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CHECK report for SingleR on malbec1

This page was generated on 2021-05-06 12:29:11 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SingleR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1726/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SingleR 1.4.1  (landing page)
Aaron Lun
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SingleR
Branch: RELEASE_3_12
Last Commit: 5b9704c
Last Changed Date: 2021-02-02 03:46:49 -0400 (Tue, 02 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SingleR
Version: 1.4.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SingleR_1.4.1.tar.gz
StartedAt: 2021-05-06 06:07:39 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:15:25 -0400 (Thu, 06 May 2021)
EllapsedTime: 466.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SingleR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:SingleR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings SingleR_1.4.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/SingleR.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SingleR/DESCRIPTION’ ... OK
* this is package ‘SingleR’ version ‘1.4.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SingleR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plotScoreDistribution 13.592  0.032  13.657
plotDeltaDistribution  8.024  0.084   8.128
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/SingleR.Rcheck/00check.log’
for details.

Installation output

SingleR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL SingleR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘SingleR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fine_tune_de.cpp -o fine_tune_de.o
fine_tune_de.cpp: In constructor ‘de_markers::de_markers(Rcpp::List)’:
fine_tune_de.cpp:6:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<marker_genes.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~~~
fine_tune_de.cpp:9:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t j=0; j<internals.size(); ++j) {
                              ~^~~~~~~~~~~~~~~~~
fine_tune_de.cpp: In function ‘Rcpp::List fine_tune_label_de(Rcpp::RObject, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::List)’:
fine_tune_de.cpp:41:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                      ~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_de.cpp:2:0:
fine_tuner.h: In instantiation of ‘tuned_stats fine_tuner::assign(int, beachmat::lin_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = de_markers; tuned_stats = std::tuple<int, double, double>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix> >]’:
fine_tune_de.cpp:54:95:   required from here
fine_tuner.h:39:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from fine_tune_de.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
fine_tune_de.cpp:61:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
fine_tune_de.cpp:61:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
fine_tune_de.cpp:61:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
fine_tune_de.cpp:61:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fine_tune_sd.cpp -o fine_tune_sd.o
fine_tune_sd.cpp: In function ‘Rcpp::List fine_tune_label_sd(SEXP, Rcpp::NumericMatrix, Rcpp::List, double, double, Rcpp::NumericMatrix, double)’:
fine_tune_sd.cpp:46:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t i=0; i<References.size(); ++i) {
                      ~^~~~~~~~~~~~~~~~~~
In file included from fine_tune_sd.cpp:2:0:
fine_tuner.h: In instantiation of ‘tuned_stats fine_tuner::assign(int, beachmat::lin_matrix*, Rcpp::NumericMatrix, const matrix_list&, double, double, const PICKER&) [with PICKER = sd_markers; tuned_stats = std::tuple<int, double, double>; Rcpp::NumericMatrix = Rcpp::Matrix<14>; matrix_list = std::vector<std::unique_ptr<beachmat::lin_matrix> >]’:
fine_tune_sd.cpp:59:95:   required from here
fine_tuner.h:39:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t i=0; i<cur_scores.size(); ++i) {
                          ~^~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from fine_tune_sd.cpp:1:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
fine_tune_sd.cpp:66:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
fine_tune_sd.cpp:66:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
fine_tune_sd.cpp:66:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
fine_tune_sd.cpp:66:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c recompute_scores.cpp -o recompute_scores.o
recompute_scores.cpp: In function ‘Rcpp::RObject recompute_scores(Rcpp::List, Rcpp::RObject, Rcpp::IntegerMatrix, Rcpp::List, Rcpp::List, double)’:
recompute_scores.cpp:38:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Labels.nrow()!=nref) {
         ~~~~~~~~~~~~~^~~~~~
recompute_scores.cpp:41:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Labels.ncol()!=ncells) {
         ~~~~~~~~~~~~~^~~~~~~~
recompute_scores.cpp:45:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (Genes.size()!=nref) {
         ~~~~~~~~~~~~^~~~~~
In file included from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12:0,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from recompute_scores.cpp:2:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:56:   required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39:   required from ‘std::unique_ptr<_Codecvt> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = beachmat::lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (nnz != x.size()) {
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
                                 ~~^~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
recompute_scores.cpp:134:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’
recompute_scores.cpp:134:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:82:   required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
recompute_scores.cpp:134:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’:
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:73:   required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:85:   required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’
recompute_scores.cpp:134:1:   required from here
/home/biocbuild/bbs-3.12-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o SingleR.so RcppExports.o fine_tune_de.o fine_tune_sd.o recompute_scores.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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)

Tests output

SingleR.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("SingleR")
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum

[ FAIL 0 | WARN 10 | SKIP 0 | PASS 520 ]
> 
> proc.time()
   user  system elapsed 
208.064   1.724 252.180

Example timings

SingleR.Rcheck/SingleR-Ex.timings

nameusersystemelapsed
SingleR1.9680.0201.990
aggregateReference3.0440.0363.082
classifySingleR0.4440.0000.444
combineCommonResults0.8960.0040.899
combineRecomputedResults0.7560.0000.756
getClassicMarkers0.2680.0040.272
getDeltaFromMedian1.0760.0161.109
matchReferences2.3920.0042.402
mockData0.0280.0000.030
plotDeltaDistribution8.0240.0848.128
plotScoreDistribution13.592 0.03213.657
plotScoreHeatmap3.6880.0283.726
pruneScores0.9640.0080.969
trainSingleR2.0160.0042.026