* installing *source* package ‘tidylda’ ...
** package ‘tidylda’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/tidylda/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/include' -I/usr/local/include   -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes  -c init.c -o init.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppProgress/include' -I'/data/gannet/ripley/R/test-dev/RcppThread/include' -I/usr/local/include   -fopenmp -DARMA_64BIT_WORD=1 -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c lda_gibbs2.cpp -o lda_gibbs2.o
In file included from lda_gibbs2.cpp:19:
matrix_conversions.h: In function 'Rcpp::NumericMatrix vec_to_mat(const std::vector<std::vector<double> >&, const bool&)':
matrix_conversions.h:82:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare]
   82 |   for (auto j = 0; j < n_cols; j++) {
      |                    ~~^~~~~~~~
matrix_conversions.h:83:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare]
   83 |     for (auto k = 0; k < n_rows; k++) {
      |                      ~~^~~~~~~~
matrix_conversions.h: In function 'Rcpp::IntegerMatrix vec_to_mat(const std::vector<std::vector<long int> >&, const bool&)':
matrix_conversions.h:106:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare]
  106 |   for (auto j = 0; j < n_cols; j++) {
      |                    ~~^~~~~~~~
matrix_conversions.h:107:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::size_t' {aka 'long unsigned int'} [-Wsign-compare]
  107 |     for (auto k = 0; k < n_rows; k++) {
      |                      ~~^~~~~~~~
In file included from lda_gibbs2.cpp:20:
parallel_gibbs_utils.h: In function 'std::vector<std::vector<long unsigned int> > allocate_batch_indices(const std::size_t&, const std::size_t&)':
parallel_gibbs_utils.h:30:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
   30 |   for (auto j = 0; j < threads; j++) {
      |                    ~~^~~~~~~~~
parallel_gibbs_utils.h: In function 'std::vector<long int> add_integer_vectors(const std::vector<std::vector<long int> >&)':
parallel_gibbs_utils.h:97:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
   97 |   for (auto j = 0; j < vec_length; j++) {
      |                    ~~^~~~~~~~~~~~
parallel_gibbs_utils.h:101:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<long int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  101 |   for (auto i = 0; i < vector_list.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
parallel_gibbs_utils.h:102:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  102 |     for (auto j = 0; j < vec_length; j++) {
      |                      ~~^~~~~~~~~~~~
parallel_gibbs_utils.h: In function 'std::vector<std::vector<long int> > add_integer_matrices(const std::vector<std::vector<std::vector<long int> > >&)':
parallel_gibbs_utils.h:132:22: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  132 |   for (auto k = 0; k < ncol; k++) {
      |                    ~~^~~~~~
parallel_gibbs_utils.h:134:24: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  134 |     for (auto j = 0; j < num_mats; j++) {
      |                      ~~^~~~~~~~~~
parallel_gibbs_utils.h: In function 'std::vector<long int> update_global_Ck(const std::vector<long int>&, const std::vector<std::vector<long int> >&, const std::size_t&)':
parallel_gibbs_utils.h:160:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  160 |   for (auto j = 0; j < Ck.size(); j++) {
      |                    ~~^~~~~~~~~~~
parallel_gibbs_utils.h: In function 'std::vector<std::vector<long int> > update_global_Cv(const std::vector<std::vector<long int> >&, const std::vector<std::vector<std::vector<long int> > >&, const std::size_t&)':
parallel_gibbs_utils.h:183:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<long int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  183 |   for (auto j = 0; j < Cv.size(); j++) {
      |                    ~~^~~~~~~~~~~
parallel_gibbs_utils.h:187:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  187 |     for (auto k = 0; k < tmp.size(); k++) {
      |                      ~~^~~~~~~~~~~~
lda_gibbs2.cpp: In function 'Rcpp::List create_lexicon(const Rcpp::IntegerMatrix&, const Rcpp::NumericMatrix&, const arma::sp_mat&, const std::vector<double>&, const bool&)':
lda_gibbs2.cpp:98:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
   98 |   for (auto d = 0; d < Nd; d++) {
      |                    ~~^~~~
lda_gibbs2.cpp:106:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  106 |     for (auto v = 0; v < Nv; v++) {
      |                      ~~^~~~
lda_gibbs2.cpp:116:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  116 |     for (auto v = 0; v < Nv; v++) {
      |                      ~~^~~~
lda_gibbs2.cpp:120:28: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  120 |         for (auto k = 0; k < Nk; k++) {
      |                          ~~^~~~
lda_gibbs2.cpp:151:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  151 |   for (auto k = 0; k < Nk; k++) {
      |                    ~~^~~~
lda_gibbs2.cpp:159:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  159 |   for (auto v = 0; v < Nv; v++) {
      |                    ~~^~~~
lda_gibbs2.cpp:161:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  161 |     for (auto k = 0; k < Nk; k++) {
      |                      ~~^~~~
lda_gibbs2.cpp:173:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  173 |   for (auto d = 0; d < Nd; d++) {
      |                    ~~^~~~
lda_gibbs2.cpp:181:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  181 |     for (auto k = 0; k < Nk; k++) {
      |                      ~~^~~~
lda_gibbs2.cpp:188:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  188 |       for (auto n = 0; n < zd.size(); n++) {
      |                        ~~^~~~~~~~~~~
lda_gibbs2.cpp:196:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  196 |       for (auto n = 0; n < zd.size(); n++) {
      |                        ~~^~~~~~~~~~~
