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This page was generated on 2021-10-15 15:06:52 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the scran package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scran.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1713/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scran 1.20.1 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: scran |
Version: 1.20.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scran |
StartedAt: 2021-10-14 09:24:45 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:26:22 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 96.9 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL scran ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘scran’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c choose_effect_size.cpp -o choose_effect_size.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c combine_rho.cpp -o combine_rho.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c compute_blocked_stats.cpp -o compute_blocked_stats.o In file included from compute_blocked_stats.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.1/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c compute_residual_stats.cpp -o compute_residual_stats.o In file included from compute_residual_stats.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.1/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c compute_rho_null.cpp -o compute_rho_null.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c cyclone_scores.cpp -o cyclone_scores.o In file included from cyclone_scores.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.1/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/Resources/library/beachmat/include/beachmat3/lin_matrix.h:95:27: note: hidden overloaded virtual function 'beachmat::lin_matrix::get_row' declared here: different number of parameters (4 vs 3) virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; ^ 8 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c overlap_exprs.cpp -o overlap_exprs.o In file included from overlap_exprs.cpp:3: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include/beachmat3/beachmat.h:24: In file included from /Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include/beachmat3/read_lin_block.h:11: /Library/Frameworks/R.framework/Versions/4.1/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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; ^ overlap_exprs.cpp:202:18: warning: unused variable 'ngroups' [-Wunused-variable] const size_t ngroups=groups.size(); ^ 9 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/dqrng/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/scuttle/include' -I/usr/local/include -fPIC -Wall -g -O2 -c rand_custom.cpp -o rand_custom.o clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o scran.so RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-scran/00new/scran/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scran)