############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL iscream ### ############################################################################## ############################################################################## * 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 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)’: parsers.cpp:46:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::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 >::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 query_intervals(const char*, const std::vector >&)’: query.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::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 >&)’: query.cpp:156:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::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::QueryAll(std::vector >&, std::vector >&, BSType, int, bool, bool, int, int) [with Mat = arma::SpMat]’: 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 >::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::QueryAll(std::vector >&, std::vector >&, BSType, int, bool, bool, int, int) [with Mat = arma::Mat]’: 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 >::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::QueryAll(std::vector >&, std::vector >&, BSType, int, bool, bool, int, int) [with Mat = arma::SpMat]’: 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 >::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::QueryAll(std::vector >&, std::vector >&, BSType, int, bool, bool, int, int) [with Mat = arma::Mat]’: 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 >::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 >&, ssize_t, std::vector >, const std::vector >&, BSType, bool)’: summarize_regions.cpp:68:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::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 >&, ssize_t, std::vector >, const std::vector >&, bool)’: summarize_regions.cpp:92:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::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 init_result_cols(ssize_t, ssize_t, const std::vector >&, bool)’: summarize_regions.cpp:123:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::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 >&, const Rcpp::CharacterVector&, const std::vector >&, const std::vector >&, const std::vector >&, const std::string&, bool, bool, int)’: summarize_regions.cpp:221:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::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 >::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::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 >::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)