[R-pkg-devel] How to use O4 flag in an RCpp project?

[Peiyuan Zhu]

Ok now I replaced all -g -O2 with -O3 in Makeconf then it seems to have
worked. Not sure which line exactly that has led to it working tho.

> load_all(".")
ℹ Loading dst
Exports from /Users/garyzhubc/Work/dst-1/src/belplauHFast.cpp:
   NumericMatrix belplauHFast(NumericVector MACC, const arma::sp_mat& W2,
NumericMatrix h, bool display_progress = false)

Exports from /Users/garyzhubc/Work/dst-1/src/closure.cpp:
   LogicalMatrix closure(IntegerMatrix ttx, bool computeJoin = true, bool
display_progress = false)

Exports from /Users/garyzhubc/Work/dst-1/src/closureSparse.cpp:
   arma::sp_mat closureSparse(arma::sp_mat ttx, bool computeJoin = true,
bool display_progress = false)

Exports from /Users/garyzhubc/Work/dst-1/src/commSparse.cpp:
   NumericVector commSparse(arma::sp_mat x, arma::sp_mat x_c, double a,
bool display_progress = false)

Exports from /Users/garyzhubc/Work/dst-1/src/iotaSparse.cpp:
   arma::sp_mat iotaSparse(arma::sp_mat tt, bool display_progress = false)

Exports from /Users/garyzhubc/Work/dst-1/src/treeFast.cpp:
   SEXP buildTreeFast(const arma::sp_mat& tt, const Rcpp::NumericVector& q,
bool display_progress = false, Rcpp::Nullable<Rcpp::IntegerVector> indices
= R_NilValue)
   SEXP updateTreeFast(SEXP tree_ptr, LogicalVector xx_vec, LogicalVector
s_vec)
   SEXP supersetFast(SEXP node_ptr, LogicalVector z_vec)
   NumericVector unravelTreeFast(SEXP tree_ptr)
   List inspectNode(SEXP tree_ptr)
   Rcpp::List inspectNodes(Rcpp::List trees)
   Rcpp::List buildTreesFast(const arma::sp_mat& tt, const
Rcpp::NumericVector& q)
   Rcpp::NumericVector unravelTreesFast(Rcpp::List trees)
   Rcpp::List updateTreesFast(Rcpp::List trees, Rcpp::NumericVector xx_vec,
Rcpp::NumericVector s_vec)

/Users/garyzhubc/Work/dst-1/src/RcppExports.cpp updated.
/Users/garyzhubc/Work/dst-1/R/RcppExports.R updated.
ℹ Re-compiling dst
── R CMD INSTALL
──────────────────────────────────────────────────────────────────────────────────────
─  installing *source* package ‘dst’ ...
   ** using staged installation
   ** libs
   using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’
   using SDK: ‘’
   clang++ -arch x86_64 -std=gnu++17
-I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include'
-I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include'
-I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include'
-I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include'
-I/opt/R/x86_64/include   -O3 -fPIC  -falign-functions=64 -Wall -O3   -c
RcppExports.cpp -o RcppExports.o


On Wed, May 21, 2025 at 1:08 PM Peiyuan Zhu <garyzhubc using gmail.com> wrote:

> The closest I got is the below after putting:
>
> PKG_CXXFLAGS = -O3
> PKG_CFLAGS = -O3
>
> in Makevars. Still I'm seeing "-falign-functions=64 -Wall -g -O2" after
> -O3 so the last flag always wins.
>
>
> > load_all(".")
> ℹ Loading dst
> Exports from /Users/garyzhubc/Work/dst-1/src/belplauHFast.cpp:
>    NumericMatrix belplauHFast(NumericVector MACC, const arma::sp_mat& W2,
> NumericMatrix h, bool display_progress = false)
>
> Exports from /Users/garyzhubc/Work/dst-1/src/closure.cpp:
>    LogicalMatrix closure(IntegerMatrix ttx, bool computeJoin = true, bool
> display_progress = false)
>
> Exports from /Users/garyzhubc/Work/dst-1/src/closureSparse.cpp:
>    arma::sp_mat closureSparse(arma::sp_mat ttx, bool computeJoin = true,
> bool display_progress = false)
>
> Exports from /Users/garyzhubc/Work/dst-1/src/commSparse.cpp:
>    NumericVector commSparse(arma::sp_mat x, arma::sp_mat x_c, double a,
> bool display_progress = false)
>
> Exports from /Users/garyzhubc/Work/dst-1/src/iotaSparse.cpp:
>    arma::sp_mat iotaSparse(arma::sp_mat tt, bool display_progress = false)
>
> Exports from /Users/garyzhubc/Work/dst-1/src/treeFast.cpp:
>    SEXP buildTreeFast(const arma::sp_mat& tt, const Rcpp::NumericVector&
> q, bool display_progress = false, Rcpp::Nullable<Rcpp::IntegerVector>
> indices = R_NilValue)
>    SEXP updateTreeFast(SEXP tree_ptr, LogicalVector xx_vec, LogicalVector
> s_vec)
>    SEXP supersetFast(SEXP node_ptr, LogicalVector z_vec)
>    NumericVector unravelTreeFast(SEXP tree_ptr)
>    List inspectNode(SEXP tree_ptr)
>    Rcpp::List inspectNodes(Rcpp::List trees)
>    Rcpp::List buildTreesFast(const arma::sp_mat& tt, const
> Rcpp::NumericVector& q)
>    Rcpp::NumericVector unravelTreesFast(Rcpp::List trees)
>    Rcpp::List updateTreesFast(Rcpp::List trees, Rcpp::NumericVector
> xx_vec, Rcpp::NumericVector s_vec)
>
> /Users/garyzhubc/Work/dst-1/src/RcppExports.cpp updated.
> /Users/garyzhubc/Work/dst-1/R/RcppExports.R updated.
> ℹ Re-compiling dst
> ── R CMD INSTALL
> ──────────────────────────────────────────────────────────────────────────────────────
> ─  installing *source* package ‘dst’ ... (1.4s)
>    ** using staged installation
>    ** libs
>    using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.0.13.3)’
>    using SDK: ‘’
>    clang++ -arch x86_64 -std=gnu++17
> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
>  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include'
> -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include'
> -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include'
> -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include'
> -I/opt/R/x86_64/include   -O3 -fPIC  -falign-functions=64 -Wall -g -O2   -c
> RcppExports.cpp -o RcppExports.o
>
>
>
> On Wed, May 21, 2025 at 12:57 PM Dirk Eddelbuettel <edd using debian.org> wrote:
>
>>
>> On 21 May 2025 at 09:34, Peiyuan Zhu wrote:
>> | I'm happy to just use O3 but it sounds like this isn't something doable
>> in C++.
>>
>> It is called -O3, not 'O3'. (Also Rcpp, not RCpp.)
>>
>> We do not know what you did because you never posted anything even
>> remotely
>> close to reproducible.
>>
>> | Maybe I should just give up RCpp and move the program entirely to C++
>> from now
>> | on.
>>
>> Whatever works for you. You could also look at some existing projects and
>> see
>> what they do; I just did a quick recursive search below my git directory
>> on
>> the machine and saw at least two packages set -O3.  So it works for some
>> of us.
>>
>> Good luck either way.
>>
>> Best, Dirk
>>
>> --
>> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>>
>

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