Aaron Lun
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/SingleR |
| git_branch: RELEASE_3_17 |
| git_last_commit: 6b09f4c |
| git_last_commit_date: 2023-04-25 11:12:06 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 | ||||
| Package 1936/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SingleR 2.2.0 (landing page) Aaron Lun
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the SingleR package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SingleR |
| Version: 2.2.0 |
| 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_2.2.0.tar.gz |
| StartedAt: 2023-10-19 01:48:02 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 01:58:05 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 603.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SingleR.Rcheck |
| Warnings: 1 |
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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_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SingleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘2.2.0’
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
Not all R platforms support C++17
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/SingleR/libs/SingleR.so’:
Found ‘_sprintf’, possibly from ‘sprintf’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotScoreDistribution 10.496 0.157 18.840
plotDeltaDistribution 6.329 0.151 11.534
plotScoreHeatmap 3.022 0.069 5.513
* 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 WARNING
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SingleR.Rcheck/00check.log’
for details.
SingleR.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SingleR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c find_classic_markers.cpp -o find_classic_markers.o
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
output = parse_dgCMatrix<Data, Index>(x);
^
find_classic_markers.cpp:27:37: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
ref_vec.push_back(raticate::parse<double, int>(ref[r], true));
^
In file included from find_classic_markers.cpp:2:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
output = parse_lgCMatrix<Data, Index>(x);
^
find_classic_markers.cpp:27:37: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
ref_vec.push_back(raticate::parse<double, int>(ref[r], true));
^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrate_build.cpp -o integrate_build.o
In file included from integrate_build.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
output = parse_dgCMatrix<Data, Index>(x);
^
integrate_build.cpp:24:33: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto parsed = raticate::parse<double, int>(curref, true);
^
In file included from integrate_build.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
output = parse_lgCMatrix<Data, Index>(x);
^
integrate_build.cpp:24:33: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto parsed = raticate::parse<double, int>(curref, true);
^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c integrate_run.cpp -o integrate_run.o
In file included from integrate_run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
output = parse_dgCMatrix<Data, Index>(x);
^
integrate_run.cpp:12:30: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto curtest = raticate::parse<double, int>(test, true);
^
In file included from integrate_run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
output = parse_lgCMatrix<Data, Index>(x);
^
integrate_run.cpp:12:30: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto curtest = raticate::parse<double, int>(test, true);
^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c prebuild.cpp -o prebuild.o
In file included from prebuild.cpp:4:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from prebuild.cpp:4:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
output = parse_dgCMatrix<Data, Index>(x);
^
prebuild.cpp:37:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto parsed = raticate::parse<double, int>(ref, true);
^
In file included from prebuild.cpp:4:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
output = parse_lgCMatrix<Data, Index>(x);
^
prebuild.cpp:37:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto parsed = raticate::parse<double, int>(ref, true);
^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BiocNeighbors/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c run.cpp -o run.o
In file included from run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:10:
In file included from ../inst/include/singlepp/Classifier.hpp:6:
In file included from ../inst/include/singlepp/BasicScorer.hpp:5:
In file included from ../inst/include/singlepp/annotate_cells.hpp:9:
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable 'NR' [-Wunused-variable]
size_t NR = curref.index->ndim();
^
In file included from run.cpp:3:
In file included from ./utils.h:24:
In file included from ../inst/include/singlepp/singlepp.hpp:15:
../inst/include/singlepp/load_references.hpp:348:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable 'continuing' [-Wunused-variable]
bool continuing = false;
^
In file included from run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:113:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<14>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:94:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, std::vector<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(v), decltype(i), decltype(p)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SparseArraySeed.hpp:116:18: note: in instantiation of function template specialization 'raticate::parse_SparseArraySeed<double, int, Rcpp::Vector<13>>' requested here
output = parse_SparseArraySeed<Data, Index>(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:320:23: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
auto parsed = parse_SparseArraySeed<Data, Index>(val0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/UnknownMatrix.hpp:554:24: note: in instantiation of member function 'raticate::UnknownEvaluator<double, int>::harvest' requested here
ex.harvest();
