Compilation error ("use of undeclared identifier")

[julianqz]

Hi there. I was trying to install presto and ran into the following problem.

> devtools::install_github("immunogenomics/presto")
Downloading GitHub repo immunogenomics/presto@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/5h/wjwzrklx5pvgg_n7qwc2f4rm0000gn/T/RtmpNQpHJV/remotes9f2b57aaf2b4/immunogenomics-presto-7636b3d/DESCRIPTION’ ...
─  preparing ‘presto’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘presto_1.0.0.tar.gz’
   
* installing *source* package ‘presto’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
using C++11
using SDK: ‘MacOSX15.2.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo:126:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_elem_check.hpp:27:32: error: use of undeclared identifier 'u8'
   27 |     arma_static_check( (sizeof(u8) != 1), "error: type 'u8' has unsupported size" );
      |                                ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_elem_check.hpp:28:32: error: use of undeclared identifier 's8'
   28 |     arma_static_check( (sizeof(s8) != 1), "error: type 's8' has unsupported size" );
      |                                ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_elem_check.hpp:30:32: error: use of undeclared identifier 'u16'
   30 |     arma_static_check( (sizeof(u16) != 2), "error: type 'u16' has unsupported size" );
      |                                ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_elem_check.hpp:31:32: error: use of undeclared identifier 's16'
   31 |     arma_static_check( (sizeof(s16) != 2), "error: type 's16' has unsupported size" );
      |                                ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_elem_check.hpp:33:32: error: use of undeclared identifier 'u32'
   33 |     arma_static_check( (sizeof(u32) != 4), "error: type 'u32' has unsupported size" );
      |                                ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_elem_check.hpp:34:32: error: use of undeclared identifier 's32'
   34 |     arma_static_check( (sizeof(s32) != 4), "error: type 's32' has unsupported size" );
      |                                ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_elem_check.hpp:36:32: error: use of undeclared identifier 'u64'
   36 |     arma_static_check( (sizeof(u64) != 8), "error: type 'u64' has unsupported size" );
      |                                ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_elem_check.hpp:37:32: error: use of undeclared identifier 's64'
   37 |     arma_static_check( (sizeof(s64) != 8), "error: type 's64' has unsupported size" );
      |                                ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo:127:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:29:14: error: use of undeclared identifier 'u32'
   29 | typedef Mat <u32> u32_mat;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:30:14: error: use of undeclared identifier 'u32'
   30 | typedef Col <u32> u32_vec;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:31:14: error: use of undeclared identifier 'u32'
   31 | typedef Col <u32> u32_colvec;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:32:14: error: use of undeclared identifier 'u32'
   32 | typedef Row <u32> u32_rowvec;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:33:14: error: use of undeclared identifier 'u32'
   33 | typedef Cube<u32> u32_cube;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:35:14: error: use of undeclared identifier 's32'
   35 | typedef Mat <s32> s32_mat;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:36:14: error: use of undeclared identifier 's32'
   36 | typedef Col <s32> s32_vec;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:37:14: error: use of undeclared identifier 's32'
   37 | typedef Col <s32> s32_colvec;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:38:14: error: use of undeclared identifier 's32'
   38 | typedef Row <s32> s32_rowvec;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:39:14: error: use of undeclared identifier 's32'
   39 | typedef Cube<s32> s32_cube;
      |              ^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include/armadillo_bits/typedef_mat.hpp:41:14: error: use of undeclared identifier 'u64'
   41 | typedef Mat <u64> u64_mat;
      |              ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘presto’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/presto’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/5h/wjwzrklx5pvgg_n7qwc2f4rm0000gn/T//RtmpNQpHJV/file9f2b68b5fb14/presto_1.0.0.tar.gz’ had non-zero exit status

Here's the session info:

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.3

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/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/Toronto
tzcode source: internal

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

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       cli_3.6.3         rlang_1.1.4       processx_3.8.5    purrr_1.0.2       pkgload_1.4.0    
 [7] promises_1.3.2    shiny_1.10.0      xtable_1.8-4      glue_1.8.0        htmltools_0.5.8.1 httpuv_1.6.15    
[13] ps_1.8.1          pkgbuild_1.4.6    ellipsis_0.3.2    fastmap_1.2.0     lifecycle_1.0.4   memoise_2.0.1    
[19] compiler_4.3.1    miniUI_0.1.1.1    fs_1.6.5          sessioninfo_1.2.2 htmlwidgets_1.6.4 Rcpp_1.0.14      
[25] rstudioapi_0.17.1 urlchecker_1.0.1  later_1.4.1       digest_0.6.37     R6_2.5.1          curl_6.1.0       
[31] usethis_3.1.0     callr_3.7.6       magrittr_2.0.3    tools_4.3.1       mime_0.12         devtools_2.4.5   
[37] profvis_0.4.0     desc_1.4.3        cachem_1.1.0      remotes_2.5.0   

Lastly, I googled "use of undeclared identifier" and saw something about c++; but I'm not sure what to do with that info..

$ c++ -v
Apple clang version 16.0.0 (clang-1600.0.26.6)
Target: arm64-apple-darwin24.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Thanks!

[julianqz]

Quick update: I downgraded RcppArmadillo from 14.2.2-1 to 14.0.2-1 and was then able to install presto. I also dropped Rcpp from 1.0.14 to 1.0.13, but not sure if that helped.