rmarkdown knit pdf failed due to Rcpp

[zhiruiwang]

When I knit a pdf using rmarkdown, it always return such error:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Rcpp/libs/Rcpp.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Rcpp/libs/Rcpp.so, 6): Library not loaded: /usr/local/clang4/lib/libc++abi.dylib
  Referenced from: /Library/Frameworks/R.framework/Resources/lib/libc++.1.dylib
  Reason: image not found
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

sessionInfo():

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
[6] methods   base     

loaded via a namespace (and not attached):
 [1] compiler_3.4.1   backports_1.1.0  magrittr_1.5    
 [4] RevoUtils_10.0.5 rprojroot_1.2    htmltools_0.3.6 
 [7] tools_3.4.1      yaml_2.1.14      Rcpp_0.12.12    
[10] stringi_1.1.5    rmarkdown_1.6    knitr_1.17      
[13] stringr_1.2.0    digest_0.6.12    evaluate_0.10.1

[coatless]

Not an Rcpp problem. Toolchain issue. Does:

Rcpp::evalCpp("1+1")

give the correct answer?

[eddelbuettel]

That's peculiar because @coatless and I have been working A LOT on rmarkdown use lately. And he uses macOS. And he just beat me...

[eddelbuettel]

Library not loaded: /usr/local/clang4/lib/libc++abi.dylib

You probably just have a hash of pre-built and locally-built components. "If it breaks, rebuild."

[zhiruiwang]

It seems like a problem of clang. How could I fix it?

> Rcpp::evalCpp('1+1')
/bin/sh: /usr/local/clang4/bin/clang++: No such file or directory
make: *** [file3e76680fbd3c.o] Error 127
/usr/local/clang4/bin/clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I"/Library/Frameworks/R.framework/Versions/3.4.1-MRO/Resources/library/Rcpp/include" -I"/private/var/folders/1v/wz_prgn52n91b5x1byjxwnl00000gn/T/RtmpXqL3rj/sourceCpp-x86_64-apple-darwin15.6.0-0.12.12" -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include   -fPIC  -DU_STATIC_IMPLEMENTATION -Wall -mtune=core2 -g -O2 -I/opt/X11/include  -c file3e76680fbd3c.cpp -o file3e76680fbd3c.o
Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir = cacheDir,  : 
  Error 1 occurred building shared library.

[coatless]

You can get the necessary compiler here:

https://github.com/coatless/r-macos-clang

@eddelbuettel please close the ticket.

[zhiruiwang]

@coatless it works. Thank you!