Multiple platform build/check report for BioC 3.19 - CHECK results for ppcseq on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4748
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4484
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4514
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"	4480
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: ppcseq

Version: 1.12.0

Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ppcseq.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ppcseq_1.12.0.tar.gz

StartedAt: 2024-05-09 10:39:28 -0000 (Thu, 09 May 2024)

EndedAt: 2024-05-09 10:44:15 -0000 (Thu, 09 May 2024)

EllapsedTime: 286.5 seconds

RetCode: 0

Status: OK

CheckDir: ppcseq.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:ppcseq.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings ppcseq_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ppcseq.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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 ‘ppcseq/DESCRIPTION’ ... OK
* this is package ‘ppcseq’ version ‘1.12.0’
* 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 ‘ppcseq’ 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 96.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  94.0Mb
* 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 code 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 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 ... NOTE
add_partition: no visible binding for global variable ‘.’
add_scaled_counts_bulk.calcNormFactor: no visible binding for global
  variable ‘transcript’
add_scaled_counts_bulk.get_low_expressed: no visible binding for global
  variable ‘transcript’
check_if_within_posterior: no visible binding for global variable
  ‘.lower’
check_if_within_posterior: no visible binding for global variable
  ‘.upper’
check_if_within_posterior: no visible binding for global variable ‘ppc’
do_inference: no visible binding for global variable ‘idx_MPI’
do_inference: no visible binding for global variable
  ‘read_count_MPI_row’
do_inference: no visible binding for global variable ‘.’
do_inference: no visible binding for global variable ‘symbol MPI row’
draws_to_tibble_x: no visible binding for global variable ‘.’
draws_to_tibble_x: no visible binding for global variable ‘dummy’
draws_to_tibble_x: no visible binding for global variable ‘.variable’
draws_to_tibble_x: no visible binding for global variable ‘.chain’
draws_to_tibble_x: no visible binding for global variable ‘.iteration’
draws_to_tibble_x: no visible binding for global variable ‘.draw’
draws_to_tibble_x: no visible binding for global variable ‘.value’
draws_to_tibble_x_y: no visible binding for global variable ‘.’
draws_to_tibble_x_y: no visible binding for global variable ‘dummy’
draws_to_tibble_x_y: no visible binding for global variable ‘.variable’
draws_to_tibble_x_y: no visible binding for global variable ‘.chain’
draws_to_tibble_x_y: no visible binding for global variable
  ‘.iteration’
draws_to_tibble_x_y: no visible binding for global variable ‘.draw’
draws_to_tibble_x_y: no visible binding for global variable ‘.value’
find_optimal_number_of_chains: no visible binding for global variable
  ‘tot’
find_optimal_number_of_chains: no visible binding for global variable
  ‘chains’
fit_to_counts_rng: no visible binding for global variable ‘.variable’
fit_to_counts_rng: no visible binding for global variable ‘S’
fit_to_counts_rng: no visible binding for global variable ‘G’
fit_to_counts_rng: no visible binding for global variable ‘.’
fit_to_counts_rng_approximated: no visible binding for global variable
  ‘.’
fit_to_counts_rng_approximated: no visible binding for global variable
  ‘S’
fit_to_counts_rng_approximated: no visible binding for global variable
  ‘G’
fit_to_counts_rng_approximated: no visible binding for global variable
  ‘CI’
format_for_MPI: no visible binding for global variable ‘.’
format_for_MPI: no visible binding for global variable ‘G’
format_for_MPI: no visible binding for global variable ‘idx_MPI’
format_input: no visible binding for global variable ‘.’
format_results: no visible binding for global variable
