* installing *source* package ‘tidylda’ ...
** package ‘tidylda’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (GCC) 14.2.0’
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/tidylda/src'
g++-14 -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 -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from /data/gannet/ripley/R/test-dev/RcppThread/include/RcppThread.h:9,
from ../inst/include/tidylda_RcppExports.h:8,
from ../inst/include/tidylda.h:7,
from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: "R_NO_REMAP" redefined
10 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
gcc-14 -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 -DC99_INLINE_SEMANTICS=0 -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++-14 -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 -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c lda_gibbs2.cpp -o lda_gibbs2.o
In file included from /data/gannet/ripley/R/test-dev/RcppThread/include/RcppThread.h:9,
from lda_gibbs2.cpp:27:
/data/gannet/ripley/R/test-dev/RcppThread/include/RcppThread/RMonitor.hpp:10:9: warning: "R_NO_REMAP" redefined
10 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
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++-14 -std=gnu++17 -shared -L/usr/local/gcc14/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)