Aaron Lun
| Snapshot Date: 2023-10-15 14:00:13 -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 Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:47 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the SingleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SingleR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SingleR_2.2.0.tar.gz |
| StartedAt: 2023-10-16 01:10:19 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 01:16:15 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 356.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SingleR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SingleR_2.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SingleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
libs 8.8Mb
* 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 loading without being on the library search path ... 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 ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/SingleR/libs/SingleR.so’:
Found ‘__sprintf_chk’, 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 8.985 0.281 9.265
plotDeltaDistribution 5.151 0.119 5.270
* 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 ...
‘SingleR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SingleR.Rcheck/00check.log’
for details.
SingleR.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SingleR
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c find_classic_markers.cpp -o find_classic_markers.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/sums.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:19,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:220: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
220 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:234: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
234 | #pragma omp for schedule(static)
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:267: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
267 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:278: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
278 | #pragma omp for schedule(static)
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
163 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
77 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
49 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
92 | #pragma omp parallel for
|
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from find_classic_markers.cpp:2:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:30:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
30 | if (i != best_label && next_score < val) {
| ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:56:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
56 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
In file included from ../inst/include/singlepp/IntegratedScorer.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:12,
from utils.h:24,
from find_classic_markers.cpp:2:
../inst/include/singlepp/IntegratedBuilder.hpp: In member function ‘std::vector<singlepp::IntegratedReference> singlepp::IntegratedBuilder::finish()’:
../inst/include/singlepp/IntegratedBuilder.hpp:438:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
438 | if (it->second < first) {
| ~~~~~~~~~~~^~~~~~~
../inst/include/singlepp/IntegratedBuilder.hpp:441:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
441 | if (it->second > last) {
| ~~~~~~~~~~~^~~~~~
find_classic_markers.cpp: In function ‘Rcpp::List find_classic_markers(int, int, Rcpp::List, Rcpp::List, int, int)’:
find_classic_markers.cpp:13:14: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
13 | if (nref != labels.size()) {
| ~~~~~^~~~~~~~~~~~~~~~
find_classic_markers.cpp:28:43: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
28 | if (ref_vec.back().matrix->nrow() != ngenes) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
find_classic_markers.cpp:34:35: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
34 | if (lab_vec.back().size() != ref_vec.back().matrix->ncol()) {
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
116 | for (INDEX_t i = 1; i < ncenters; ++i) {
| ~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
133 | for (INDEX_t c = 0; c < ncenters; ++c) {
| ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from find_classic_markers.cpp:2:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:120:36: required from here
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable ‘NR’ [-Wunused-variable]
136 | size_t NR = curref.index->ndim();
| ^~
In file included from ../inst/include/singlepp/singlepp.hpp:15,
from utils.h:24,
from find_classic_markers.cpp:2:
../inst/include/singlepp/load_references.hpp: In instantiation of ‘singlepp::Markers singlepp::load_markers_internal(std::size_t, std::size_t, Reader&) [with Reader = byteme::RawFileReader; singlepp::Markers = std::vector<std::vector<std::vector<int> > >; std::size_t = long unsigned int]’:
../inst/include/singlepp/load_references.hpp:598:33: required from here
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable ‘continuing’ [-Wunused-variable]
490 | bool continuing = false;
| ^~~~~~~~~~
In file included from ../inst/include/singlepp/singlepp.hpp:14,
from utils.h:24,
from find_classic_markers.cpp:2:
../inst/include/singlepp/ChooseClassicMarkers.hpp: In instantiation of ‘singlepp::Markers singlepp::ChooseClassicMarkers::run(const std::vector<const Matrix*>&, const std::vector<const Label*>&) const [with Matrix = tatami::Matrix<double, int>; Label = int; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
find_classic_markers.cpp:42:25: required from here
../inst/include/singlepp/ChooseClassicMarkers.hpp:197:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
197 | for (int g = 0; g < ngenes; ++g, ++sIt) {
| ~~^~~~~~~~
../inst/include/singlepp/ChooseClassicMarkers.hpp:214:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
214 | for (int g = 0; g < ngenes; ++g, ++lptr, ++rptr, ++sIt) {
| ~~^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:11,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_DelayedAbind(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:76:53: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp:19:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
19 | for (size_t s = 0; s < seeds.size(); ++s) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:6,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
