densvis, scuttle, scatter cannot be installed

[Jeffchingg]

Hi,

I am new to R. During the installing Catalyst, there are error message as below. Can you let me know what I should do? I am using Mac Ventura 13.2.

Thanks a lot.

Jeff

devtools::install_github("HelenaLC/CATALYST") Downloading GitHub repo HelenaLC/CATALYST@HEAD These packages have more recent versions available. It is recommended to update all of them. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: scuttle (1.9.4 -> 1.10.3) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 2 densvis (NA -> 1.10.3) [CRAN] scuttle (1.9.4 -> 1.10.3) [CRAN] scater (NA -> 1.28.0) [CRAN] Installing 3 packages: densvis, scuttle, scater

There is a binary version available but the source version is later: binary source needs_compilation scuttle 1.9.4 1.10.3 TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) y Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘densvis’ Do you want to attempt to install these from sources? (Yes/no/cancel) y installing the source packages ‘densvis’, ‘scuttle’, ‘scater’

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/densvis_1.10.3.tar.gz' Content type 'application/x-gzip' length 1731202 bytes (1.7 MB)

downloaded 1.7 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/scuttle_1.10.3.tar.gz' Content type 'application/x-gzip' length 1029617 bytes (1005 KB)

downloaded 1005 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/scater_1.28.0.tar.gz' Content type 'application/x-gzip' length 4089325 bytes (3.9 MB)

downloaded 3.9 MB

• installing source package ‘densvis’ ... using non-staged installation via StagedInstall field libs using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++14 using SDK: ‘MacOSX13.3.sdk’ clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densne.cpp -o densne.o densne.cpp:181:24: warning: variable 'row_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized] for(int i = 0; i < N N; i++) P[i] /= sum_P; ^~~~~ densne.cpp:201:33: note: uninitialized use occurs here computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift); ^~~~~ densne.cpp:181:24: note: remove the condition if it is always true for(int i = 0; i < N N; i++) P[i] /= sum_P; ^~~~~ densne.cpp:154:35: note: initialize the variable 'row_P' to silence this warning double P; unsigned int row_P; unsigned int col_P; double val_P; double val_D; ^ = nullptr densne.cpp:181:24: warning: variable 'col_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized] for(int i = 0; i < N N; i++) P[i] /= sum_P; ^~~~~ densne.cpp:201:40: note: uninitialized use occurs here computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift); ^~~~~ densne.cpp:181:24: note: remove the condition if it is always true for(int i = 0; i < N N; i++) P[i] /= sum_P; ^~~~~ densne.cpp:154:56: note: initialize the variable 'col_P' to silence this warning double P; unsigned int row_P; unsigned int col_P; double val_P; double val_D; ^ = nullptr densne.cpp:181:24: warning: variable 'val_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized] for(int i = 0; i < N N; i++) P[i] /= sum_P; ^~~~~ densne.cpp:201:47: note: uninitialized use occurs here computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift); ^~~~~ densne.cpp:181:24: note: remove the condition if it is always true for(int i = 0; i < N N; i++) P[i] /= sum_P; ^~~~~ densne.cpp:154:71: note: initialize the variable 'val_P' to silence this warning double P; unsigned int row_P; unsigned int col_P; double val_P; double val_D; ^ = nullptr densne.cpp:181:24: warning: variable 'val_D' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized] for(int i = 0; i < N N; i++) P[i] /= sum_P; ^~~~~ densne.cpp:201:54: note: uninitialized use occurs here computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift); ^~~~~ densne.cpp:181:24: note: remove the condition if it is always true for(int i = 0; i < N N; i++) P[i] /= sum_P; ^~~~~ densne.cpp:154:86: note: initialize the variable 'val_D' to silence this warning double P; unsigned int row_P; unsigned int col_P; double val_P; double val_D; ^ = nullptr 4 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c densvis.cpp -o densvis.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sptree.cpp -o sptree.o clang++ -arch arm64 -std=gnu++14 -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 densvis.so RcppExports.o densne.o densvis.o sptree.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: *** [densvis.so] Error 1 ERROR: compilation failed for package ‘densvis’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/densvis’
• installing source package ‘scuttle’ ... using staged installation libs using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’ using C++11 using SDK: ‘MacOSX13.3.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’
• restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/scuttle’ ERROR: dependency ‘densvis’ is not available for package ‘scater’
• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/scater’

The downloaded source packages are in ‘/private/var/folders/4g/k4jqbl916jv_ml53s141yfswjy8k6x/T/RtmpJcSr5K/downloaded_packages’ ── R CMD build ────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/private/var/folders/4g/k4jqbl916jv_ml53s141yfswjy8k6x/T/RtmpJcSr5K/remotes1983621b7165/HelenaLC-CATALYST-f3e294e/DESCRIPTION’ ... ─ preparing ‘CATALYST’: ✔ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘CATALYST_1.24.0.tar.gz’ Warning: invalid uid value replaced by that for user 'nobody' Warning: invalid gid value replaced by that for user 'nobody'

ERROR: dependency ‘scater’ is not available for package ‘CATALYST’

• removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CATALYST’ Warning messages: 1: In i.p(...) : installation of package ‘densvis’ had non-zero exit status 2: In i.p(...) : installation of package ‘scuttle’ had non-zero exit status 3: In i.p(...) : installation of package ‘scater’ had non-zero exit status 4: In i.p(...) : installation of package ‘/var/folders/4g/k4jqbl916jv_ml53s141yfswjy8k6x/T//RtmpJcSr5K/file19834dd9daaf/CATALYST_1.24.0.tar.gz’ had non-zero exit status

[SamGG]

Hi, I am not a Mac user, but a Windows user. Whatever I install, I never update while installing. Either I install a package, either I update installed packages. So, you should try without updating, ie option 3: None. Best.

[markrobinsonuzh]

Maybe a couple other things to say:

• I would recommend installing CATALYST in the standard way, as it suggests here with the command BiocManager::install("CATALYST") (assumes BiocManager is installed)
• Try answering 'no' to any of the questions about compiling from source; for most day-to-day R use on a Mac, there are binaries and you should not need to compile from source.

[Jeffchingg]

Thanks Mark and Sam for the comments. The problem to answer "no" for those questions will cause the installation exit automatically. Eventually I solved the problem. I used Homedrew to install gcc which made this compilation issue. Everything is working now