Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-16 11:05:52 -0400 (Tue, 16 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4378
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4161
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4169
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

CHECK results for scran on nebbiolo2


To the developers/maintainers of the scran package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scran.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1783/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scran 1.25.0  (landing page)
Aaron Lun
Snapshot Date: 2022-08-15 14:00:06 -0400 (Mon, 15 Aug 2022)
git_url: https://git.bioconductor.org/packages/scran
git_branch: master
git_last_commit: 935072d
git_last_commit_date: 2022-04-26 11:31:31 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: scran
Version: 1.25.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings scran_1.25.0.tar.gz
StartedAt: 2022-08-15 21:48:09 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 21:59:22 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 672.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scran.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings scran_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/scran.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.25.0’
* 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 ‘scran’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'combinePValues' is deprecated.
  Warning: 'combinePValues' is deprecated.
  Warning: 'combinePValues' is deprecated.
  Warning: 'combinePValues' is deprecated.
  Warning: 'correlateNull' is deprecated.
  Warning: 'correlateNull' is deprecated.
  Warning: 'correlateNull' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
cyclone       10.021  0.136  10.157
buildSNNGraph  6.886  0.198   7.084
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/scran.Rcheck/00check.log’
for details.



Installation output

scran.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL scran
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘scran’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c choose_effect_size.cpp -o choose_effect_size.o
choose_effect_size.cpp: In instantiation of ‘size_t instantiate_list(Rcpp::List, std::vector<T>&, std::string) [with V = Rcpp::Vector<13>; size_t = long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’:
choose_effect_size.cpp:38:67:   required from here
choose_effect_size.cpp:13:23: 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 c=0; c<input.size(); ++c) {
      |                      ~^~~~~~~~~~~~~
choose_effect_size.cpp: In instantiation of ‘size_t instantiate_list(Rcpp::List, std::vector<T>&, std::string) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; size_t = long unsigned int; Rcpp::List = Rcpp::Vector<19>; std::string = std::__cxx11::basic_string<char>]’:
choose_effect_size.cpp:67:70:   required from here
choose_effect_size.cpp:13:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c combine_rho.cpp -o combine_rho.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_blocked_stats.cpp -o compute_blocked_stats.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from compute_blocked_stats.cpp:2:
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
  250 |             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
      |                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_residual_stats.cpp -o compute_residual_stats.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from compute_residual_stats.cpp:2:
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
  250 |             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
      |                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c compute_rho_null.cpp -o compute_rho_null.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/size_type.hpp:20,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/size.hpp:21,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/random.hpp:70,
                 from rand_custom.h:6,
                 from compute_rho_null.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c cyclone_scores.cpp -o cyclone_scores.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/algorithm.hpp:29,
                 from cyclone_scores.cpp:4:
/home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from cyclone_scores.cpp:3:
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
  250 |             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
      |                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c overlap_exprs.cpp -o overlap_exprs.o
overlap_exprs.cpp: In function ‘Rcpp::NumericMatrix overlap_exprs_paired(Rcpp::RObject, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::List, double)’:
overlap_exprs.cpp:214:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  214 |         for (size_t i=0; i<left.size(); ++i, ++oIt) {
      |                          ~^~~~~~~~~~~~
overlap_exprs.cpp:202:18: warning: unused variable ‘ngroups’ [-Wunused-variable]
  202 |     const size_t ngroups=groups.size();
      |                  ^~~~~~~
In file included from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24,
                 from overlap_exprs.cpp:3:
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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-3.16-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  535 |         if (nnz != x.size()) {
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                       ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  551 |                     if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) {
      |                                                                   ~~~~~~^~~~
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
  593 |                 for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) {
      |                                 ~~^~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
  250 |             if (idex != *pIt && static_cast<size_t>(i[idex]) == r) {
      |                 ~~~~~^~~~~~~
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]’
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/beachmat/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/dqrng/include' -I'/home/biocbuild/bbs-3.16-bioc/R/library/scuttle/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rand_custom.cpp -o rand_custom.o
In file included from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/size_type.hpp:20,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/size.hpp:21,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/random.hpp:70,
                 from rand_custom.h:6,
                 from rand_custom.cpp:1:
/home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o scran.so RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.16-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/library/00LOCK-scran/00new/scran/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 (scran)

Tests output

scran.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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.

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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(scran)
Loading required package: SingleCellExperiment
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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

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

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: scuttle
> test_check("scran")
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, scale, sweep

In file included from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/range/algorithm.hpp:29,
                 from file3ba400fd9c0b1.cpp:3:
/home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.16-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
[ FAIL 0 | WARN 194 | SKIP 1 | PASS 4478 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• monocle is a little broken because of clusterApply (1)

[ FAIL 0 | WARN 194 | SKIP 1 | PASS 4478 ]
> 
> proc.time()
   user  system elapsed 
337.073  14.783 417.357 

Example timings

scran.Rcheck/scran-Ex.timings

nameusersystemelapsed
DM0.0430.0040.047
buildSNNGraph6.8860.1987.084
clusterCells1.3580.1041.462
combineBlocks1.0930.0201.113
combineMarkers2.2990.1882.487
combinePValues0.0300.0040.034
combineVar1.0480.0721.121
computeMinRank0.0010.0000.002
convertTo2.5790.0362.615
correlateGenes1.9730.0402.014
correlateNull0.2240.0000.224
correlatePairs1.7610.0401.826
cyclone10.021 0.13610.157
decideTestsPerLabel3.1080.0563.164
defunct0.0010.0000.000
denoisePCA1.4300.0081.438
findMarkers2.1820.0162.199
fitTrendCV20.6520.0040.655
fitTrendPoisson0.1890.0040.193
fitTrendVar0.7200.0040.724
fixedPCA1.2170.0001.218
getClusteredPCs3.2150.0013.215
getMarkerEffects0.9560.0150.972
getTopHVGs0.7820.0040.786
getTopMarkers0.8880.0040.892
logBH0.0000.0000.001
modelGeneCV20.9480.0000.948
modelGeneCV2WithSpikes0.9930.0121.005
modelGeneVar1.1130.0161.128
modelGeneVarByPoisson1.0380.0041.043
modelGeneVarWithSpikes1.2330.0041.238
multiMarkerStats1.8560.0001.856
pairwiseBinom0.8440.0000.843
pairwiseTTests0.8340.0040.837
pairwiseWilcox0.6980.0440.742
pseudoBulkDGE3.8200.1123.933
pseudoBulkSpecific4.8240.0444.868
quickCluster1.8270.0161.844
quickSubCluster4.7140.0204.734
rhoToPValue0.0000.0000.001
sandbag0.6650.0000.665
scaledColRanks1.1910.0121.203
scoreMarkers0.9870.0120.999
summaryMarkerStats0.8300.0040.834
testLinearModel0.0580.0040.062