23 | if (nnz != val.size()) {
| ~~~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:119:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<IDX> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
73 | INDEX_t counter = 0;
| ^~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
344 | if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:12,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<double>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
127 | if (indices[i] == -1) {
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<int>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 0; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 0; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:28:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | if (chosen != indices.size()) {
| ~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 1; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 1; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:38:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:40:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_dgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:63:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:46:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_lgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:65:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
find_classic_markers.cpp:27:55: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:12,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:200:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
187 | if (obj.size() != last - first) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:205:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:210:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:298:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
246 | if (obj.size() != nnzero) {
| ~~~~~~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:303:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:308:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from find_classic_markers.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c integrate_build.cpp -o integrate_build.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/sums.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:19,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:220: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
220 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:234: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
234 | #pragma omp for schedule(static)
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:267: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
267 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:278: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
278 | #pragma omp for schedule(static)
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
163 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
77 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
49 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
92 | #pragma omp parallel for
|
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_build.cpp:3:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:30:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
30 | if (i != best_label && next_score < val) {
| ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:56:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
56 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
In file included from ../inst/include/singlepp/IntegratedScorer.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:12,
from utils.h:24,
from integrate_build.cpp:3:
../inst/include/singlepp/IntegratedBuilder.hpp: In member function ‘std::vector<singlepp::IntegratedReference> singlepp::IntegratedBuilder::finish()’:
../inst/include/singlepp/IntegratedBuilder.hpp:438:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
438 | if (it->second < first) {
| ~~~~~~~~~~~^~~~~~~
../inst/include/singlepp/IntegratedBuilder.hpp:441:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
441 | if (it->second > last) {
| ~~~~~~~~~~~^~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
116 | for (INDEX_t i = 1; i < ncenters; ++i) {
| ~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
133 | for (INDEX_t c = 0; c < ncenters; ++c) {
| ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_build.cpp:3:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:120:36: required from here
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable ‘NR’ [-Wunused-variable]
136 | size_t NR = curref.index->ndim();
| ^~
In file included from ../inst/include/singlepp/singlepp.hpp:15,
from utils.h:24,
from integrate_build.cpp:3:
../inst/include/singlepp/load_references.hpp: In instantiation of ‘singlepp::Markers singlepp::load_markers_internal(std::size_t, std::size_t, Reader&) [with Reader = byteme::RawFileReader; singlepp::Markers = std::vector<std::vector<std::vector<int> > >; std::size_t = long unsigned int]’:
../inst/include/singlepp/load_references.hpp:598:33: required from here
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable ‘continuing’ [-Wunused-variable]
490 | bool continuing = false;
| ^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:11,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_DelayedAbind(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:76:53: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp:19:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
19 | for (size_t s = 0; s < seeds.size(); ++s) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:6,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
23 | if (nnz != val.size()) {
| ~~~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:119:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<IDX> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
73 | INDEX_t counter = 0;
| ^~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
344 | if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:12,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<double>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
127 | if (indices[i] == -1) {
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<int>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 0; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 0; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:28:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | if (chosen != indices.size()) {