  ‘sample_wise_data’
get_scaled_counts_bulk: no visible binding for global variable ‘med’
get_scaled_counts_bulk: no visible binding for global variable
  ‘tot_filt’
get_scaled_counts_bulk: no visible binding for global variable ‘nf’
get_scaled_counts_bulk: no visible binding for global variable ‘.’
get_scaled_counts_bulk: no visible binding for global variable ‘tot’
identify_outliers: no visible binding for global variable ‘.’
identify_outliers: no visible binding for global variable ‘do_check___’
identify_outliers: no visible binding for global variable ‘multiplier’
identify_outliers: no visible binding for global variable
  ‘exposure_rate’
identify_outliers: no visible binding for global variable
  ‘write_on_disk’
identify_outliers: no visible binding for global variable ‘.variable’
identify_outliers: no visible binding for global variable ‘S’
identify_outliers: no visible binding for global variable ‘G’
identify_outliers: no visible binding for global variable ‘.lower’
identify_outliers: no visible binding for global variable ‘.upper’
identify_outliers_1_step: no visible binding for global variable ‘.’
identify_outliers_1_step: no visible global function definition for
  ‘scale_abundance’
identify_outliers_1_step: no visible binding for global variable ‘TMM’
identify_outliers_1_step: no visible binding for global variable
  ‘multiplier’
identify_outliers_1_step: no visible binding for global variable ‘l’
identify_outliers_1_step: no visible binding for global variable ‘l %>%
  sd’
identify_outliers_1_step: no visible binding for global variable ‘cc’
identify_outliers_1_step: no visible binding for global variable
  ‘write_on_disk’
identify_outliers_1_step: no visible binding for global variable
  ‘.variable’
identify_outliers_1_step: no visible binding for global variable ‘S’
identify_outliers_1_step: no visible binding for global variable ‘G’
identify_outliers_1_step: no visible binding for global variable
  ‘.lower’
identify_outliers_1_step: no visible binding for global variable
  ‘.upper’
identify_outliers_1_step: no visible binding for global variable ‘ppc’
identify_outliers_1_step: no visible binding for global variable
  ‘exposure_rate’
inits_fx: no visible binding for global variable ‘res_discovery’
inits_fx: no visible binding for global variable ‘.variable’
inits_fx: no visible binding for global variable ‘S’
inits_fx: no visible binding for global variable ‘G’
inits_fx: no visible binding for global variable ‘init’
merge_results: no visible binding for global variable ‘.variable’
merge_results: no visible binding for global variable ‘S’
merge_results: no visible binding for global variable ‘G’
merge_results: no visible binding for global variable ‘slope’
merge_results: no visible binding for global variable ‘exposure_rate’
merge_results: no visible binding for global variable ‘multiplier’
merge_results: no visible binding for global variable ‘.lower’
merge_results: no visible binding for global variable ‘.upper’
merge_results: no visible binding for global variable ‘ppc’
plot_credible_intervals: no visible binding for global variable
  ‘sample_wise_data’
produce_plots: no visible binding for global variable ‘.upper’
select_to_check_and_house_keeping: no visible binding for global
  variable ‘.’
summary_to_tibble: no visible binding for global variable ‘.’
Undefined global functions or variables:
  . .chain .draw .iteration .lower .upper .value .variable CI G S TMM
  cc chains do_check___ dummy exposure_rate idx_MPI init l l %>% sd med
  multiplier nf ppc read_count_MPI_row res_discovery sample_wise_data
  scale_abundance slope symbol MPI row tot tot_filt transcript
  write_on_disk
Consider adding
  importFrom("base", "row")
  importFrom("stats", "sd")
to your NAMESPACE file.
* 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
identify_outliers       25.602  0.395  26.057
plot_credible_intervals 24.480  0.207  24.738
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ppcseq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL ppcseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘ppcseq’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17


