Aaron Lun
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/SingleR |
| git_branch: RELEASE_3_16 |
| git_last_commit: f36aaf5 |
| git_last_commit_date: 2022-11-01 11:20:26 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:27 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the SingleR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1891/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SingleR 2.0.0 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SingleR |
| Version: 2.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SingleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SingleR_2.0.0.tar.gz |
| StartedAt: 2023-04-10 22:44:46 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 22:49:09 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 263.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SingleR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SingleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SingleR_2.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SingleR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘2.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SingleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotScoreDistribution 7.512 0.13 7.661
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/SingleR.Rcheck/00check.log’
for details.
SingleR.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR
###
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##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c find_classic_markers.cpp -o find_classic_markers.o
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
output = parse_dgCMatrix<Data, Index>(x);
^
find_classic_markers.cpp:27:37: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
ref_vec.push_back(raticate::parse<double, int>(ref[r], true));
^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c integrate_build.cpp -o integrate_build.o
In file included from integrate_build.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
output = parse_dgCMatrix<Data, Index>(x);
^
integrate_build.cpp:24:33: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto parsed = raticate::parse<double, int>(curref, true);
^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c integrate_run.cpp -o integrate_run.o
In file included from integrate_run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c prebuild.cpp -o prebuild.o
In file included from prebuild.cpp:4:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from prebuild.cpp:4:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
output = parse_dgCMatrix<Data, Index>(x);
^
prebuild.cpp:37:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto parsed = raticate::parse<double, int>(ref, true);
^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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++ -mmacosx-version-min=10.13 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocNeighbors/include' -I/usr/local/include -fPIC -Wall -g -O2 -c run.cpp -o run.o
In file included from run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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/4.2/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.2/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.2/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++ -mmacosx-version-min=10.13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SingleR.so RcppExports.o find_classic_markers.o integrate_build.o integrate_run.o prebuild.o run.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-SingleR/00new/SingleR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SingleR)
SingleR.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SingleR)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
> test_check("SingleR")
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, rowsum, scale, sweep
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 294 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 294 ]
>
> proc.time()
user system elapsed
58.626 1.371 99.450
SingleR.Rcheck/SingleR-Ex.timings
| name | user | system | elapsed | |
| SingleR | 1.347 | 0.064 | 1.415 | |
| aggregateReference | 1.413 | 0.036 | 1.451 | |
| classifySingleR | 0.158 | 0.002 | 0.161 | |
| combineCommonResults | 0.384 | 0.006 | 0.392 | |
| combineRecomputedResults | 0.893 | 0.008 | 0.904 | |
| getClassicMarkers | 0.139 | 0.002 | 0.143 | |
| getDeltaFromMedian | 0.217 | 0.003 | 0.222 | |
| matchReferences | 0.384 | 0.023 | 0.408 | |
| mockData | 0.027 | 0.002 | 0.029 | |
| plotDeltaDistribution | 4.755 | 0.118 | 4.885 | |
| plotScoreDistribution | 7.512 | 0.130 | 7.661 | |
| plotScoreHeatmap | 2.938 | 0.068 | 3.019 | |
| pruneScores | 0.278 | 0.004 | 0.282 | |
| rebuildIndex | 0.071 | 0.002 | 0.073 | |
| trainSingleR | 1.127 | 0.027 | 1.160 | |