| ~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 1; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 1; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:38:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:40:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_dgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:63:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:46:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_lgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:65:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_build.cpp:24:51: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:12,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:200:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
187 | if (obj.size() != last - first) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:205:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:210:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:298:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
246 | if (obj.size() != nnzero) {
| ~~~~~~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:303:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:308:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_build.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c integrate_run.cpp -o integrate_run.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/sums.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:19,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:220: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
220 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:234: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
234 | #pragma omp for schedule(static)
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:267: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
267 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:278: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
278 | #pragma omp for schedule(static)
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
163 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
77 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
49 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
92 | #pragma omp parallel for
|
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_run.cpp:3:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:30:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
30 | if (i != best_label && next_score < val) {
| ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:56:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
56 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
In file included from ../inst/include/singlepp/IntegratedScorer.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:12,
from utils.h:24,
from integrate_run.cpp:3:
../inst/include/singlepp/IntegratedBuilder.hpp: In member function ‘std::vector<singlepp::IntegratedReference> singlepp::IntegratedBuilder::finish()’:
../inst/include/singlepp/IntegratedBuilder.hpp:438:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
438 | if (it->second < first) {
| ~~~~~~~~~~~^~~~~~~
../inst/include/singlepp/IntegratedBuilder.hpp:441:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
441 | if (it->second > last) {
| ~~~~~~~~~~~^~~~~~
integrate_run.cpp: In function ‘SEXPREC* integrate_run(Rcpp::RObject, Rcpp::List, SEXP, double, int)’:
integrate_run.cpp:18:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
18 | for (size_t r = 0; r < results.size(); ++r) {
| ~~^~~~~~~~~~~~~~~~
integrate_run.cpp:24:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
24 | for (size_t r = 0; r < results.size(); ++r) {
| ~~^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
116 | for (INDEX_t i = 1; i < ncenters; ++i) {
| ~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
133 | for (INDEX_t c = 0; c < ncenters; ++c) {
| ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_run.cpp:3:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:120:36: required from here
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable ‘NR’ [-Wunused-variable]
136 | size_t NR = curref.index->ndim();
| ^~
In file included from ../inst/include/singlepp/singlepp.hpp:15,
from utils.h:24,
from integrate_run.cpp:3:
../inst/include/singlepp/load_references.hpp: In instantiation of ‘singlepp::Markers singlepp::load_markers_internal(std::size_t, std::size_t, Reader&) [with Reader = byteme::RawFileReader; singlepp::Markers = std::vector<std::vector<std::vector<int> > >; std::size_t = long unsigned int]’:
../inst/include/singlepp/load_references.hpp:598:33: required from here
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable ‘continuing’ [-Wunused-variable]
490 | bool continuing = false;
| ^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:11,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_DelayedAbind(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:76:53: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp:19:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
19 | for (size_t s = 0; s < seeds.size(); ++s) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:6,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
23 | if (nnz != val.size()) {
| ~~~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:119:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<IDX> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
73 | INDEX_t counter = 0;
| ^~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
344 | if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:12,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<double>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
127 | if (indices[i] == -1) {
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<int>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 0; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 0; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:28:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | if (chosen != indices.size()) {
| ~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 1; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 1; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:38:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:40:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_dgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:63:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:46:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_lgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:65:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
