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This page was generated on 2022-07-11 11:06:57 -0400 (Mon, 11 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4168
kjohnsonmacOS 12.4 Montereyarm644.2.1 (2022-06-23) -- "Funny-Looking Kid" 3545
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INSTALL results for SingleR on kjohnson


To the developers/maintainers of the SingleR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1847/2130HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 1.99.1  (landing page)
Aaron Lun
Snapshot Date: 2022-07-10 14:00:02 -0400 (Sun, 10 Jul 2022)
git_url: https://git.bioconductor.org/packages/SingleR
git_branch: master
git_last_commit: 59d97fa
git_last_commit_date: 2022-06-26 21:57:17 -0400 (Sun, 26 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  OK    NA    NA    NA  

Summary

Package: SingleR
Version: 1.99.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR
StartedAt: 2022-07-10 19:05:47 -0400 (Sun, 10 Jul 2022)
EndedAt: 2022-07-10 19:08:51 -0400 (Sun, 10 Jul 2022)
EllapsedTime: 183.9 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c custom_parallel.cpp -o custom_parallel.o
In file included from custom_parallel.cpp:1:
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:7:
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 custom_parallel.cpp:1:
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 custom_parallel.cpp:1:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
In file included from custom_parallel.cpp:1:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -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:7:
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
            output = parse_dgCMatrix<Data, Index>(x);
                     ^
find_classic_markers.cpp:27:37: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
        ref_vec.push_back(raticate::parse<double, int>(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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
            output = parse_lgCMatrix<Data, Index>(x);
                     ^
find_classic_markers.cpp:27:37: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
        ref_vec.push_back(raticate::parse<double, int>(ref[r], true));
                                    ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -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:7:
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
            output = parse_dgCMatrix<Data, Index>(x);
                     ^
integrate_build.cpp:24:33: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
        auto parsed = raticate::parse<double, int>(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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
            output = parse_lgCMatrix<Data, Index>(x);
                     ^
integrate_build.cpp:24:33: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
        auto parsed = raticate::parse<double, int>(curref, true);
                                ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -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:7:
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
            output = parse_dgCMatrix<Data, Index>(x);
                     ^
integrate_run.cpp:13:30: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
    auto curtest = raticate::parse<double, int>(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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
            output = parse_lgCMatrix<Data, Index>(x);
                     ^
integrate_run.cpp:13:30: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
    auto curtest = raticate::parse<double, int>(test, true);
                             ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -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:7:
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
            output = parse_dgCMatrix<Data, Index>(x);
                     ^
prebuild.cpp:37:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
    auto parsed = raticate::parse<double, int>(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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
            output = parse_lgCMatrix<Data, Index>(x);
                     ^
prebuild.cpp:37:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
    auto parsed = raticate::parse<double, int>(ref, true);
                            ^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -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:7:
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::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-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
        output = parse_SparseArraySeed<Data, Index>(seed, y);
                 ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:451:42: note: in instantiation of function template specialization 'raticate::UnknownMatrixCore<double, int>::buffered_sparse_extractor_raw<true>' requested here
                        parent->template buffered_sparse_extractor_raw<true>(index, first, last, work);
                                         ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
                    ex.harvest();
                       ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
                                    ^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/annotate_cells.hpp:63:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/annotate_cells.hpp:63:34)>' 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 
                                 ^
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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
            output = parse_dgCMatrix<Data, Index>(x);
                     ^
run.cpp:15:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
    auto parsed = raticate::parse<double, int>(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-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2-arm64/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-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
        auto obtained = primary_dimension(i, first, last, otherdim);
                        ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
            primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::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-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
        new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
            ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
    return parse_CSparseMatrix(seed, y);
           ^
/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
            output = parse_lgCMatrix<Data, Index>(x);
                     ^
run.cpp:15:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
    auto parsed = raticate::parse<double, int>(test, true);
                            ^
7 warnings generated.
clang++ -arch arm64 -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/opt/R/arm64/lib -o SingleR.so RcppExports.o custom_parallel.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-arm64/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)