;
> LAPACK version 3.11.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> time zone: America/Chicago
> tzcode source: internal
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] compiler_4.3.0
> >
>
> OpenMP Build: LLVM 14.0.6
>
> $ codesign -d -vv /usr/local/lib/libomp.dylib
>
> Executable=/usr/local/lib/libomp.dylib
>
> Identifier=libomp
>
> Format=Mach-O universal (x86_64 arm64)
>
> CodeDirectory v=20400 size=6506 flags=0x0(none) hashes=198+2
> location=embedded
>
> Signature size=8977
>
> Authority=Developer ID Application: Simon Urbanek (VZLD955F6P)
>
> Authority=Developer ID Certification Authority
>
> Authority=Apple Root CA
>
> Timestamp=Feb 5, 2023 at 4:26:54 PM
>
> Info.plist=not bound
>
> TeamIdentifier=VZLD955F6P
>
> Sealed Resources=none
>
> Internal requirements count=1 size=168
>
> --
> Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
> Director, Wisconsin Chapter of the American Statistical Association
> Institute for Health and Equity, Division of Biostatistics
> Medical College of Wisconsin, Milwaukee Campus
>
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>
>         [[alternative HTML version deleted]]
>
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>

-- 
Best,
Kasper

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