integrate_run.cpp:12:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:12,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:200:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
187 | if (obj.size() != last - first) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:205:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:210:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:298:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
246 | if (obj.size() != nnzero) {
| ~~~~~~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:303:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:308:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from integrate_run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c prebuild.cpp -o prebuild.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/sums.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:19,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:220: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
220 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:234: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
234 | #pragma omp for schedule(static)
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:267: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
267 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:278: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
278 | #pragma omp for schedule(static)
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
163 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
77 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
49 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
92 | #pragma omp parallel for
|
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from prebuild.cpp:4:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:30:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
30 | if (i != best_label && next_score < val) {
| ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:56:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
56 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
In file included from ../inst/include/singlepp/IntegratedScorer.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:12,
from utils.h:24,
from prebuild.cpp:4:
../inst/include/singlepp/IntegratedBuilder.hpp: In member function ‘std::vector<singlepp::IntegratedReference> singlepp::IntegratedBuilder::finish()’:
../inst/include/singlepp/IntegratedBuilder.hpp:438:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
438 | if (it->second < first) {
| ~~~~~~~~~~~^~~~~~~
../inst/include/singlepp/IntegratedBuilder.hpp:441:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
441 | if (it->second > last) {
| ~~~~~~~~~~~^~~~~~
prebuild.cpp: In function ‘SEXPREC* prebuild(Rcpp::RObject, Rcpp::IntegerVector, Rcpp::List, bool, int)’:
prebuild.cpp:24:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
24 | for (size_t m = 0; m < markers.size(); ++m) {
| ~~^~~~~~~~~~~~~~~~
prebuild.cpp:29:30: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
29 | for (size_t n = 0; n < curmarkers.size(); ++n) {
| ~~^~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
116 | for (INDEX_t i = 1; i < ncenters; ++i) {
| ~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
133 | for (INDEX_t c = 0; c < ncenters; ++c) {
| ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from prebuild.cpp:4:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:120:36: required from here
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable ‘NR’ [-Wunused-variable]
136 | size_t NR = curref.index->ndim();
| ^~
In file included from ../inst/include/singlepp/singlepp.hpp:15,
from utils.h:24,
from prebuild.cpp:4:
../inst/include/singlepp/load_references.hpp: In instantiation of ‘singlepp::Markers singlepp::load_markers_internal(std::size_t, std::size_t, Reader&) [with Reader = byteme::RawFileReader; singlepp::Markers = std::vector<std::vector<std::vector<int> > >; std::size_t = long unsigned int]’:
../inst/include/singlepp/load_references.hpp:598:33: required from here
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable ‘continuing’ [-Wunused-variable]
490 | bool continuing = false;
| ^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:11,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_DelayedAbind(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:76:53: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp:19:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
19 | for (size_t s = 0; s < seeds.size(); ++s) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:6,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
23 | if (nnz != val.size()) {
| ~~~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:119:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<IDX> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
73 | INDEX_t counter = 0;
| ^~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
344 | if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:12,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<double>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
127 | if (indices[i] == -1) {
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<int>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 0; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 0; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:28:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | if (chosen != indices.size()) {
| ~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 1; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 1; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:38:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:40:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_dgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:63:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:46:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_lgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:65:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
prebuild.cpp:37:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:12,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:200:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
