##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf scuttle.buildbin-libdir && mkdir scuttle.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scuttle_1.8.4.tar.gz /Library/Frameworks/R.framework/Resources/bin/R scuttle.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scuttle.buildbin-libdir scuttle_1.8.4.tar.gz'
>>>>>>> 

* installing *source* package ‘scuttle’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/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/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cumulative_prop.cpp -o cumulative_prop.o
In file included from cumulative_prop.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from cumulative_prop.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c downsample_counts.cpp -o downsample_counts.o
In file included from downsample_counts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from downsample_counts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c fit_linear_model.cpp -o fit_linear_model.o
In file included from fit_linear_model.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from fit_linear_model.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pool_size_factors.cpp -o pool_size_factors.o
In file included from pool_size_factors.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from pool_size_factors.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c sum_counts.cpp -o sum_counts.o
In file included from sum_counts.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
In file included from sum_counts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:218:43: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:236:43: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i, size_t first, size_t last) = 0;
                                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:254:46: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 5)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:272:46: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    virtual sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i, size_t first, size_t last) = 0;
                                             ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 5)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:287:35: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_col(size_t c, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:304:35: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i) {
                                  ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:321:38: warning: 'beachmat::lin_sparse_matrix::get_col' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_col(size_t c, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:52:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:81:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_col' declared here: different number of parameters (4 vs 3)
    virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0;
                          ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:338:38: warning: 'beachmat::lin_sparse_matrix::get_row' hides overloaded virtual functions [-Woverloaded-virtual]
    sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i) {
                                     ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:66:24: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0;
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3)
    virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0;
                          ^
9 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c utils.cpp -o utils.o
In file included from utils.cpp:1:
In file included from ./utils.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168:
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    ::sprintf(buff, "%02x", from);
      ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o scuttle.so RcppExports.o cumulative_prop.o downsample_counts.o fit_linear_model.o pool_size_factors.o sum_counts.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/scuttle.buildbin-libdir/00LOCK-scuttle/00new/scuttle/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scuttle)


>>>>>>> 
>>>>>>> FIXING LINKS FOR scuttle.buildbin-libdir/scuttle/libs/scuttle.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "scuttle.buildbin-libdir/scuttle/libs/scuttle.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "scuttle.buildbin-libdir/scuttle/libs/scuttle.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "scuttle.buildbin-libdir/scuttle/libs/scuttle.so"
install_name_tool -change "/opt/R/arm64/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "scuttle.buildbin-libdir/scuttle/libs/scuttle.so"
install_name_tool -change "/opt/R/arm64/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "scuttle.buildbin-libdir/scuttle/libs/scuttle.so"