* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ondisc’ ...
** this is package ‘ondisc’ version ‘1.3.5’
** package ‘ondisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDwb6oS/R.INSTALLb67d1489c2b0/ondisc/src'
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c h5_import_data_functs.cpp -o h5_import_data_functs.o
h5_import_data_functs.cpp: In function ‘void decrement_vector(Rcpp::IntegerVector)’:
h5_import_data_functs.cpp:19:36: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   19 |   for (unsigned long long i = 0; i < v.size(); i ++) v[i] --;
      |                                  ~~^~~~~~~~~~
h5_import_data_functs.cpp: In function ‘void add_value_to_vector(Rcpp::IntegerVector, int)’:
h5_import_data_functs.cpp:26:36: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   26 |   for (unsigned long long i = 0; i < v.size(); i ++) v[i] += to_add;
      |                                  ~~^~~~~~~~~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c h5_initialize_functs.cpp -o h5_initialize_functs.o
h5_initialize_functs.cpp: In function ‘void create_odm_r_matrix_cpp(const std::string&, Rcpp::StringVector, int, int, int, int, int, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&)’:
h5_initialize_functs.cpp:156:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  156 |   for (int i = 0; i < p.size(); i ++) row_ptr[i] = static_cast<unsigned long long>(p[i]);
      |                   ~~^~~~~~~~~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c h5_load_row.cpp -o h5_load_row.o
h5_load_row.cpp: In function ‘Rcpp::IntegerVector load_row_cpp(const std::string&, SEXP, int, int)’:
h5_load_row.cpp:15:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   15 |   for (int i = 0; i < m_x.size(); i ++) out[m_j[i]] = m_x[i];
      |                   ~~^~~~~~~~~~~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c h5_simple_read.cpp -o h5_simple_read.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c sceptre_functs.cpp -o sceptre_functs.o
sceptre_functs.cpp: In function ‘Rcpp::IntegerVector threshold_count_matrix_cpp(const std::string&, SEXP, int, int)’:
sceptre_functs.cpp:14:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   14 |   for (int k = 0; k < x.size(); k ++) if (x[k] >= threshold) n_gte_threshold ++;
      |                   ~~^~~~~~~~~~
sceptre_functs.cpp:16:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   16 |   for (int k = 0; k < x.size(); k ++) if (x[k] >= threshold) out[counter ++] = j[k] + 1;
      |                   ~~^~~~~~~~~~
sceptre_functs.cpp: In function ‘void load_nonzero_posits_odm(const std::string&, SEXP, int, std::vector<bool>&, std::vector<bool>&, std::vector<int>&)’:
sceptre_functs.cpp:26:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   26 |   for (int k = 0; k < y_orig.size(); k ++) y_orig[k] = false;
      |                   ~~^~~~~~~~~~~~~~~
sceptre_functs.cpp:27:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   27 |   for (int k = 0; k < j.size(); k ++) y_orig[j[k]] = true;
      |                   ~~^~~~~~~~~~
sceptre_functs.cpp:28:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   28 |   for (int k = 0; k < y_sub.size(); k++) y_sub[k] = y_orig[cells_in_use_zero_idx[k]];
      |                   ~~^~~~~~~~~~~~~~
sceptre_functs.cpp: In function ‘Rcpp::List compute_nt_nonzero_matrix_and_n_ok_pairs_ondisc(const std::string&, SEXP, int, int, int, Rcpp::List, Rcpp::List, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, Rcpp::IntegerVector)’:
sceptre_functs.cpp:45:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |   for (int i = 0; i < cells_in_use_zero_idx.size(); i ++) cells_in_use_zero_idx[i] = cells_in_use[i] - 1;
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sceptre_functs.cpp:70:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   70 |       for (int k = 0; k < y_sub.size(); k++) if (y_sub[k]) n_nonzero_tot[row_idx] ++;
      |                       ~~^~~~~~~~~~~~~~
sceptre_functs.cpp: In function ‘Rcpp::IntegerMatrix compute_n_trt_cells_matrix_ondisc(const std::string&, SEXP, int, int, int, Rcpp::List, Rcpp::IntegerVector)’:
sceptre_functs.cpp:105:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  105 |   for (int i = 0; i < cells_in_use_zero_idx.size(); i ++) cells_in_use_zero_idx[i] = cells_in_use[i] - 1;
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sceptre_functs.cpp: In function ‘Rcpp::List compute_n_ok_pairs_ondisc(const std::string&, SEXP, int, int, int, Rcpp::List, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, Rcpp::IntegerVector, Rcpp::IntegerVector)’:
sceptre_functs.cpp:139:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  139 |   for (int i = 0; i < cells_in_use_zero_idx.size(); i ++) cells_in_use_zero_idx[i] = cells_in_use[i] - 1;
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sceptre_functs.cpp:152:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  152 |       for (int k = 0; k < y_sub.size(); k++) if (y_sub[k]) n_nonzero_tot ++;
      |                       ~~^~~~~~~~~~~~~~
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c shared_functs.cpp -o shared_functs.o
g++-16 -std=gnu++20 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c utility_functs.cpp -o utility_functs.o
utility_functs.cpp: In function ‘void print_ull_vect(SEXP)’:
utility_functs.cpp:15:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   15 |   for (int i = 0; i < (*v).size(); i ++) {
      |                   ~~^~~~~~~~~~~~~
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o ondisc.so RcppExports.o h5_import_data_functs.o h5_initialize_functs.o h5_load_row.o h5_simple_read.o sceptre_functs.o shared_functs.o utility_functs.o /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/lib/libhdf5_cpp.a /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/lib/libhdf5.a -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rhdf5lib/lib -lsz -lm -ldl -lcurl -lssl -lcrypto -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDwb6oS/R.INSTALLb67d1489c2b0/ondisc/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDwb6oS/R.INSTALLb67d1489c2b0/ondisc/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDwb6oS/R.INSTALLb67d1489c2b0/ondisc/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ondisc/00new/ondisc/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘ondisc’
    finding HTML links ... done
    create_odm_from_cellranger              html  
    create_odm_from_r_matrix                html  
    dim-odm-method                          html  
    initialize_odm_from_backing_file        html  
    ondisc-package                          html  
    rownames-odm-method                     html  
    sub-odm-ANY-missing-missing-method      html  
    write_example_cellranger_dataset        html  
*** 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 (ondisc)