187 | if (obj.size() != last - first) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:205:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:210:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:298:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
246 | if (obj.size() != nnzero) {
| ~~~~~~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:303:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:308:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from prebuild.cpp:4:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include' -I/usr/local/include -fpic -g -O2 -Wall -c run.cpp -o run.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/sums.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:19,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:220: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
220 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:234: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
234 | #pragma omp for schedule(static)
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:267: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
267 | #pragma omp parallel
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/stats/apply.hpp:278: warning: ignoring ‘#pragma omp for’ [-Wunknown-pragmas]
278 | #pragma omp for schedule(static)
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:163: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
163 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:77: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
77 | #pragma omp parallel for
|
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:49: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
49 | #pragma omp parallel for
|
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/utils/find_nearest_neighbors.hpp:92: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
92 | #pragma omp parallel for
|
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from run.cpp:3:
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::fill_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:30:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
30 | if (i != best_label && next_score < val) {
| ~~^~~~~~~~~~~~~
../inst/include/singlepp/fine_tune.hpp: In function ‘std::pair<int, double> singlepp::replace_labels_in_use(const std::vector<double>&, double, std::vector<int>&)’:
../inst/include/singlepp/fine_tune.hpp:56:15: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
56 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
In file included from ../inst/include/singlepp/IntegratedScorer.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:12,
from utils.h:24,
from run.cpp:3:
../inst/include/singlepp/IntegratedBuilder.hpp: In member function ‘std::vector<singlepp::IntegratedReference> singlepp::IntegratedBuilder::finish()’:
../inst/include/singlepp/IntegratedBuilder.hpp:438:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
438 | if (it->second < first) {
| ~~~~~~~~~~~^~~~~~~
../inst/include/singlepp/IntegratedBuilder.hpp:441:36: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
441 | if (it->second > last) {
| ~~~~~~~~~~~^~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp: In instantiation of ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’:
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
116 | for (INDEX_t i = 1; i < ncenters; ++i) {
| ~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:133:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
133 | for (INDEX_t c = 0; c < ncenters; ++c) {
| ~~^~~~~~~~~~
In file included from ../inst/include/singlepp/annotate_cells.hpp:9,
from ../inst/include/singlepp/BasicScorer.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:6,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from run.cpp:3:
../inst/include/singlepp/fine_tune.hpp: In instantiation of ‘std::pair<int, double> singlepp::FineTuner::run(singlepp::RankedVector<double, int>&, const std::vector<singlepp::Reference>&, const Markers&, std::vector<double>&, double, double) [with bool test = false; singlepp::RankedVector<double, int> = std::vector<std::pair<double, int>, std::allocator<std::pair<double, int> > >; singlepp::Markers = std::vector<std::vector<std::vector<int> > >]’:
../inst/include/singlepp/annotate_cells.hpp:120:36: required from here
../inst/include/singlepp/fine_tune.hpp:136:24: warning: unused variable ‘NR’ [-Wunused-variable]
136 | size_t NR = curref.index->ndim();
| ^~
In file included from ../inst/include/singlepp/singlepp.hpp:15,
from utils.h:24,
from run.cpp:3:
../inst/include/singlepp/load_references.hpp: In instantiation of ‘singlepp::Markers singlepp::load_markers_internal(std::size_t, std::size_t, Reader&) [with Reader = byteme::RawFileReader; singlepp::Markers = std::vector<std::vector<std::vector<int> > >; std::size_t = long unsigned int]’:
../inst/include/singlepp/load_references.hpp:598:33: required from here
../inst/include/singlepp/load_references.hpp:490:10: warning: unused variable ‘continuing’ [-Wunused-variable]
490 | bool continuing = false;
| ^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:11,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_DelayedAbind(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:76:53: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedAbind.hpp:19:26: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
19 | for (size_t s = 0; s < seeds.size(); ++s) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:6,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
23 | if (nnz != val.size()) {
| ~~~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp: In instantiation of ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:119:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:23:13: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<IDX> kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:136:25: required from ‘CLUSTER_t kmeans::InitializeKmeansPP<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:91:32: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp:73:21: warning: variable ‘counter’ set but not used [-Wunused-but-set-variable]
73 | INDEX_t counter = 0;
| ^~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/build_indices.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:5,
