Multiple platform build/check report for BioC 3.22 - CHECK results for iscream on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4658
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for iscream on nebbiolo2

To the developers/maintainers of the iscream package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/iscream.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.

raw results

Summary

Package: iscream

Version: 0.99.8

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:iscream.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings iscream_0.99.8.tar.gz

StartedAt: 2025-10-25 00:49:30 -0400 (Sat, 25 Oct 2025)

EndedAt: 2025-10-25 00:51:16 -0400 (Sat, 25 Oct 2025)

EllapsedTime: 106.1 seconds

RetCode: 1

Status: ERROR

CheckDir: iscream.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:iscream.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings iscream_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/iscream.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘iscream/DESCRIPTION’ ... OK
* this is package ‘iscream’ version ‘0.99.8’
* 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 ‘iscream’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking 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 whether startup messages can be suppressed ... 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 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
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
make_mat_bsseq 8.671  0.309    8.98
* 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 ‘TSS.Rmd’ using rmarkdown
File figure/tss_plot-1.png not found in resource path
Error: processing vignette 'TSS.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘TSS.Rmd’

--- re-building ‘data_structures.Rmd’ using rmarkdown
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘data_structures.Rmd’

--- re-building ‘htslib.rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/iscream.Rcheck/vign_test/iscream/vignettes/htslib_files/figure-html/unnamed-chunk-2-1.png" but not available.
--- finished re-building ‘htslib.rmd’

--- re-building ‘iscream.Rmd’ using rmarkdown
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘iscream.Rmd’

--- re-building ‘manuscript_data.Rmd’ using rmarkdown
--- finished re-building ‘manuscript_data.Rmd’

--- re-building ‘performance.Rmd’ using rmarkdown
--- finished re-building ‘performance.Rmd’

--- re-building ‘tabix.Rmd’ using rmarkdown
File figure/bench_1_raw-1.png not found in resource path
Error: processing vignette 'tabix.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘tabix.Rmd’

SUMMARY: processing the following files failed:
  ‘TSS.Rmd’ ‘tabix.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/iscream.Rcheck/00check.log’
for details.

