error in batchelor installation

[wonliy]

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

• install.packages("BiocManager")
  

BiocManager::install("batchelor")
'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) 'batchelor'
also installing the dependency ‘scuttle’

Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘scuttle’
‘batchelor’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source packages ‘scuttle’, ‘batchelor’

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

trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/batchelor_1.10.0.tar.gz'
Content type 'application/x-gzip' length 1996990 bytes (1.9 MB)

downloaded 1.9 MB

• 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’
  ERROR: dependency ‘scuttle’ is not available for package ‘batchelor’
• removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/batchelor’

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]:
n
Warning messages:
1: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
2: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
3: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
4: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
5: In .inet_warning(msg) :
unable to access index for repository https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1:
cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
6: In .inet_warning(msg) :
installation of package ‘scuttle’ had non-zero exit status
7: In .inet_warning(msg) :
installation of package ‘batchelor’ had non-zero exit status

[PeteHaitch]

See LTLA/scuttle#14 (comment)