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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scuttle
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘scuttle’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cumulative_prop.cpp -o cumulative_prop.o
In file included from cumulative_prop.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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;
^
8 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c downsample_counts.cpp -o downsample_counts.o
In file included from downsample_counts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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;
^
8 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c fit_linear_model.cpp -o fit_linear_model.o
In file included from fit_linear_model.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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;
^
8 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pool_size_factors.cpp -o pool_size_factors.o
In file included from pool_size_factors.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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;
^
8 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c sum_counts.cpp -o sum_counts.o
In file included from sum_counts.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
/Library/Frameworks/R.framework/Versions/4.2/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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;
^
8 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -mmacosx-version-min=10.13 -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/usr/local/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/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (10.14) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (10.14) than being linked (10.13)
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/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)
