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This page was generated on 2024-05-04 11:41:05 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1913/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scran 1.32.0  (landing page)
Aaron Lun
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/scran
git_branch: RELEASE_3_19
git_last_commit: 03deb61
git_last_commit_date: 2024-04-30 10:50:14 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for scran on kunpeng2


To the developers/maintainers of the scran package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: scran
Version: 1.32.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings scran_1.32.0.tar.gz
StartedAt: 2024-05-04 11:48:49 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 12:04:49 -0000 (Sat, 04 May 2024)
EllapsedTime: 959.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scran.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:scran.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings scran_1.32.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/scran.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scran/DESCRIPTION’ ... OK
* this is package ‘scran’ version ‘1.32.0’
* 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
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in combinePValues(p1, p2, p3) : 'combinePValues' 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             32.944  0.152  33.154
quickSubCluster      7.711  0.032   7.762
pseudoBulkSpecific   7.503  0.020   7.544
buildSNNGraph        6.195  0.008   6.215
decideTestsPerLabel  5.749  0.135   5.896
pseudoBulkDGE        5.674  0.100   5.791
getClusteredPCs      5.125  0.004   5.141
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/scran.Rcheck/00check.log’
for details.


Installation output

scran.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL scran
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘scran’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/scuttle/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/beachmat.h:24,
                 from compute_blocked_stats.cpp:2:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/beachmat.h:24,
                 from compute_residual_stats.cpp:2:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/size_type.hpp:20,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/size.hpp:21,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/random.hpp:70,
                 from rand_custom.h:6,
                 from compute_rho_null.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/algorithm.hpp:29,
                 from cyclone_scores.cpp:4:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/beachmat.h:24,
                 from cyclone_scores.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/beachmat.h:24,
                 from overlap_exprs.cpp:3:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/read_lin_block.h:65:63:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54:   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/R/R-beta-2024-04-15_r86425/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/beachmat/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/dqrng/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/iterator/iterator_concepts.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/concepts.hpp:20,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/size_type.hpp:20,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/range/size.hpp:21,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/random/hyperexponential_distribution.hpp:29,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/random.hpp:70,
                 from rand_custom.h:6,
                 from rand_custom.cpp:1:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-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/R/R-beta-2024-04-15_r86425/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 -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.
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> 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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

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

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


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: scuttle
> test_check("scran")
Loading required package: Matrix

Attaching package: 'Matrix'

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

    expand

Loading required package: S4Arrays
Loading required package: abind

Attaching package: 'S4Arrays'

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

    abind

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

    rowsum

Loading required package: SparseArray

Attaching package: 'DelayedArray'

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

    apply, scale, sweep

[ FAIL 0 | WARN 192 | SKIP 1 | PASS 4479 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• monocle is a little broken because of clusterApply (1): 'test-convert.R:71:5'

[ FAIL 0 | WARN 192 | SKIP 1 | PASS 4479 ]
> 
> proc.time()
   user  system elapsed 
490.684  16.751 588.723 

Example timings

scran.Rcheck/scran-Ex.timings

nameusersystemelapsed
DM0.0710.0000.072
buildSNNGraph6.1950.0086.215
clusterCells2.8200.2083.034
combineBlocks1.4670.0361.506
combineMarkers2.1740.0802.262
combinePValues0.0410.0000.041
combineVar1.4690.0081.480
computeMinRank0.0020.0000.001
convertTo1.7300.0551.794
correlateGenes1.2070.0241.234
correlateNull0.2540.0000.255
correlatePairs2.1110.2752.392
cyclone32.944 0.15233.154
decideTestsPerLabel5.7490.1355.896
defunct0.0010.0000.001
denoisePCA1.4010.0081.412
findMarkers2.8640.0042.874
fitTrendCV20.7990.0200.820
fitTrendPoisson0.2110.0040.215
fitTrendVar0.9140.0080.924
fixedPCA1.2150.0041.222
getClusteredPCs5.1250.0045.141
getMarkerEffects1.1930.0121.206
getTopHVGs1.0870.0041.092
getTopMarkers1.2360.0001.238
logBH0.0010.0000.001
modelGeneCV21.2530.0001.254
modelGeneCV2WithSpikes1.2850.0001.288
modelGeneVar1.4630.0041.470
modelGeneVarByPoisson1.2530.0241.280
modelGeneVarWithSpikes1.4620.0041.469
multiMarkerStats2.0110.0002.015
pairwiseBinom1.1150.0001.116
pairwiseTTests1.2380.0121.252
pairwiseWilcox1.0850.0041.092
pseudoBulkDGE5.6740.1005.791
pseudoBulkSpecific7.5030.0207.544
quickCluster1.9070.0041.916
quickSubCluster7.7110.0327.762
rhoToPValue000
sandbag0.9710.0150.990
scaledColRanks1.1150.0041.122
scoreMarkers1.5540.0041.562
summaryMarkerStats1.2090.0071.220
testLinearModel0.0860.0000.087