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This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1936/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 2.2.0  (landing page)
Aaron Lun
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SingleR
git_branch: RELEASE_3_17
git_last_commit: 6b09f4c
git_last_commit_date: 2023-04-25 11:12:06 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

BUILD BIN results for SingleR on kjohnson2


To the developers/maintainers of the SingleR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: SingleR
Version: 2.2.0
Command: rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SingleR_2.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SingleR.buildbin-libdir
StartedAt: 2023-10-19 17:19:21 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 17:23:38 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 256.9 seconds
RetCode: 0
Status:   OK  
PackageFile: SingleR_2.2.0.tgz
PackageFileSize: 1.028 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SingleR.buildbin-libdir && mkdir SingleR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SingleR_2.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SingleR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SingleR.buildbin-libdir SingleR_2.2.0.tar.gz'
>>>>>>> 

* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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:12:30: 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/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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:12:30: 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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from prebuild.cpp:4:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
                size_t NR = curref.index->ndim();
                       ^
In file included from run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
    bool continuing = false;
         ^
In file included from run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        auto parsed = parse_SparseArraySeed<Data, Index>(val0);
                      ^
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/build_indices.hpp:68:34)>' 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/build_indices.hpp:68:34)>' requested here
    raticate::parallelize<double, int>(n, function, num_threads);
              ^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
    SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
    ^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize 
                                 ^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
            subref = build_indices(
                     ^
In file included from run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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:14:29: 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/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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:14:29: 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 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 /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SingleR.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SingleR.buildbin-libdir/SingleR/libs/SingleR.so
>>>>>>> 

>>>>>>> Paths before fix:
SingleR.buildbin-libdir/SingleR/libs/SingleR.so:
	SingleR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "SingleR.buildbin-libdir/SingleR/libs/SingleR.so"

>>>>>>> Paths after fix:

SingleR.buildbin-libdir/SingleR/libs/SingleR.so:
	SingleR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)