############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’ * installing *source* package ‘SingleR’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c find_classic_markers.cpp -o find_classic_markers.o In file included from find_classic_markers.cpp:2: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:6: In file included from ../inst/include/singlepp/BasicScorer.hpp:5: In file included from ../inst/include/singlepp/annotate_cells.hpp:9: ../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from find_classic_markers.cpp:2: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ ../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ In file included from find_classic_markers.cpp:2: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from find_classic_markers.cpp:2: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from find_classic_markers.cpp:2: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix' requested here output = parse_dgCMatrix(x); ^ find_classic_markers.cpp:27:37: note: in instantiation of function template specialization 'raticate::parse' requested here ref_vec.push_back(raticate::parse(ref[r], true)); ^ In file included from find_classic_markers.cpp:2: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix' requested here output = parse_lgCMatrix(x); ^ find_classic_markers.cpp:27:37: note: in instantiation of function template specialization 'raticate::parse' requested here ref_vec.push_back(raticate::parse(ref[r], true)); ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c integrate_build.cpp -o integrate_build.o In file included from integrate_build.cpp:3: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:6: In file included from ../inst/include/singlepp/BasicScorer.hpp:5: In file included from ../inst/include/singlepp/annotate_cells.hpp:9: ../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from integrate_build.cpp:3: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ ../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ In file included from integrate_build.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from integrate_build.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from integrate_build.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix' requested here output = parse_dgCMatrix(x); ^ integrate_build.cpp:24:33: note: in instantiation of function template specialization 'raticate::parse' requested here auto parsed = raticate::parse(curref, true); ^ In file included from integrate_build.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix' requested here output = parse_lgCMatrix(x); ^ integrate_build.cpp:24:33: note: in instantiation of function template specialization 'raticate::parse' requested here auto parsed = raticate::parse(curref, true); ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c integrate_run.cpp -o integrate_run.o In file included from integrate_run.cpp:3: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:6: In file included from ../inst/include/singlepp/BasicScorer.hpp:5: In file included from ../inst/include/singlepp/annotate_cells.hpp:9: ../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from integrate_run.cpp:3: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ ../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ In file included from integrate_run.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from integrate_run.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from integrate_run.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix' requested here output = parse_dgCMatrix(x); ^ integrate_run.cpp:12:30: note: in instantiation of function template specialization 'raticate::parse' requested here auto curtest = raticate::parse(test, true); ^ In file included from integrate_run.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix' requested here output = parse_lgCMatrix(x); ^ integrate_run.cpp:12:30: note: in instantiation of function template specialization 'raticate::parse' requested here auto curtest = raticate::parse(test, true); ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c prebuild.cpp -o prebuild.o In file included from prebuild.cpp:4: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:6: In file included from ../inst/include/singlepp/BasicScorer.hpp:5: In file included from ../inst/include/singlepp/annotate_cells.hpp:9: ../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from prebuild.cpp:4: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ ../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ In file included from prebuild.cpp:4: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from prebuild.cpp:4: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from prebuild.cpp:4: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix' requested here output = parse_dgCMatrix(x); ^ prebuild.cpp:37:29: note: in instantiation of function template specialization 'raticate::parse' requested here auto parsed = raticate::parse(ref, true); ^ In file included from prebuild.cpp:4: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix' requested here output = parse_lgCMatrix(x); ^ prebuild.cpp:37:29: note: in instantiation of function template specialization 'raticate::parse' requested here auto parsed = raticate::parse(ref, true); ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c run.cpp -o run.o In file included from run.cpp:3: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:10: In file included from ../inst/include/singlepp/Classifier.hpp:6: In file included from ../inst/include/singlepp/BasicScorer.hpp:5: In file included from ../inst/include/singlepp/annotate_cells.hpp:9: ../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable] size_t NR = curref.index->ndim(); ^ In file included from run.cpp:3: In file included from ./utils.h:24: In file included from ../inst/include/singlepp/singlepp.hpp:15: ../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ ../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable] bool continuing = false; ^ In file included from run.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from run.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed>' requested here output = parse_SparseArraySeed(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) auto parsed = parse_SparseArraySeed(val0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator::harvest' requested here ex.harvest(); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run' requested here parallel_coordinator().template run(njobs, fun, nthreads); ^ ./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize' requested here raticate::parallelize(n, function, num_threads); ^ ../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void { ^ ./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL' #define SINGLEPP_CUSTOM_PARALLEL parallelize ^ ../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here subref = build_indices( ^ In file included from run.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix' requested here output = parse_dgCMatrix(x); ^ run.cpp:14:29: note: in instantiation of function template specialization 'raticate::parse' requested here auto parsed = raticate::parse(test, true); ^ In file included from run.cpp:3: In file included from ./utils.h:13: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5: /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable] auto xIt = values.begin() + pstart; ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension' requested here auto obtained = primary_dimension(i, first, last, otherdim); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::primary_dimension_expanded' requested here primary_dimension_expanded(c, first, last, this->nrows, buffer, 0); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::column' requested here CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) { ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix, tatami::ArrayView, tatami::ArrayView>::CompressedSparseMatrix' requested here new tatami::CompressedSparseMatrix( ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix>' requested here return parse_CSparseMatrix(seed, y); ^ /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix' requested here output = parse_lgCMatrix(x); ^ run.cpp:14:29: note: in instantiation of function template specialization 'raticate::parse' requested here auto parsed = raticate::parse(test, true); ^ 7 warnings generated. clang++ -mmacosx-version-min=10.13 -std=gnu++17 -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 SingleR.so RcppExports.o find_classic_markers.o integrate_build.o integrate_run.o prebuild.o run.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-SingleR/00new/SingleR/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 (SingleR)