##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:scMET.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings scMET_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/scMET.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scMET/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scMET’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scMET’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... OK
  Not all R platforms support C++17
* checking installed package size ... NOTE
  installed size is 55.1Mb
  sub-directories of 1Mb or more:
    libs  53.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
scmet_plot_estimated_vs_true 27.367  0.180  27.592
scmet                        18.927  0.280  19.249
scmet_plot_efdr_efnr_grid    18.268  0.255  18.554
scmet_plot_mean_var          18.110  0.168  18.306
scmet_hvf_lvf                18.000  0.224  18.249
scmet_plot_vf_tail_prob      17.404  0.111  17.544
sce_to_scmet                  8.579  0.303   8.898
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/scMET.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL scMET
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘scMET’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17


g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o


g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -Wall -c stanExports_scmet.cc -o stanExports_scmet.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_scmet.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_scmet.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_scmet.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_scmet.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_scmet.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_scmet.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_scmet.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/callbacks/writer.hpp:4,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/filtered_values.hpp:4,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:23,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:110,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp: In function ‘Eigen::Matrix<typename stan::value_type<T>::type, EigMat::ColsAtCompileTime, EigMat::RowsAtCompileTime> stan::math::generalized_inverse(const EigMat&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp:34:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs]
   34 |   using value_t = value_type_t<EigMat>;
      |         ^~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:319,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp: In function ‘std::vector<T> stan::math::tail(const std::vector<T>&, size_t)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp:46:9: warning: typedef ‘using idx_t = stan::math::index_type_t<std::vector<T> >’ locally defined but not used [-Wunused-local-typedefs]
   46 |   using idx_t = index_type_t<std::vector<T>>;
      |         ^~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
      |                                        ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_scmet.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_log.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::bernoulli_logit_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp:59:9: warning: typedef ‘using T_y_val = std::conditional_t<stan::is_vector<T2>::value, Eigen::Matrix<typename stan::partials_return_type<T_y>::type, -1, 1>, typename stan::partials_return_type<T_y>::type>’ locally defined but not used [-Wunused-local-typedefs]
   59 |   using T_y_val =
      |         ^~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_log.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:31,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_lpdf(const T_y&, const T_scale_succ&, const T_scale_fail&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp:50:9: warning: typedef ‘using T_partials_matrix = class Eigen::Matrix<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   50 |   using T_partials_matrix = Eigen::Matrix<T_partials_return, Eigen::Dynamic, 1>;
      |         ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_log.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:37,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_proportion_lpdf(const T_y&, const T_loc&, const T_prec&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp:55:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   55 |   using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
      |         ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_log.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:63,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::cauchy_lpdf(const T_y&, const T_loc&, const T_scale&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp:45:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   45 |   using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
      |         ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_log.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:74,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpdf(const T_prob&, const T_prior_size&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_n, T_prob>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   60 |   using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
      |         ^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_log.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:91,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::double_exponential_lpdf(const T_y&, const T_loc&, const T_scale&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:44:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   44 |   using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
      |         ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:111,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp: In function ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::frechet_cdf(const T_y&, const T_shape&, const T_scale&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp:30:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   30 |   using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
      |         ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_log.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:245,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp: In function ‘stan::return_type_t<T_shared_param, T_job_param> stan::math::ordered_logistic_lpmf(const T_y&, const T_loc&, const T_cut&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp:76:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_loc, T_cut>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
   76 |   using T_partials_array = Eigen::Array<T_partials_return, -1, 1>;
      |         ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_log.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:277,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp:62:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T_prob>::value, Eigen::Array<typename stan::partials_return_type<T_cut>::type, -1, 1>, typename stan::partials_return_type<T_cut>::type>’ locally defined but not used [-Wunused-local-typedefs]
   62 |   using T_alpha_val = typename std::conditional_t<
      |         ^~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:32,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp: In lambda function:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp:83:11: warning: typedef ‘using Block_ = class Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>’ locally defined but not used [-Wunused-local-typedefs]
   83 |     using Block_ = Eigen::Block<Eigen::MatrixXd>;
      |           ^~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:34,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp: In function ‘stan::math::var_value<Eigen::Matrix<double, -1, -1> > stan::math::cholesky_factor_constrain(const T&, int, int)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp:32:9: warning: typedef ‘using T_scalar = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs]
   32 |   using T_scalar = value_type_t<T>;
      |         ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:71,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp: In function ‘auto stan::math::generalized_inverse(const VarMat&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp:64:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs]
   64 |   using value_t = value_type_t<VarMat>;
      |         ^~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:8,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15,
                 from stanExports_scmet.h:11,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp: In function ‘void stan::model::assign(Mat1&&, const stan::model::cons_index_list<stan::model::index_multi, stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list> >&, const Mat2&, const char*, int)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp:349:9: warning: typedef ‘using pair_type = struct std::pair<int, std::vector<int, stan::math::arena_allocator<int> > >’ locally defined but not used [-Wunused-local-typedefs]
  349 |   using pair_type = std::pair<int, arena_vec>;
      |         ^~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:96:75:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   73 |     for (int i = 0; i < dims.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’:
stanExports_scmet.cc:30:89:   required from here
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20:   required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
  158 |   for (size_t i = 0; i < x.size(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, -1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20:   required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:222:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  222 |   for (size_t i = 0; i < x.rows(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:223:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  223 |     for (size_t j = 0; j < x.cols(); j++) {