lda_gibbs2.cpp: In function 'Rcpp::List fit_lda_c(const std::vector<std::vector<long unsigned int> >&, const std::vector<std::vector<long unsigned int> >&, const Rcpp::IntegerMatrix&, const Rcpp::IntegerMatrix&, const std::vector<long int>&, std::vector<double>, const Rcpp::NumericMatrix&, const std::size_t&, const int&, const bool&, const bool&, const Rcpp::NumericMatrix&, const bool&, const std::size_t&, const bool&)':
lda_gibbs2.cpp:332:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  332 |   for (auto k = 0; k < Nk; k++) {
      |                    ~~^~~~
lda_gibbs2.cpp:340:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  340 |   for (auto d = 0; d < Nd; d++) {
      |                    ~~^~~~
lda_gibbs2.cpp:341:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  341 |     for (auto k = 0; k < Nk; k++) {
      |                      ~~^~~~
lda_gibbs2.cpp:350:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  350 |   for (auto k = 0; k < Nk; k++) {
      |                    ~~^~~~
lda_gibbs2.cpp:351:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  351 |     for (auto v = 0; v < Nv; v++) {
      |                      ~~^~~~
lda_gibbs2.cpp:368:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  368 |   for (auto j = 0; j < threads; j++) {
      |                    ~~^~~~~~~~~
lda_gibbs2.cpp:381:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  381 |   for (auto t = 0; t < iterations; t++) { // fill in empty likelihood
      |                    ~~^~~~~~~~~~~~
lda_gibbs2.cpp:392:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  392 |     for (auto v = 0; v < Nv; v++) {
      |                      ~~^~~~
lda_gibbs2.cpp:398:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  398 |     for (auto k = 0; k < Nk; k++) {
      |                      ~~^~~~
lda_gibbs2.cpp:409:22: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  409 |   for (auto t = 0; t < iterations; t++) { // for each iteration
      |                    ~~^~~~~~~~~~~~
lda_gibbs2.cpp:412:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  412 |     for (auto j = 0; j < threads; j++) {
      |                      ~~^~~~~~~~~
lda_gibbs2.cpp:417:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  417 |     for (auto j = 0; j < threads; j++) { // for each thread (used to be parallel)
      |                      ~~^~~~~~~~~
lda_gibbs2.cpp:435:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  435 |         for (auto n = 0; n < doc.size(); n++) { // for each word in that document
      |                          ~~^~~~~~~~~~~~
lda_gibbs2.cpp:447:32: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  447 |             for (auto k = 0; k < Nk; k++) {
      |                              ~~^~~~
lda_gibbs2.cpp:470:32: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  470 |             for (auto k = 0; k < Nk; k++) {
      |                              ~~^~~~
lda_gibbs2.cpp:525:26: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  525 |       for (auto d = 0; d < Nd; d++) {
      |                        ~~^~~~
lda_gibbs2.cpp:526:28: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  526 |         for (auto k = 0; k < Nk; k++) {
      |                          ~~^~~~
lda_gibbs2.cpp:534:28: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  534 |         for (auto k = 0; k < Nk; k++) {
      |                          ~~^~~~
lda_gibbs2.cpp:535:30: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  535 |           for (auto v = 0; v < Nv; v++) {
      |                            ~~^~~~
lda_gibbs2.cpp:555:26: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  555 |       for (auto k = 0; k < Nk; k++) {
      |                        ~~^~~~
lda_gibbs2.cpp:562:28: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  562 |         for (auto v = 0; v < Nv; v++) {
      |                          ~~^~~~
lda_gibbs2.cpp:567:28: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  567 |         for (auto v = 0; v < Nv; v++) {
      |                          ~~^~~~
lda_gibbs2.cpp:582:26: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  582 |       for (auto d = 0; d < Nd; d++) {
      |                        ~~^~~~
lda_gibbs2.cpp:592:28: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  592 |         for (auto k = 0; k < Nk; k++) {
      |                          ~~^~~~
lda_gibbs2.cpp:596:28: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  596 |         for (auto k = 0; k < Nk; k++) {
      |                          ~~^~~~
lda_gibbs2.cpp:602:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<long unsigned int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  602 |         for (auto n = 0; n < doc.size(); n++) {
      |                          ~~^~~~~~~~~~~~
lda_gibbs2.cpp:606:30: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  606 |           for (auto k = 0; k < Nk; k++) {
      |                            ~~^~~~
lda_gibbs2.cpp:631:26: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  631 |       for (auto k = 0; k < Nk; k++) {
      |                        ~~^~~~
lda_gibbs2.cpp:654:24: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  654 |     for (auto d = 0; d < Nd; d++) {
      |                      ~~^~~~
lda_gibbs2.cpp:655:26: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  655 |       for (auto k = 0; k < Nk; k++) {
      |                        ~~^~~~
lda_gibbs2.cpp:661:26: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  661 |       for (auto k = 0; k < Nk; k++) {
      |                        ~~^~~~
lda_gibbs2.cpp:662:28: warning: comparison of integer expressions of different signedness: 'int' and 'const std::size_t' {aka 'const long unsigned int'} [-Wsign-compare]
  662 |         for (auto v = 0; v < Nv; v++) {
      |                          ~~^~~~
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o tidylda.so RcppExports.o init.o lda_gibbs2.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/tidylda/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/tidylda/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/tidylda/src'
installing to /data/gannet/ripley/R/packages/tests-devel/tidylda.Rcheck/00LOCK-tidylda/00new/tidylda/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (tidylda)