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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:HiSpaR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings HiSpaR_0.99.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/HiSpaR.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-19 04:45:24 UTC
* checking for file ‘HiSpaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiSpaR’ version ‘0.99.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HiSpaR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Matrix’
A package should be listed in only one of these fields.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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
File ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/HiSpaR/libs/HiSpaR.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/HiSpaR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL HiSpaR
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘HiSpaR’ ...
** this is package ‘HiSpaR’ version ‘0.99.5’
** using staged installation
Configuring HiSpaR for platform: Linux
  Detected Linux
  Found Armadillo via pkg-config
Checking for OpenMP support...
  OpenMP support: NO
  WARNING: OpenMP is required for HiSpaR. Package may not function correctly.
Writing src/Makevars
Configuration complete
** libs
specified C++17
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I../inst/include  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I../inst/include  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c chromosome.cpp -o chromosome.o
chromosome.cpp: In member function ‘void Chromosome::assign_clusters(int)’:
chromosome.cpp:155:19: warning: comparison of integer expressions of different signedness: ‘arma::uword’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  155 |         if (label >= num_clusters) {
      |             ~~~~~~^~~~~~~~~~~~~~~
chromosome.cpp: In member function ‘void Chromosome::build_cluster_relationships_by_distance(int)’:
chromosome.cpp:335:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  335 |     for (int c = 0; c < num_clusters; ++c) {
      |                     ~~^~~~~~~~~~~~~~
chromosome.cpp:339:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  339 |         for (int other_c = 0; other_c < num_clusters; ++other_c) {
      |                               ~~~~~~~~^~~~~~~~~~~~~~
chromosome.cpp: In member function ‘void Chromosome::log_memory_usage()’:
chromosome.cpp:1270:24: warning: unused variable ‘memory_mb’ [-Wunused-variable]
 1270 |                 double memory_mb = static_cast<double>(memory_kb) / 1024.0;
      |                        ^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I../inst/include  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c hispa_rcpp.cpp -o hispa_rcpp.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o HiSpaR.so RcppExports.o chromosome.o hispa_rcpp.o -larmadillo -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-HiSpaR/00new/HiSpaR/libs
** R
** data
** 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 (HiSpaR)

R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
Type 'q()' to quit R.

> library(testthat)
> library(HiSpaR)
Consider using the `HiContacts` package to perform advanced genomic operations 
on `HiCExperiment` objects.

Read "Orchestrating Hi-C analysis with Bioconductor" online book to learn more:
https://js2264.github.io/OHCA/
> 
> test_check("HiSpaR")
[ FAIL 0 | WARN 0 | SKIP 8 | PASS 3 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• On CRAN (8): 'test-hispa.R:22:3', 'test-hispa.R:66:3', 'test-hispa.R:105:3',
  'test-hispa.R:146:3', 'test-hispa.R:177:3', 'test-hispa.R:207:3',
  'test-hispa.R:236:3', 'test-hispa.R:263:3'

[ FAIL 0 | WARN 0 | SKIP 8 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 10.698   0.602  11.291