g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include' -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include' -I/usr/local/include    -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -g -O2  -Wall  -c stanExports_negBinomial_MPI.cc -o stanExports_negBinomial_MPI.o
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_negBinomial_MPI.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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:251:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  251 | 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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_negBinomial_MPI.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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:508:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  508 |     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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_negBinomial_MPI.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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:521:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  521 |     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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_negBinomial_MPI.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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:604:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  604 |     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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_negBinomial_MPI.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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:613:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  613 |     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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_negBinomial_MPI.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-beta-2024-04-15_r86425/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:615:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  615 |         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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_negBinomial_MPI.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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combination(std::vector<int>&, const int&, const int&, const int&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:73:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   73 |   for (std::size_t i = 0; i < p - 1; i++) {
      |                           ~~^~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:79:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   79 |     } while (k < x);
      |              ~~^~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::combos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:102:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  102 |   for (std::size_t i = 1; i != choose_dimk + 1; i++) {
      |                           ~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:105:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  105 |     for (std::size_t j = 0; j != k; j++) {
      |                             ~~^~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::increment(std::vector<bool>&, const int&, const double&, const std::vector<int>&, std::vector<double>&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:126:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  126 |     for (std::size_t j = 0; j != k; j++) {
      |                             ~~^~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  132 |   while ((first_zero < index.size()) && index[first_zero]) {
      |           ~~~~~~~~~~~^~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<bool>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  135 |   if (first_zero == index.size()) {
      |       ~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:143:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  143 |     for (std::size_t i = 0; i != first_zero + 1; i++) {
      |                             ~~^~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp: In function ‘void stan::math::internal::signcombos(const int&, const double&, const int&, std::vector<std::vector<double> >&)’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/hcubature.hpp:168:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  168 |   for (std::size_t i = 1; i != choose_dimk + 1; i++) {
      |                           ~~^~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/apply.hpp:24,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_optimization.hpp:18,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array_wrapper.hpp:21,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/serialization/array.hpp:26,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/storage.hpp:22,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/ublas/vector.hpp:21,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rcpp/include/Rcpp.h:27,
                 from stanExports_negBinomial_MPI.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-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::dump::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:694:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  694 |       for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
      |                                          ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  707 |              real_iter < val_i->second.first.size();
      |              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp:85:40: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   85 |         for (Eigen::Index pos = 0; pos < l_tri_size; pos++) {
      |                                    ~~~~^~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:49,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::random_var_context::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/random_var_context.hpp:111:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  111 |       for (comp_iter = 0, real_iter = 0; real_iter < val_r.size();
      |                                          ~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In member function ‘virtual std::vector<std::complex<double> > stan::io::array_var_context::vals_c(const string&) const’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:304:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  304 |       for (comp_iter = 0, real_iter = 0; real_iter < val_r->second.first.size();
      |                                          ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:317:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  317 |              real_iter < val_i->second.first.size();
      |              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: 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]
   74 |     for (int i = 0; i < dims.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_cholesky_factor.hpp:9,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp: In instantiation of ‘void stan::math::check_matching_dims(const char*, const char*, const T1&, const char*, const T2&) [with T1 = double; T2 = double; stan::require_all_not_matrix_t<T1, T2>* <anonymous> = 0; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T1, T2>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/offset_multiplier_constrain.hpp:98:24:   required from ‘auto stan::math::offset_multiplier_constrain(const T&, const M&, const S&, stan::return_type_t<T_x, T_sigma, T_l>&) [with T = double; M = double; S = int; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T, M, S>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:475:41:   required from ‘auto stan::io::deserializer<T>::read_constrain_offset_multiplier(const Offset&, const Mult&, LP&, Sizes ...) [with Ret = double; bool Jacobian = false; Offset = double; Mult = int; LP = double; Sizes = {}; T = double]’
stanExports_negBinomial_MPI.h:1293:72:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:37:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   37 |       for (int i = 1; i < y1_d.size(); i++) {
