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List: r-sig-mac
Subject: Re: [R-SIG-Mac] symbol not found in flat namespace '___kmpc_critical'
From: "Sparapani, Rodney via R-SIG-Mac" <r-sig-mac () r-project ! org>
Date: 2023-04-29 22:31:43
Message-ID: CO6PR01MB7452095DD9B7EC5CF3BD5326CB689 () CO6PR01MB7452 ! prod ! exchangelabs ! com
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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@r-project.org> on behalf of Sparapani, Rodney via \
R-SIG-Mac <r-sig-mac@r-project.org>
Date: Saturday, April 29, 2023 at 4:18 PM
To: r-sig-mac@r-project.org <r-sig-mac@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!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1Er \
Xx7PLOgKyTDw$<https://urldefense.com/v3/__https:/github.com/rsparapa/bnptools.git__;!! \
H8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$>
So, to demonstrate, you just need to do something like this�
$ git clone https://urldefense.com/v3/__https://github.com/rsparapa/bnptools.git__;!!H \
8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErX \
x7PLOgKyTDw$<https://urldefense.com/v3/__https:/github.com/rsparapa/bnptools.git__;!!H \
8mHWRdzp34!4rScCMt0gCJ2ZzuZjzo9CEWXYOBECh814z0fzF0OiVjfFcc609ThiLvNcCYt4sIk7wrZhld1ErXx7PLOgKyTDw$> \
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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