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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL iscream
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘iscream’ ...
** this is package ‘iscream’ version ‘1.1.7’
** 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
     /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 version 14.2.0 meets minimum requirements!
**** Compilation flags
     Using PKG_CFLAGS=-D_FILE_OFFSET_BITS=64
     Using PKG_LIBS='/home/biocbuild/R/R-devel_2025-02-19/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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppSpdlog/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppSpdlog/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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++) {
      |                     ~~^~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppSpdlog/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security  -c get_threads.cpp -o get_threads.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppSpdlog/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/stringfish/include' -I/usr/local/include   -fopenmp -fPIC  -g -O2  -Wall -Werror=format-security  -c log.cpp -o log.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppSpdlog/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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()) {
      |         ~~~~~~~~^~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppSpdlog/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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:71:23: 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]
   71 |     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:159:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<RegionQuery>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  159 |     for (int i = 0; i < intervals.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppSpdlog/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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
  286 |                 QueryAll query = QueryAll<arma::sp_umat>(bedfiles, regions, bstype, valInd, merged, sparse, prealloc, nthreads);
      |                                                                                                                               ^
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
  289 |                 QueryAll query = QueryAll<arma::umat>(bedfiles, regions, bstype, valInd, merged, sparse, prealloc, nthreads);
      |                                                                                                                            ^
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
  295 |                 QueryAll query = QueryAll<arma::sp_fmat>(bedfiles, regions, bstype, valInd, merged, sparse, prealloc, nthreads);
      |                                                                                                                               ^
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
  298 |                 QueryAll query = QueryAll<arma::fmat>(bedfiles, regions, bstype, valInd, merged, sparse, prealloc, nthreads);
      |                                                                                                                            ^
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); } \
      |                    ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppProgress/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppSpdlog/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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:121:23: 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]
  121 |     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:145:23: 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]
  145 |     for (int i = 0; i < cpgs.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
summarize_regions.cpp:147:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  147 |         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:176:35: 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]
  176 |     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 Rcpp::DataFrame&, const std::string&, bool, int)’:
summarize_regions.cpp:297:39: 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]
  297 |     for (int bedfile_n = 0; bedfile_n < bedfiles.size(); bedfile_n++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
summarize_regions.cpp:333:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<arma::Col<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  333 |                     for (int i = 0; i < input_data.size(); i++) {
      |                                     ~~^~~~~~~~~~~~~~~~~~~
summarize_regions.cpp:361:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ComputedFunVecs>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  361 |     for (int i = 0; i < computed_vecs.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~
summarize_regions.cpp:363:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  363 |         for (int j = 0; j < vecs.computed_vecs.size(); j++) {
      |                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o iscream.so RcppExports.o decode_mat.o get_threads.o log.o parsers.o query.o query_all.o summarize_regions.o /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -fopenmp -L/home/biocbuild/R/R/lib -lR
/usr/bin/ld: cannot find -lcurl: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/home/biocbuild/R/R/share/make/shlib.mk:10: iscream.so] Error 1
ERROR: compilation failed for package ‘iscream’
* removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/iscream’