Installation output

iscream.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL iscream
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘iscream’ ...
** this is package ‘iscream’ version ‘0.99.8’
** using staged installation
*** Configuring for package installation...
**** Trying pkg-config to use system htslib headers...
     Found pkg-config cflags and libs for htslib!
**** Checking GCC version
     gcc -std=gnu2x version meets minimum requirements!
**** Checking htslib version
     htslib version meets minimum requirements!
**** Compilation flags
     Using PKG_CFLAGS=
     Using PKG_LIBS=-lhts 
**** Checking if htslib was compiled with libdeflate
     htslib compiled with libdeflate!
**** Success!
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c decode_mat.cpp -o decode_mat.o
decode_mat.cpp: In function ‘void get_cov(Rcpp::NumericMatrix&, int)’:
decode_mat.cpp:33:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   33 |     for (int coln = 0; coln < M.n_cols; coln++) {
      |                        ~~~~~^~~~~~~~~~
decode_mat.cpp: In function ‘void get_m(Rcpp::NumericMatrix&, int)’:
decode_mat.cpp:47:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   47 |     for (int coln = 0; coln < M.n_cols; coln++) {
      |                        ~~~~~^~~~~~~~~~
decode_mat.cpp: In function ‘void get_beta(Rcpp::NumericMatrix&, int)’:
decode_mat.cpp:64:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   64 |     for (int coln = 0; coln < M.n_cols; coln++) {
      |                        ~~~~~^~~~~~~~~~
decode_mat.cpp: In function ‘void get_cov_sparse(Rcpp::S4&)’:
decode_mat.cpp:76:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
   76 |     for (int i = 0; i < x.size(); i++) {
      |                     ~~^~~~~~~~~~
decode_mat.cpp: In function ‘void get_m_sparse(Rcpp::S4&)’:
decode_mat.cpp:88:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
   88 |     for (int i = 0; i < x.size(); i++) {
      |                     ~~^~~~~~~~~~
decode_mat.cpp: In function ‘void get_beta_sparse(Rcpp::S4&)’:
decode_mat.cpp:104:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
  104 |     for (int i = 0; i < x.size(); i++) {
      |                     ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c get_threads.cpp -o get_threads.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c log.cpp -o log.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c parsers.cpp -o parsers.o
parsers.cpp: In function ‘BedRecord parseBedRecord(const std::string&, std::vector<int>)’:
parsers.cpp:46:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   46 |         for (i = 0; i < valInd.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~
parsers.cpp: In function ‘BedRecord parseBedRecord(const std::string&, int)’:
parsers.cpp:59:17: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   59 |     if (valInd1 >= fields.size()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c query.cpp -o query.o
query.cpp: In function ‘std::vector<RegionQuery> query_intervals(const char*, const std::vector<std::__cxx11::basic_string<char> >&)’:
query.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for (int i = 0; i < regions.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~
query.cpp: In function ‘Rcpp::List scan_tabix(const std::string&, const std::vector<std::__cxx11::basic_string<char> >&)’:
query.cpp:156:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<RegionQuery>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  156 |     for (int i = 0; i < intervals.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c query_all.cpp -o query_all.o
query_all.cpp: In instantiation of ‘QueryAll<Mat>::QueryAll(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, BSType, int, bool, bool, int, int) [with Mat = arma::SpMat<long long unsigned int>]’:
query_all.cpp:286:127:   required from here
query_all.cpp:45:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |     for (int bedfile_n = 0; bedfile_n < bedfile_vec.size(); bedfile_n++) {
      |                                                          ^
query_all.cpp:111:23: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  111 |     if (bitmat.n_rows > mapsize) {
      |         ~~~~~~~~~~~~~~^~~~~~~~~
query_all.cpp: In instantiation of ‘QueryAll<Mat>::QueryAll(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, BSType, int, bool, bool, int, int) [with Mat = arma::Mat<long long unsigned int>]’:
query_all.cpp:289:124:   required from here
query_all.cpp:45:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |     for (int bedfile_n = 0; bedfile_n < bedfile_vec.size(); bedfile_n++) {
      |                                                          ^
query_all.cpp:111:23: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  111 |     if (bitmat.n_rows > mapsize) {
      |         ~~~~~~~~~~~~~~^~~~~~~~~
query_all.cpp: In instantiation of ‘QueryAll<Mat>::QueryAll(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, BSType, int, bool, bool, int, int) [with Mat = arma::SpMat<float>]’:
query_all.cpp:295:127:   required from here
query_all.cpp:45:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |     for (int bedfile_n = 0; bedfile_n < bedfile_vec.size(); bedfile_n++) {
      |                                                          ^
query_all.cpp:111:23: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  111 |     if (bitmat.n_rows > mapsize) {
      |         ~~~~~~~~~~~~~~^~~~~~~~~
query_all.cpp: In instantiation of ‘QueryAll<Mat>::QueryAll(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, BSType, int, bool, bool, int, int) [with Mat = arma::Mat<float>]’:
query_all.cpp:298:124:   required from here
query_all.cpp:45:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |     for (int bedfile_n = 0; bedfile_n < bedfile_vec.size(); bedfile_n++) {
      |                                                          ^
query_all.cpp:111:23: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const long long unsigned int’} and ‘int’ [-Wsign-compare]
  111 |     if (bitmat.n_rows > mapsize) {
      |         ~~~~~~~~~~~~~~^~~~~~~~~
In file included from query_all.hpp:30,
                 from query_all.cpp:1:
query_all.hpp:56:34: warning: ‘int khmap_del(khmap_t*, khint_t)’ defined but not used [-Wunused-function]
   56 | KHASHL_MAP_INIT(static, khmap_t, khmap, CpG, int, kh_hash_cpg, kh_eq_cpg);
      |                                  ^~~~~
../inst/include/khashl.h:352:19: note: in definition of macro ‘KHASHL_MAP_INIT’
  352 |         SCOPE int prefix##_del(HType *h, khint_t k) { return prefix##_m_del(h, k); } \
      |                   ^~~~~~
query_all.hpp:56:34: warning: ‘void khmap_destroy(khmap_t*)’ defined but not used [-Wunused-function]
   56 | KHASHL_MAP_INIT(static, khmap_t, khmap, CpG, int, kh_hash_cpg, kh_eq_cpg);
      |                                  ^~~~~
../inst/include/khashl.h:350:20: note: in definition of macro ‘KHASHL_MAP_INIT’
  350 |         SCOPE void prefix##_destroy(HType *h) { prefix##_m_destroy(h); } \
      |                    ^~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -Werror=format-security  -c summarize_regions.cpp -o summarize_regions.o
summarize_regions.cpp: In function ‘InputCols make_BSdata_vecs(const std::vector<std::__cxx11::basic_string<char> >&, ssize_t, std::vector<int, std::allocator<int> >, const std::vector<std::__cxx11::basic_string<char> >&, BSType, bool)’:
summarize_regions.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   68 |     for (int i = 0; i < cpgs.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
summarize_regions.cpp: In function ‘InputCols make_data_vecs(const std::vector<std::__cxx11::basic_string<char> >&, ssize_t, std::vector<int, std::allocator<int> >, const std::vector<std::__cxx11::basic_string<char> >&, bool)’:
summarize_regions.cpp:92:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   92 |     for (int i = 0; i < cpgs.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
summarize_regions.cpp:94:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   94 |         for (int dp = 0; dp < parsed_cpg.size; dp++) {
      |                          ~~~^~~~~~~~~~~~~~~~~
summarize_regions.cpp: In function ‘std::vector<ComputedFunVecs> init_result_cols(ssize_t, ssize_t, const std::vector<std::__cxx11::basic_string<char> >&, bool)’:
summarize_regions.cpp:123:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  123 |     for (int fun_ind = 0; fun_ind < fun_vec.size(); fun_ind++) {
      |                           ~~~~~~~~^~~~~~~~~~~~~~~~
summarize_regions.cpp: In function ‘Rcpp::DataFrame Cpp_summarize_regions(const std::vector<std::__cxx11::basic_string<char> >&, const Rcpp::CharacterVector&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::__cxx11::basic_string<char> >&, const std::string&, bool, bool, int)’:
summarize_regions.cpp:221:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  221 |     for (int bedfile_n = 0; bedfile_n < bedfiles.size(); bedfile_n++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
summarize_regions.cpp:252:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<arma::Col<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |                     for (int i = 0; i < input_data.size(); i++) {
      |                                     ~~^~~~~~~~~~~~~~~~~~~
summarize_regions.cpp:273:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ComputedFunVecs>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  273 |     for (int i = 0; i < computed_vecs.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~
summarize_regions.cpp:275:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  275 |         for (int j = 0; j < vecs.computed_vecs.size(); j++) {
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o iscream.so RcppExports.o decode_mat.o get_threads.o log.o parsers.o query.o query_all.o summarize_regions.o -lhts -fopenmp -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-iscream/00new/iscream/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (iscream)

Tests output

iscream.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(iscream)
iscream using 1 thread by default but parallelly::availableCores() detects 2 possibly available threads. See `?set_threads` for information on multithreading before trying to use more.
> 
> test_check("iscream")
Corrected 2 invalid 'chr:start' region strings to 'chr:start-start'
iscream now using 1 of 2 available threads.
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
iscream now using 1 of 2 available threads.
iscream now using 2 of 2 available threads.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
> 
> proc.time()
   user  system elapsed 
 11.811   0.727  12.479

Example timings

iscream.Rcheck/iscream-Ex.timings

name	user	system	elapsed
get_df_string	0.022	0.003	0.027
get_granges_string	2.170	0.069	2.239
get_threads	0.002	0.001	0.002
htslib_version	0.001	0.000	0.001
make_mat	0.041	0.001	0.044
make_mat_bsseq	8.671	0.309	8.980
query_chroms	0.001	0.000	0.002
set_log_level	0.002	0.000	0.003
set_threads	0.002	0.000	0.002
summarize_meth_regions	0.025	0.002	0.026
summarize_regions	0.052	0.007	0.059
tabix	0.263	0.062	0.327
validate_log_level	0.002	0.000	0.002