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/parallelize.hpp:37:37: note: in instantiation of function template specialization 'raticate::ParallelCoordinator::run<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
parallel_coordinator().template run<Data, Index>(njobs, fun, nthreads);
^
./utils.h:17:15: note: in instantiation of function template specialization 'raticate::parallelize<double, int, (lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
raticate::parallelize<double, int>(n, function, num_threads);
^
../inst/include/singlepp/build_indices.hpp:68:5: note: in instantiation of function template specialization 'parallelize<(lambda at ../inst/include/singlepp/build_indices.hpp:68:34)>' requested here
SINGLEPP_CUSTOM_PARALLEL(NC, [&](size_t start, size_t end) -> void {
^
./utils.h:21:34: note: expanded from macro 'SINGLEPP_CUSTOM_PARALLEL'
#define SINGLEPP_CUSTOM_PARALLEL parallelize
^
../inst/include/singlepp/BasicBuilder.hpp:88:22: note: in instantiation of function template specialization 'singlepp::build_indices<(lambda at ../inst/include/singlepp/BasicBuilder.hpp:92:17)>' requested here
subref = build_indices(
^
In file included from run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:40:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<14>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:63:22: note: in instantiation of function template specialization 'raticate::parse_dgCMatrix<double, int>' requested here
output = parse_dgCMatrix<Data, Index>(x);
^
run.cpp:14:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto parsed = raticate::parse<double, int>(test, true);
^
In file included from run.cpp:3:
In file included from ./utils.h:13:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:5:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/SimpleMatrix.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/utils.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/tatami.h:5:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:188:14: warning: unused variable 'xIt' [-Wunused-variable]
auto xIt = values.begin() + pstart;
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:226:25: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension' requested here
auto obtained = primary_dimension(i, first, last, otherdim);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:88:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::primary_dimension_expanded' requested here
primary_dimension_expanded(c, first, last, this->nrows, buffer, 0);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/tatami/utils/../base/CompressedSparseMatrix.hpp:54:5: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::column' requested here
CompressedSparseMatrix(size_t nr, size_t nc, U vals, V idx, W ptr, bool check=true) : nrows(nr), ncols(nc), values(std::move(vals)), indices(std::move(idx)), indptrs(std::move(ptr)) {
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:24:13: note: in instantiation of member function 'tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int>>::CompressedSparseMatrix' requested here
new tatami::CompressedSparseMatrix<false, Data, Index, decltype(vview), decltype(iview), decltype(pview)>(
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/CSparseMatrix.hpp:46:12: note: in instantiation of function template specialization 'raticate::parse_CSparseMatrix<double, int, Rcpp::Vector<10>>' requested here
return parse_CSparseMatrix(seed, y);
^
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/beachmat/include/raticate/raticate.hpp:65:22: note: in instantiation of function template specialization 'raticate::parse_lgCMatrix<double, int>' requested here
output = parse_lgCMatrix<Data, Index>(x);
^
run.cpp:14:29: note: in instantiation of function template specialization 'raticate::parse<double, int>' requested here
auto parsed = raticate::parse<double, int>(test, true);
^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SingleR.so RcppExports.o find_classic_markers.o integrate_build.o integrate_run.o prebuild.o run.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-SingleR/00new/SingleR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SingleR)
SingleR.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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'
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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'
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as.data.frame, basename, cbind, colnames, dirname, do.call,
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lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
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Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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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'
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> test_check("SingleR")
Loading required package: Matrix
Attaching package: 'Matrix'
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expand
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
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Attaching package: 'DelayedArray'
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[ FAIL 0 | WARN 5 | SKIP 0 | PASS 294 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 294 ]
>
> proc.time()
user system elapsed
83.051 2.335 239.661
SingleR.Rcheck/SingleR-Ex.timings
| name | user | system | elapsed | |
| SingleR | 1.677 | 0.085 | 3.132 | |
| aggregateReference | 2.304 | 0.051 | 4.223 | |
| classifySingleR | 0.184 | 0.003 | 0.333 | |
| combineCommonResults | 0.505 | 0.006 | 0.882 | |
| combineRecomputedResults | 0.489 | 0.020 | 0.901 | |
| getClassicMarkers | 0.231 | 0.026 | 0.461 | |
| getDeltaFromMedian | 0.333 | 0.007 | 0.602 | |
| matchReferences | 0.481 | 0.007 | 0.864 | |
| mockData | 0.034 | 0.000 | 0.060 | |
| plotDeltaDistribution | 6.329 | 0.151 | 11.534 | |
| plotScoreDistribution | 10.496 | 0.157 | 18.840 | |
| plotScoreHeatmap | 3.022 | 0.069 | 5.513 | |
| pruneScores | 0.343 | 0.006 | 0.641 | |
| rebuildIndex | 0.102 | 0.002 | 0.189 | |
| trainSingleR | 1.575 | 0.038 | 2.935 | |