      |                       ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:45:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |       for (int i = 1; i < y2_d.size(); i++) {
      |                       ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:56:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   56 |     for (int i = 0; i < y1_d.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp: In instantiation of ‘void stan::math::check_matching_dims(const char*, const char*, const T1&, const char*, const T2&) [with T1 = double; T2 = int; stan::require_all_not_matrix_t<T1, T2>* <anonymous> = 0; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T1, T2>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/offset_multiplier_constrain.hpp:101:24:   required from ‘auto stan::math::offset_multiplier_constrain(const T&, const M&, const S&, stan::return_type_t<T_x, T_sigma, T_l>&) [with T = double; M = double; S = int; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T, M, S>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:475:41:   required from ‘auto stan::io::deserializer<T>::read_constrain_offset_multiplier(const Offset&, const Mult&, LP&, Sizes ...) [with Ret = double; bool Jacobian = false; Offset = double; Mult = int; LP = double; Sizes = {}; T = double]’
stanExports_negBinomial_MPI.h:1293:72:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:37:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   37 |       for (int i = 1; i < y1_d.size(); i++) {
      |                       ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:45:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |       for (int i = 1; i < y2_d.size(); i++) {
      |                       ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:56:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   56 |     for (int i = 0; i < y1_d.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
In file included from stanExports_negBinomial_MPI.cc:5:
stanExports_negBinomial_MPI.h: In instantiation of ‘void model_negBinomial_MPI_namespace::model_negBinomial_MPI::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = std::vector<double>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_negBinomial_MPI.h:1876:36:   required from here
stanExports_negBinomial_MPI.h:1422:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
 1422 |       int pos__ = std::numeric_limits<int>::min();
      |           ^~~~~
stanExports_negBinomial_MPI.h: In instantiation of ‘void model_negBinomial_MPI_namespace::model_negBinomial_MPI::unconstrain_array_impl(const VecVar&, const VecI&, VecVar&, std::ostream*) const [with VecVar = Eigen::Matrix<double, -1, 1>; VecI = std::vector<int>; stan::require_vector_t<T_y>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’:
stanExports_negBinomial_MPI.h:1886:36:   required from here
stanExports_negBinomial_MPI.h:1422:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:30:89:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
  153 |   for (size_t i = 0; i < x.size(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:207:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  207 |   for (size_t i = 0; i < x.rows(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:208:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  208 |     for (size_t j = 0; j < x.cols(); j++) {
      |                        ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
  153 |   for (size_t i = 0; i < x.size(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/core.hpp:4,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:10,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&, Idxs ...) [with T_y = long unsigned int; T_high = long int; stan::require_all_stan_scalar_t<U, V>* <anonymous> = 0; Idxs = {}]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36:   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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:39:20: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘const long int’ [-Wsign-compare]
   39 |   if (unlikely(!(y <= high))) {
      |                 ~~~^~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/meta/compiler_attributes.hpp:9:41: note: in definition of macro ‘unlikely’
    9 | #define unlikely(x) __builtin_expect(!!(x), 0)
      |                                         ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:68,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:30:89:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:55:22: 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]
   55 |   if (p_names.size() != draws.cols()) {
      |       ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:71:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   71 |   for (size_t i = 0; i < draws.rows(); ++i) {
      |                      ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::detail::hypergeometric_pFq_checked_series_impl(const Seq&, const Seq&, const Real&, const Policy&, const Terminal&, long long int&) [with Seq = std::vector<double>; Real = 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>; Terminal = boost::math::detail::iteration_terminator]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:107:   required from ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector<double>; Real = 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<Real, typename Seq::value_type>::type = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:72:35:   required from ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*) [with Seq = std::vector<double>; Real = double; typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:55:41:   required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, -1, 1>; Tb = Eigen::Matrix<double, -1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:125:28:   required from ‘auto stan::math::hypergeometric_3F2(const Ta&, const Tb&, const Tz&) [with Ta = std::vector<double>; Tb = std::vector<double>; Tz = double; stan::require_all_vector_t<T_y, T_high>* <anonymous> = 0; stan::require_stan_scalar_t<T2>* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_3F2.hpp:148:28:   required from ‘auto stan::math::hypergeometric_3F2(const std::initializer_list<_Tp>&, const std::initializer_list<_Up>&, const Tz&) [with Ta = double; Tb = double; Tz = double; stan::require_all_stan_scalar_t<Ta, Tb, Tz>* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/hypergeometric_pFq_checked_series.hpp:122:28: 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
  122 |      std::pair<Real, Real> hypergeometric_pFq_checked_series_impl(const Seq& aj, const Seq& bj, const Real& z, const Policy& pol, const Terminal& termination, long long& log_scale)
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:35:15:   required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30:   required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39:   required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57:   required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
