Aaron Lun
| Snapshot Date: 2023-10-23 14:05:08 -0400 (Mon, 23 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/SingleR |
| git_branch: devel |
| git_last_commit: 8337ab6 |
| git_last_commit_date: 2023-09-11 05:26:14 -0400 (Mon, 11 Sep 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-10-24 11:41:33 -0400 (Tue, 24 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4724 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4459 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4473 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4461 |
| 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 1971/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SingleR 2.3.7 (landing page) Aaron Lun
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SingleR |
| Version: 2.3.7 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings SingleR_2.3.7.tar.gz |
| StartedAt: 2023-10-24 13:11:58 -0000 (Tue, 24 Oct 2023) |
| EndedAt: 2023-10-24 13:21:34 -0000 (Tue, 24 Oct 2023) |
| EllapsedTime: 575.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SingleR.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings SingleR_2.3.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SingleR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘2.3.7’
* 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++ (GCC) 10.3.1’
* checking C++ specification ... OK
Not all R platforms support C++17
* checking installed package size ... NOTE
installed size is 11.9Mb
sub-directories of 1Mb or more:
libs 11.4Mb
* 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/R/R-4.3.1/site-library/SingleR/libs/SingleR.so’:
Found ‘sprintf’, possibly from ‘sprintf’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotScoreDistribution 12.300 0.152 12.478
plotDeltaDistribution 7.321 0.087 7.426
* 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-3.18-bioc/meat/SingleR.Rcheck/00check.log’
for details.
SingleR.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL SingleR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from find_classic_markers.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from find_classic_markers.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from find_classic_markers.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from find_classic_markers.cpp:1:
../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:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
32 | 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:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
find_classic_markers.cpp: In function ‘Rcpp::List find_classic_markers(int, int, Rcpp::List, Rcpp::List, int, int)’:
find_classic_markers.cpp:9:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
9 | if (nref != labels.size()) {
| ~~~~~^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from find_classic_markers.cpp:1:
/home/biocbuild/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from find_classic_markers.cpp:1:
../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:101:86: required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
138 | size_t NR = curref.index->ndim();
| ^~
In file included from ../inst/include/singlepp/singlepp.hpp:14,
from utils.h:11,
from find_classic_markers.cpp:1:
../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:39:44: required from here
../inst/include/singlepp/ChooseClassicMarkers.hpp:198:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
198 | for (int g = 0; g < ngenes; ++g, ++sIt) {
| ~~^~~~~~~~
../inst/include/singlepp/ChooseClassicMarkers.hpp:225:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
225 | for (int g = 0; g < ngenes; ++g, ++lptr, ++rptr, ++sIt) {
| ~~^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from find_classic_markers.cpp:1:
/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> 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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from find_classic_markers.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c grouped_medians.cpp -o grouped_medians.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from grouped_medians.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from grouped_medians.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from grouped_medians.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from grouped_medians.cpp:1:
../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:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
32 | 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:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from grouped_medians.cpp:1:
/home/biocbuild/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from grouped_medians.cpp:1:
../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:101:86: required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
138 | size_t NR = curref.index->ndim();
| ^~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from grouped_medians.cpp:1:
/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> 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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from grouped_medians.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_build.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_build.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_build.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_build.cpp:1:
../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:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
32 | 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:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_build.cpp:1:
/home/biocbuild/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_build.cpp:1:
../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:101:86: required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
138 | size_t NR = curref.index->ndim();
| ^~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_build.cpp:1:
/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> 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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_build.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_run.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_run.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_run.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_run.cpp:1:
../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:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
32 | 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:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
integrate_run.cpp: In function ‘SEXPREC* integrate_run(Rcpp::RObject, Rcpp::List, SEXP, double, int)’:
integrate_run.cpp:13:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
13 | for (size_t r = 0; r < results.size(); ++r) {
| ~~^~~~~~~~~~~~~~~~
integrate_run.cpp:19:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
19 | for (size_t r = 0; r < results.size(); ++r) {
| ~~^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_run.cpp:1:
/home/biocbuild/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_run.cpp:1:
../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:101:86: required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
138 | size_t NR = curref.index->ndim();
| ^~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_run.cpp:1:
/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> 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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from integrate_run.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c prebuild.cpp -o prebuild.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from prebuild.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from prebuild.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from prebuild.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from prebuild.cpp:1:
../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:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
32 | 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:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
prebuild.cpp: In function ‘SEXPREC* prebuild(Rcpp::RObject, Rcpp::IntegerVector, Rcpp::List, bool, int)’:
prebuild.cpp:18:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
18 | for (size_t m = 0; m < markers.size(); ++m) {
| ~~^~~~~~~~~~~~~~~~
prebuild.cpp:23:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
23 | for (size_t n = 0; n < curmarkers.size(); ++n) {
| ~~^~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from prebuild.cpp:1:
/home/biocbuild/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from prebuild.cpp:1:
../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:101:86: required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
138 | size_t NR = curref.index->ndim();
| ^~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from prebuild.cpp:1:
/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> 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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from prebuild.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I../inst/include/ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include' -I/usr/local/include -fPIC -g -O2 -Wall -c run.cpp -o run.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from run.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from run.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:19,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from run.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from run.cpp:1:
../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:32:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
32 | 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:58:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
58 | if (i != best_index && next_score < val) {
| ~~^~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from run.cpp:1:
/home/biocbuild/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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:11,
from ../inst/include/singlepp/BasicScorer.hpp:8,
from ../inst/include/singlepp/Classifier.hpp:9,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from run.cpp:1:
../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:101:86: required from here
../inst/include/singlepp/fine_tune.hpp:138:24: warning: unused variable ‘NR’ [-Wunused-variable]
138 | size_t NR = curref.index->ndim();
| ^~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from run.cpp:1:
/home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/InitializeKmeansPP.hpp: In instantiation of ‘std::vector<Index_> 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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/site-library/BiocNeighbors/include/kmeans/Kmeans.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/Kmknn/Kmknn.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/BiocNeighbors/include/knncolle/knncolle.hpp:8,
from ../inst/include/singlepp/BasicBuilder.hpp:6,
from ../inst/include/singlepp/Classifier.hpp:8,
from ../inst/include/singlepp/singlepp.hpp:10,
from utils.h:11,
from run.cpp:1:
/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/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:107:127: required from here
/home/biocbuild/R/R-4.3.1/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) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o SingleR.so RcppExports.o find_classic_markers.o grouped_medians.o integrate_build.o integrate_run.o prebuild.o run.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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: aarch64-unknown-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
Loading required package: SparseArray
Attaching package: 'DelayedArray'
The following objects are masked from 'package:base':
apply, scale, sweep
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 295 ]
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 295 ]
>
> proc.time()
user system elapsed
100.585 2.911 163.362
SingleR.Rcheck/SingleR-Ex.timings
| name | user | system | elapsed | |
| SingleR | 1.311 | 0.060 | 1.372 | |
| aggregateReference | 2.847 | 0.040 | 2.893 | |
| classifySingleR | 0.207 | 0.000 | 0.207 | |
| combineCommonResults | 0.568 | 0.028 | 0.597 | |
| combineRecomputedResults | 0.526 | 0.000 | 0.527 | |
| getClassicMarkers | 0.221 | 0.000 | 0.221 | |
| getDeltaFromMedian | 0.358 | 0.000 | 0.359 | |
| matchReferences | 0.540 | 0.000 | 0.542 | |
| mockData | 0.064 | 0.000 | 0.065 | |
| plotDeltaDistribution | 7.321 | 0.087 | 7.426 | |
| plotScoreDistribution | 12.300 | 0.152 | 12.478 | |
| plotScoreHeatmap | 3.528 | 0.016 | 3.551 | |
| pruneScores | 0.391 | 0.000 | 0.391 | |
| rebuildIndex | 0.102 | 0.000 | 0.101 | |
| trainSingleR | 1.716 | 0.008 | 1.728 | |