      |                        ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20:   required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
  158 |   for (size_t i = 0; i < x.size(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20:   required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_scmet_namespace::model_scmet; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1253:46:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_scmet.cc:30:89:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:89:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   89 |   if (p_names.size() != draws.cols()) {
      |       ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:107:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  107 |   for (size_t i = 0; i < draws.rows(); ++i) {
      |                      ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_cholesky_factor.hpp:7,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:7,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:74:74:   required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:78:36:   required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:23:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘std::decay_t<long int>’ {aka ‘long int’} [-Wsign-compare]
   23 |       if (!(y <= high_vec[n])) {
      |            ~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:8,
                 from stanExports_scmet.h:11,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp: In instantiation of ‘T stan::io::reader<T>::scalar() [with T = double]’:
stanExports_scmet.h:903:28:   required from ‘void model_scmet_namespace::model_scmet::write_array_impl(RNG&, VecR&, VecI&, VecVar&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; VecR = std::vector<double>; VecI = std::vector<int>; VecVar = std::vector<double>; stan::require_vector_like_vt<std::is_floating_point, VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::require_std_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’
stanExports_scmet.h:1362:23:   required from ‘void model_scmet_namespace::model_scmet::write_array(RNG&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1105:23:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::constrain_pars(SEXP) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_scmet.cc:26:89:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp:139:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Map<const Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare]
  139 |     if (pos_ >= data_r_.size()) {
      |         ~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp: In instantiation of ‘T stan::io::reader<T>::scalar() [with T = stan::math::var_value<double>]’:
stanExports_scmet.h:710:28:   required from ‘stan::scalar_type_t<T2> model_scmet_namespace::model_scmet::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_scmet.h:1374:49:   required from ‘T__ model_scmet_namespace::model_scmet::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79:   required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_scmet_namespace::model_scmet; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_scmet.cc:23:88:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp:139:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Map<const Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:20:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:252:31:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68:   required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44:   required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:2128:35:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55:   required from here
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  299 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:240,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46:   required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36:   required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38:   required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24:   required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77:   required from here
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  543 |          std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol)
      |                          ^~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:123:20:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:156:31:   required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:729:54:   required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1367:36:   required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1404:20:   required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1543:93:   required from ‘typename boost::math::tools::promote_args<RT1, RT2, A>::type boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2, A>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:28:56:   required from here
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:692:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  692 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20:   required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:69:16:   required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Matrix<double, -1, 1>; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = stan::math::var_value<double>]’
stanExports_scmet.h:805:45:   required from ‘stan::scalar_type_t<T2> model_scmet_namespace::model_scmet::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_scmet.h:1374:49:   required from ‘T__ model_scmet_namespace::model_scmet::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79:   required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_scmet_namespace::model_scmet; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_scmet.cc:23:88:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Array<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
  158 |   for (size_t i = 0; i < x.size(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20:   required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:70:15:   required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Matrix<double, -1, 1>; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = stan::math::var_value<double>]’
stanExports_scmet.h:805:45:   required from ‘stan::scalar_type_t<T2> model_scmet_namespace::model_scmet::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_scmet.h:1374:49:   required from ‘T__ model_scmet_namespace::model_scmet::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79:   required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_scmet_namespace::model_scmet; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_scmet.cc:23:88:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20:   required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:70:15:   required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = stan::math::var_value<double>]’
stanExports_scmet.h:809:45:   required from ‘stan::scalar_type_t<T2> model_scmet_namespace::model_scmet::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; VecR = std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_scmet.h:1374:49:   required from ‘T__ model_scmet_namespace::model_scmet::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79:   required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_scmet_namespace::model_scmet; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_scmet.cc:23:88:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Array<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20:   required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:69:16:   required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = Eigen::Matrix<double, -1, 1>; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = double]’
stanExports_scmet.h:805:45:   required from ‘stan::scalar_type_t<T2> model_scmet_namespace::model_scmet::log_prob_impl(VecR&, VecI&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; VecR = std::vector<double>; VecI = std::vector<int>; stan::require_vector_like_t<VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::scalar_type_t<T2> = double; std::ostream = std::basic_ostream<char>]’
stanExports_scmet.h:1374:49:   required from ‘T__ model_scmet_namespace::model_scmet::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T__ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:55:47:   required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_scmet_namespace::model_scmet]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:502:41:   required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::__cxx11::basic_string<char> >&, RNG_t&) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1215:18:   required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::call_sampler(SEXP) [with Model = model_scmet_namespace::model_scmet; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_scmet.cc:15:87:   required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:18,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_scmet.h:9,
                 from stanExports_scmet.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
  217 |    value_type v = g();
      |               ^
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o scMET.so RcppExports.o stanExports_scmet.o -L/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-scMET/00new/scMET/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (scMET)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(scMET)
> 
> test_check("scMET")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  7.864   0.254   8.121