from ../inst/include/singlepp/Classifier.hpp:5,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:24,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp: In instantiation of ‘void kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::optimal_transfer(INDEX_t&) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:235:13: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::HartiganWong<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:98:26: required from ‘kmeans::Details<DATA_t, INDEX_t> kmeans::Kmeans<DATA_t, CLUSTER_t, INDEX_t>::run(int, INDEX_t, const DATA_t*, CLUSTER_t, DATA_t*, CLUSTER_t*, kmeans::Initialize<DATA_t, CLUSTER_t, INDEX_t>*, kmeans::Refine<DATA_t, CLUSTER_t, INDEX_t>*) [with DATA_t = double; CLUSTER_t = int; INDEX_t = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:106:60: required from ‘knncolle::Kmknn<DISTANCE, INDEX_t, DISTANCE_t, QUERY_t, INTERNAL_t>::Kmknn(INDEX_t, INDEX_t, const INPUT_t*, double) [with INPUT_t = double; DISTANCE = knncolle::distances::Euclidean; INDEX_t = int; DISTANCE_t = double; QUERY_t = double; INTERNAL_t = double]’
../inst/include/singlepp/BasicBuilder.hpp:103:127: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/BiocNeighbors/include/kmeans/HartiganWong.hpp:344:41: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
344 | if (obs >= live[l1] && obs >= live[cen] || cen == l1 || cen == ll) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:12,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<double>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:113:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
127 | if (indices[i] == -1) {
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp: In instantiation of ‘std::vector<long unsigned int> tatami::compress_sparse_triplets(std::size_t, std::size_t, U&, V&, W&) [with bool ROW = false; U = std::vector<int>; V = std::vector<int>; W = std::vector<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:88:56: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<13>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SparseArraySeed.hpp:116:52: required from ‘raticate::Parsed<Data, Index> raticate::parse_SparseArraySeed(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:61:56: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/utils/compress_sparse_triplets.hpp:127:28: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int>, long unsigned int>::value_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:7,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 0; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 0; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:28:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
48 | if (chosen != indices.size()) {
| ~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp: In instantiation of ‘tatami::DelayedSubset<MARGIN, T, IDX, V>::DelayedSubset(std::shared_ptr<const tatami::Matrix<T, IDX> >, V) [with int MARGIN = 1; T = double; IDX = int; V = std::vector<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:322:9: required from ‘std::shared_ptr<_Tp> tatami::make_DelayedSubset(std::shared_ptr<_Tp>, V) [with int MARGIN = 1; MAT = tatami::Matrix<double, int>; V = std::vector<int>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/DelayedSubset.hpp:38:48: required from ‘raticate::Parsed<Data, Index> raticate::parse_DelayedSubset(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:72:54: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/DelayedSubset.hpp:48:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:40:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_dgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:63:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::check_values(bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:55:9: required from ‘tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::CompressedSparseMatrix(std::size_t, std::size_t, U, V, W, bool) [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:24:9: required from ‘raticate::Parsed<Data, Index> raticate::parse_CSparseMatrix(Rcpp::RObject, const V&) [with Data = double; Index = int; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/CSparseMatrix.hpp:46:31: required from ‘raticate::Parsed<Data, Index> raticate::parse_lgCMatrix(Rcpp::RObject) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:65:50: required from ‘raticate::Parsed<Data, Index> raticate::parse(Rcpp::RObject, bool) [with Data = double; Index = int; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
run.cpp:14:47: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:154:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
154 | if (indptrs[indptrs.size() - 1] != indices.size()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:167:32: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
167 | while (counter < indptrs[i]) {
| ~~~~~~~~^~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:12,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:200:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
187 | if (obj.size() != last - first) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:205:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_dense_dims(const Object&, std::size_t, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:210:35: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_dense_extractor_raw(std::size_t, Data*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:443:73: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:187:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<10, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:298:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
246 | if (obj.size() != nnzero) {
| ~~~~~~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<13>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:303:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp: In instantiation of ‘void raticate::UnknownMatrixCore<Data, Index>::check_quick_sparse_dims(const Object&, std::size_t) const [with Object = Rcpp::Vector<14, Rcpp::PreserveStorage>; Data = double; Index = int; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:308:36: required from ‘void raticate::UnknownMatrixCore<Data, Index>::quick_sparse_extractor_raw(std::size_t, std::size_t*, Data*, Index*, std::size_t, std::size_t) const [with bool byrow = true; Data = double; Index = int; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:457:74: required from ‘void raticate::UnknownEvaluator<Data, Index>::harvest() [with Data = double; Index = int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:554:31: required from ‘void raticate::ParallelCoordinator::run(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/parallelize.hpp:37:53: required from ‘void raticate::parallelize(std::size_t, Function, std::size_t) [with Data = double; Index = int; Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
