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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:epiregulon.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings epiregulon_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/epiregulon.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epiregulon/DESCRIPTION’ ... OK
* this is package ‘epiregulon’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘epiregulon’ can be installed ... OK
* used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
aggregateAcrossCellsFast: no visible global function definition for
  ‘spritnf’
Undefined global functions or variables:
  spritnf
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ...

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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL epiregulon
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘epiregulon’ ...
** this is package ‘epiregulon’ version ‘1.4.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c aggregate_across_cells.cpp -o aggregate_across_cells.o
aggregate_across_cells.cpp: In function ‘SEXPREC* aggregate_across_cells(SEXP, Rcpp::List, int)’:
aggregate_across_cells.cpp:19:26: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   19 |     if (groups[g].size() != NC) {
      |         ~~~~~~~~~~~~~~~~~^~~~~
In file included from aggregate_across_cells.cpp:2:
AggregateAcrossCells.h: In instantiation of ‘void scran::AggregateAcrossCells::compute_row(Index_, Index_, const Contents_&, const Factor_*, std::vector<IndexIn_>&, std::vector<Sum_*>&, std::vector<Detected_>&, std::vector<Detected_*>&) [with bool sparse_ = true; Index_ = int; Contents_ = tatami::SparseRange<double, int>; Factor_ = int; Sum_ = double; Detected_ = int]’:
AggregateAcrossCells.h:150:30:   required from ‘void scran::AggregateAcrossCells::compute(const tatami::Matrix<Value_, Index_>*, const Factor_*, std::vector<Detected_*>&, std::vector<Detected_*>&) [with bool row_ = true; bool sparse_ = true; Data_ = double; Index_ = int; Factor_ = int; Sum_ = double; Detected_ = int]’
  150 |             compute_row<true>(x, NC, ext->fetch(x, vbuffer.data(), ibuffer.data()), factor, tmp_sums, sums, tmp_detected, detected);
      |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AggregateAcrossCells.h:210:28:   required from ‘void scran::AggregateAcrossCells::run(const tatami::Matrix<Value_, Index_>*, const Factor*, std::vector<Sum*>, std::vector<Sum_*>) [with Data = double; Index = int; Factor = int; Sum = double; Detected = int]’
  210 |         compute<true, true>(input, factor, sums, detected);
      |         ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aggregate_across_cells.cpp:52:13:   required from here
   52 |   runner.run(mat.get(), fptr, sptrs, dptrs);
      |   ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AggregateAcrossCells.h:109:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  109 |       for (Index_ l = 0; l < tmp_sums.size(); ++l) {
      |                          ~~^~~~~~~~~~~~~~~~~
AggregateAcrossCells.h:127:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  127 |       for (Index_ l = 0; l < tmp_detected.size(); ++l) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~
AggregateAcrossCells.h: In instantiation of ‘void scran::AggregateAcrossCells::compute_row(Index_, Index_, const Contents_&, const Factor_*, std::vector<IndexIn_>&, std::vector<Sum_*>&, std::vector<Detected_>&, std::vector<Detected_*>&) [with bool sparse_ = false; Index_ = int; Contents_ = const double*; Factor_ = int; Sum_ = double; Detected_ = int]’:
AggregateAcrossCells.h:152:31:   required from ‘void scran::AggregateAcrossCells::compute(const tatami::Matrix<Value_, Index_>*, const Factor_*, std::vector<Detected_*>&, std::vector<Detected_*>&) [with bool row_ = true; bool sparse_ = false; Data_ = double; Index_ = int; Factor_ = int; Sum_ = double; Detected_ = int]’
  152 |             compute_row<false>(x, NC, ext->fetch(x, vbuffer.data()), factor, tmp_sums, sums, tmp_detected, detected);
      |             ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AggregateAcrossCells.h:212:29:   required from ‘void scran::AggregateAcrossCells::run(const tatami::Matrix<Value_, Index_>*, const Factor*, std::vector<Sum*>, std::vector<Sum_*>) [with Data = double; Index = int; Factor = int; Sum = double; Detected = int]’
  212 |         compute<true, false>(input, factor, sums, detected);
      |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aggregate_across_cells.cpp:52:13:   required from here
   52 |   runner.run(mat.get(), fptr, sptrs, dptrs);
      |   ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AggregateAcrossCells.h:109:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  109 |       for (Index_ l = 0; l < tmp_sums.size(); ++l) {
      |                          ~~^~~~~~~~~~~~~~~~~
AggregateAcrossCells.h:127:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  127 |       for (Index_ l = 0; l < tmp_detected.size(); ++l) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c binom.c -o binom.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c fast_chisq.cpp -o fast_chisq.o
fast_chisq.cpp: In function ‘Rcpp::List fast_chisq(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericMatrix, int, Rcpp::NumericVector, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericMatrix, int, Rcpp::IntegerVector)’:
fast_chisq.cpp:27:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   27 |     if (nrows != tf_by_peak.size()) {
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~
fast_chisq.cpp:30:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   30 |     if (nrows != target_by_peak.size()) {
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
fast_chisq.cpp:33:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   33 |     if (nrows != target_ordered.size()) {
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c fast_wilcox.cpp -o fast_wilcox.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o epiregulon.so RcppExports.o aggregate_across_cells.o binom.o fast_chisq.o fast_wilcox.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-epiregulon/00new/epiregulon/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 (epiregulon)