James Eapen
| Snapshot Date: 2025-10-31 13:40 -0400 (Fri, 31 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/iscream |
| git_branch: devel |
| git_last_commit: b1bda1c |
| git_last_commit_date: 2025-10-29 14:17:07 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4774 |
| 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 1064/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| iscream 1.1.1 (landing page) James Eapen
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
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. |
| Package: iscream |
| Version: 1.1.1 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:iscream.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings iscream_1.1.1.tar.gz |
| StartedAt: 2025-11-01 00:26:21 -0400 (Sat, 01 Nov 2025) |
| EndedAt: 2025-11-01 00:28:17 -0400 (Sat, 01 Nov 2025) |
| EllapsedTime: 116.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: iscream.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:iscream.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings iscream_1.1.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/iscream.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.1.1’
* 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 15.2Mb
sub-directories of 1Mb or more:
help 1.9Mb
libs 13.0Mb
* 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
File ‘/home/biocbuild/bbs-3.23-bioc/R/site-library/iscream/libs/iscream.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
make_mat_bsseq 8.648 0.263 8.911
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/iscream.Rcheck/00check.log’
for details.
iscream.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL iscream
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘iscream’ ...
** this is package ‘iscream’ version ‘1.1.1’
** using staged installation
*** Configuring for package installation...
**** Trying pkg-config to use system htslib headers...
Falling back to Rhtslib
Using Rhtslib cflags and libs for htslib!
**** Checking GCC version
gcc -std=gnu2x version 13.3.0 meets minimum requirements!
**** Compilation flags
Using PKG_CFLAGS=-D_FILE_OFFSET_BITS=64
Using PKG_LIBS='/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/usrlib/libhts.a' -lcurl -lbz2 -llzma -lz
**** Checking if htslib was compiled with libdeflate
NOTE: iscream queries may be slower with Rhtslib than with htslib compiled with libdeflate
See <https://huishenlab.github.io/iscream/articles/htslib.html> for more information
**** 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-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-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-3.23-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -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'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppSpdlog/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.23-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-3.23-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 /home/biocbuild/bbs-3.23-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -fopenmp -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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)
iscream.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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.
'tabix' executable not found in $PATH. tabix() will use htslib to make queries instead which can be slower. See ?tabix for details.
>
> test_check("iscream")
Corrected 2 invalid 'chr:start' region strings to 'chr:start-start'
iscream now using 1 of 2 available threads.
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iscream now using 1 of 2 available threads.
iscream now using 2 of 2 available threads.
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 355 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• tabix_installed is not TRUE (2): 'test-tabix.R:59:3', 'test-tabix.R:120:3'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 355 ]
>
> proc.time()
user system elapsed
12.200 0.690 12.789
iscream.Rcheck/iscream-Ex.timings
| name | user | system | elapsed | |
| get_df_string | 0.023 | 0.002 | 0.024 | |
| get_granges_string | 1.982 | 0.096 | 2.079 | |
| get_threads | 0.002 | 0.001 | 0.003 | |
| htslib_version | 0.000 | 0.000 | 0.001 | |
| make_mat | 0.070 | 0.007 | 0.078 | |
| make_mat_bsseq | 8.648 | 0.263 | 8.911 | |
| query_chroms | 0.001 | 0.000 | 0.001 | |
| set_log_level | 0.001 | 0.001 | 0.002 | |
| set_threads | 0.001 | 0.001 | 0.002 | |
| summarize_meth_regions | 0.022 | 0.005 | 0.028 | |
| summarize_regions | 0.050 | 0.006 | 0.056 | |
| tabix | 0.262 | 0.033 | 0.295 | |
| validate_log_level | 0.003 | 0.000 | 0.003 | |