utils.h:17:39: required from ‘void parallelize(std::size_t, Function, int) [with Function = singlepp::annotate_cells_simple(const tatami::Matrix<double, int>*, std::size_t, const int*, const std::vector<singlepp::Reference>&, const Markers&, double, bool, double, int*, std::vector<double*>&, double*, int)::<lambda(std::size_t, std::size_t)>; std::size_t = long unsigned int]’
../inst/include/singlepp/annotate_cells.hpp:64:29: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/UnknownMatrix.hpp:246:24: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.h:5,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/tatami.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/utils.hpp:15,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/SimpleMatrix.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/raticate/raticate.hpp:5,
from utils.h:13,
from run.cpp:3:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<int>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<int>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: unused variable ‘xIt’ [-Wunused-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, tatami::ArrayView<double>, tatami::ArrayView<int>, tatami::ArrayView<int> >::raw_store; bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = tatami::ArrayView<double>; V = tatami::ArrayView<int>; W = tatami::ArrayView<int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<int>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<int>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::expanded_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:380:28: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_expanded(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:79:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::row(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:75:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘std::pair<long unsigned int, long unsigned int> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension(std::size_t, std::size_t, std::size_t, std::size_t) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:226:25: required from ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::primary_dimension_expanded(std::size_t, std::size_t, std::size_t, std::size_t, T*, T) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:88:13: required from ‘const T* tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::column(std::size_t, T*, std::size_t, std::size_t, tatami::Workspace*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:84:14: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:188:14: warning: variable ‘xIt’ set but not used [-Wunused-but-set-variable]
188 | auto xIt = values.begin() + pstart;
| ^~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp: In instantiation of ‘void tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension(IDX, std::size_t, std::size_t, tatami::Workspace*, STORE&) const [with STORE = tatami::CompressedSparseMatrix<false, double, int, std::vector<double>, std::vector<int>, std::vector<long unsigned int> >::raw_store; bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’:
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:362:28: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::secondary_dimension_raw(IDX, std::size_t, std::size_t, tatami::Workspace*, T*, IDX*) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:106:20: required from ‘tatami::SparseRange<T, IDX> tatami::CompressedSparseMatrix<ROW, T, IDX, U, V, W>::sparse_row(std::size_t, T*, IDX*, std::size_t, std::size_t, tatami::Workspace*, bool) const [with bool ROW = false; T = double; IDX = int; U = std::vector<double>; V = std::vector<int>; W = std::vector<long unsigned int>; std::size_t = long unsigned int]’
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:101:25: required from here
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:312:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
312 | if (i == prev_i + 1) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:317:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
317 | } else if (i + 1 == prev_i) {
| ~~~~~~^~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:322:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
322 | } else if (i > prev_i) {
| ~~^~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/site-library/beachmat/include/tatami/base/CompressedSparseMatrix.hpp:327:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
327 | } else if (i < prev_i) {
| ~~^~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o SingleR.so RcppExports.o find_classic_markers.o integrate_build.o integrate_run.o prebuild.o run.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-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: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SingleR)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
> test_check("SingleR")
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Loading required package: S4Arrays
Loading required package: abind
Attaching package: 'S4Arrays'
The following object is masked from 'package:abind':
abind
The following object is masked from 'package:base':
rowsum
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 294 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 294 ]
>
> proc.time()
user system elapsed
71.974 2.145 114.720
SingleR.Rcheck/SingleR-Ex.timings
| name | user | system | elapsed | |
| SingleR | 1.687 | 0.077 | 1.764 | |
| aggregateReference | 1.367 | 0.072 | 1.439 | |
| classifySingleR | 0.154 | 0.007 | 0.161 | |
| combineCommonResults | 1.031 | 0.016 | 1.047 | |
| combineRecomputedResults | 0.386 | 0.004 | 0.390 | |
| getClassicMarkers | 0.174 | 0.008 | 0.182 | |
| getDeltaFromMedian | 0.259 | 0.056 | 0.314 | |
| matchReferences | 0.467 | 0.008 | 0.474 | |
| mockData | 0.028 | 0.000 | 0.028 | |
| plotDeltaDistribution | 5.151 | 0.119 | 5.270 | |
| plotScoreDistribution | 8.985 | 0.281 | 9.265 | |
| plotScoreHeatmap | 2.537 | 0.064 | 2.601 | |
| pruneScores | 0.293 | 0.008 | 0.301 | |
| rebuildIndex | 0.087 | 0.004 | 0.091 | |
| trainSingleR | 1.212 | 0.060 | 1.271 | |