unable to install scuttle

[wonliy]

if (!requireNamespace("BiocManager", quietly = TRUE))

• install.packages("BiocManager")
  

BiocManager::install("scuttle")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'scuttle'
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘scuttle’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package ‘scuttle’

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/scuttle_1.4.0.tar.gz'
Content type 'application/x-gzip' length 979954 bytes (956 KB)

downloaded 956 KB

• 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/4.1-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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;
  ^
  8 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/4.1-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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;
  ^
  8 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/4.1-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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;
  ^
  8 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/4.1-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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;
  ^
  8 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/4.1-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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/4.1-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;
  ^
  8 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/4.1-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
  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-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
  ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
  ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
  ld: library not found for -lgfortran
  clang: error: linker command failed with exit code 1 (use -v to see invocation)
  make: *** [scuttle.so] Error 1
  ERROR: compilation failed for package ‘scuttle’
• removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/scuttle’

The downloaded source packages are in
‘/private/var/folders/mq/j68g448j3j59cct30c1wb9hh0000gp/T/Rtmpp9wICn/downloaded_packages’
Old packages: 'Matrix'
Update all/some/none? [a/s/n]:

[PeteHaitch]

Are you on an M1-mac?
Bioconductor is not producing M1 binaries at the moment so the package probably hasn't received much (any?) testing on the M1 platform (except perhaps via running the intel version of R under Rosetta 2). Based on this report, it looks like it might require a little work to get everything working smoothly once Bioconductor has first-class support for the M1 Macs?

[Wenfei-Sun]

Having the same issue while installing from remote::

ld: library not found for -lquadmath
collect2: error: ld returned 1 exit status
make: *** [scuttle.so] Error 1
ERROR: compilation failed for package ‘scuttle’

[PeteHaitch]

Same question: Are you on an M1-mac?
Please also post your sessionInfo() and output of BiocManager::valid()

[Wenfei-Sun]

Thank you Peter for your quick reply!

Yes, my system is an M1-mac, was using the arm based R yesterday.

After switching to the intel version R (via rosetta), it was installed smoothly.

[hank00000]

Same question: Are you on an M1-mac?
Please also post your sessionInfo() and output of BiocManager::valid()

Is this issue still ongoing? Trying to use a package that uses scuttle as a dependency and not able to make it work. M2 mac user.

ERROR: compilation failed for package ‘scuttle’

• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/scuttle’
  Warning: installation of package ‘scuttle’ had non-zero exit status
  The downloaded source packages are in
  ‘/private/var/folders/hg/cjdjk0qj3xgdt9c82c8rc1gr0000gp/T/RtmpOAalN5/downloaded_packages’

[LTLA]

Do you have the full installation traceback? FWIW I am on an M2 and scuttle installs fine.

[hank00000]

Apologies for the extremely long traceback. I'm on R Studio 2023.09.0+463.

BiocManager::install("scuttle")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16)
Installing package(s) 'scuttle'
Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 0Warning: cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/macosx/big-sur-arm64/contrib/4.3/PACKAGES.gz': HTTP status was '404 Not Found'Package which is only available in source form, and may need compilation
of C/C++/Fortran: ‘scuttle’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘scuttle’

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/scuttle_1.11.2.tar.gz'
Content type 'application/x-gzip' length 1029681 bytes (1005 KB)

downloaded 1005 KB

• installing source package ‘scuttle’ ...
  ** using staged installation
  ** libs
  using C++ compiler: ‘Apple clang version 12.0.0 (clang-1200.0.32.29)’
  using C++11
  using SDK: ‘MacOSX11.1.sdk’
  clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
  clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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;
  ^
  8 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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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;
  ^
  8 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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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;
  ^
  8 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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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;
  ^
  8 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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sparse_summarize.cpp -o sparse_summarize.o
  clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:2:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/beachmat.h:24:
  In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11:
  /Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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;
  ^
  8 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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
  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 sparse_summarize.o sum_counts.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
  ld: warning: directory not found for option '-L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0'
  ld: warning: directory not found for option '-L/opt/gfortran/lib'
  ld: library not found for -lgfortran
  clang: error: linker command failed with exit code 1 (use -v to see invocation)
  make: *** [scuttle.so] Error 1
  ERROR: compilation failed for package ‘scuttle’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/scuttle’
  Warning: installation of package ‘scuttle’ had non-zero exit status
  The downloaded source packages are in
  ‘/private/var/folders/hg/cjdjk0qj3xgdt9c82c8rc1gr0000gp/T/RtmpdbA8ZQ/downloaded_packages’

[LTLA]

The fundamental issue is that Bioc is not yet reliably building Mac Arm binaries yet. I see some binaries for release (3.17) on the landing page, but none for devel (3.18) on the corresponding page.

As a result, the user is prompted to install from source, which you can't do without the fortran build tools. This is what I did on my machine, but I don't remember the exact steps involved. I think maybe I got it from homebrew?

Anyway, the simplest solution is to just use Rosetta. Perhaps @vjcitn could comment more on Mac Arm support.

[PeteHaitch]

FWIW I reckon you'd have probably have installed gfortran from https://mac.r-project.org/tools/ (linked from https://cran.r-project.org/bin/macosx/tools/)

[hpages]

@LTLA scuttle's unit tests fail on Mac Arm hence why there's no binary for this platform.

[vjcitn]

Here's some of the detail on my M1:

Last 13 lines of output:
  Objects equal but not identical
  ── Failure ('test-norm.R:299:5'): logNormCounts works for SCE objects (basic) ──
  `out` not identical to `sub`.
  Objects equal but not identical
  ── Failure ('test-size-factors.R:16:5'): librarySizeFactors works as expected ──
  mean(sf) not identical to 1.
  Objects equal but not identical
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1695 ]
  Error: Test failures

probing further...

[hpages]

The build report displays some details already: open https://bioconductor.org/checkResults/3.18/bioc-mac-arm64-LATEST/scuttle/kjohnson1-checksrc.html and scroll down to the "Tests output" section. This is what is displayed:

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(scuttle)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("scuttle")
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

The following object is masked from 'package:abind':

    abind

The following object is masked from 'package:base':

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    apply, scale, sweep

[ FAIL 4 | WARN 13 | SKIP 0 | PASS 1695 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-norm.R:47:5'): normalizeCounts works as expected ─────────────
`out` not identical to `sub`.
Objects equal but not identical
── Failure ('test-norm.R:248:5'): logNormCounts works for SE objects ───────────
`out` not identical to `ref`.
Objects equal but not identical
── Failure ('test-norm.R:299:5'): logNormCounts works for SCE objects (basic) ──
`out` not identical to `sub`.
Objects equal but not identical
── Failure ('test-size-factors.R:16:5'): librarySizeFactors works as expected ──
mean(sf) not identical to 1.
Objects equal but not identical

[ FAIL 4 | WARN 13 | SKIP 0 | PASS 1695 ]
Error: Test failures
Execution halted

[hpages]

Also FWIW the RELEASE_3_18 RELEASE_3_17 branch has the same problem: https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/scuttle/kjohnson2-checksrc.html

[LTLA]

Thanks @hpages. I've relaxed the tests on 1.11.3. Hopefully this should allow the devel builds to pass.