  153 |   for (size_t i = 0; i < x.size(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:36:15:   required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30:   required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39:   required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57:   required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 2, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 2, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:39:16:   required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30:   required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39:   required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57:   required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 2, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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, 0, 1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:40:16:   required from ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::hypergeometric_pFq(const Ta&, const Tb&, const Tz&) [with Ta = Eigen::Matrix<double, 2, 1>; Tb = Eigen::Matrix<double, 1, 1, 0, 1, 1>; Tz = double; stan::require_all_eigen_st<std::is_arithmetic, Ta, Tb>* <anonymous> = 0; stan::require_arithmetic_t<Tz>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:189:30:   required from ‘stan::return_type_t<Ta1, Ta1, Tb, Tz> stan::math::hypergeometric_2F1(const Ta1&, const Ta2&, const Tb&, const Tz&) [with Ta1 = double; Ta2 = double; Tb = double; Tz = double; ScalarT = double; OptT = boost::optional<double>; stan::require_all_arithmetic_t<Ta1, Ta2, Tb, Tz>* <anonymous> = 0; stan::return_type_t<Ta1, Ta1, Tb, Tz> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:190:39:   required from ‘TupleT stan::math::internal::grad_2F1_impl(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool calc_a1 = true; bool calc_a2 = true; bool calc_b1 = true; bool calc_z = true; T1 = double; T2 = double; T3 = double; T_z = double; ScalarT = double; TupleT = std::tuple<double, double, double, double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:306:57:   required from ‘auto stan::math::grad_2F1(const T1&, const T2&, const T3&, const T_z&, double, int) [with bool ReturnSameT = true; T1 = double; T2 = double; T3 = double; T_z = double; stan::require_t<std::integral_constant<bool, __v> >* <anonymous> = 0]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, 1, 1, 0, 1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1721,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp: In instantiation of ‘boost::math::detail::temme_root_finder<T>::temme_root_finder(T, T) [with T = double]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7:   required from ‘T boost::math::detail::temme_method_2_ibeta_inverse(T, T, T, T, T, const Policy&) [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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:48:   required from ‘T boost::math::detail::ibeta_inv_imp(T, T, T, T, 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:30:   required from ‘boost::math::tools::promote_args_t<T1, T2, T3, T4> boost::math::ibeta_inv(T1, T2, T3, T4*, const Policy&) [with T1 = double; T2 = double; T3 = double; T4 = 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>; boost::math::tools::promote_args_t<T1, T2, T3, T4> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:20:   required from ‘boost::math::tools::promote_args_t<RT1, RT2, A> boost::math::ibeta_inv(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>; boost::math::tools::promote_args_t<RT1, RT2, A> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable ‘x_extrema’ [-Wunused-variable]
   29 |       const T x_extrema = 1 / (1 + a);
      |               ^~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_cholesky_factor.hpp:9,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp: In instantiation of ‘void stan::math::check_matching_dims(const char*, const char*, const T1&, const char*, const T2&) [with T1 = stan::math::var_value<double>; T2 = double; stan::require_all_not_matrix_t<T1, T2>* <anonymous> = 0; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T1, T2>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/offset_multiplier_constrain.hpp:98:24:   required from ‘auto stan::math::offset_multiplier_constrain(const T&, const M&, const S&, stan::return_type_t<T_x, T_sigma, T_l>&) [with T = stan::math::var_value<double>; M = double; S = int; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T, M, S>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = stan::math::var_value<double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:475:41:   required from ‘auto stan::io::deserializer<T>::read_constrain_offset_multiplier(const Offset&, const Mult&, LP&, Sizes ...) [with Ret = stan::math::var_value<double>; bool Jacobian = true; Offset = double; Mult = int; LP = stan::math::var_value<double>; Sizes = {}; T = stan::math::var_value<double>]’
stanExports_negBinomial_MPI.h:1151:50:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:23:88:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:37:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   37 |       for (int i = 1; i < y1_d.size(); i++) {
      |                       ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:45:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |       for (int i = 1; i < y2_d.size(); i++) {
      |                       ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:56:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   56 |     for (int i = 0; i < y1_d.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp: In instantiation of ‘void stan::math::check_matching_dims(const char*, const char*, const T1&, const char*, const T2&) [with T1 = stan::math::var_value<double>; T2 = int; stan::require_all_not_matrix_t<T1, T2>* <anonymous> = 0; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T1, T2>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/offset_multiplier_constrain.hpp:101:24:   required from ‘auto stan::math::offset_multiplier_constrain(const T&, const M&, const S&, stan::return_type_t<T_x, T_sigma, T_l>&) [with T = stan::math::var_value<double>; M = double; S = int; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T, M, S>* <anonymous> = 0; stan::return_type_t<T_x, T_sigma, T_l> = stan::math::var_value<double>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:475:41:   required from ‘auto stan::io::deserializer<T>::read_constrain_offset_multiplier(const Offset&, const Mult&, LP&, Sizes ...) [with Ret = stan::math::var_value<double>; bool Jacobian = true; Offset = double; Mult = int; LP = stan::math::var_value<double>; Sizes = {}; T = stan::math::var_value<double>]’
stanExports_negBinomial_MPI.h:1151:50:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:23:88:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:37:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   37 |       for (int i = 1; i < y1_d.size(); i++) {
      |                       ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:45:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   45 |       for (int i = 1; i < y2_d.size(); i++) {
      |                       ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_matching_dims.hpp:56:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   56 |     for (int i = 0; i < y1_d.size(); i++) {
      |                     ~~^~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:2130:35:   required from ‘boost::math::tools::promote_args_t<RT1, RT2> 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>; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86:   required from ‘boost::math::tools::promote_args_t<RT1, RT2> 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>; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24:   required from ‘boost::math::tools::promote_args_t<RT1, RT2> boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; boost::math::tools::promote_args_t<RT1, RT2> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing.hpp:13,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:13,
                 from stanExports_negBinomial_MPI.h:25,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp: In instantiation of ‘stan::plain_type_t<T> stan::model::rvalue(EigMat&&, const char*, const Idx&, const stan::model::index_multi&) [with EigMat = const Eigen::Matrix<stan::math::var_value<double>, -1, -1>&; Idx = stan::model::index_omni; stan::require_eigen_dense_dynamic_t<M>* <anonymous> = 0; stan::require_not_same_t<typename std::decay<_Tp2>::type, stan::model::index_uni>* <anonymous> = 0; stan::plain_type_t<T> = std::decay<const Eigen::Matrix<stan::math::var_value<double>, -1, -1>&>::type]’:
stanExports_negBinomial_MPI.h:400:36:   required from ‘std::vector<Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, typename stan::base_type<T6__, void>::type>::type, -1, 1> > model_negBinomial_MPI_namespace::get_reference_parameters_MPI(const int&, const int&, const std::vector<int>&, const std::vector<std::vector<int> >&, const T4__&, const T5__&, const T6__&, std::ostream*) [with T4__ = Eigen::Matrix<stan::math::var_value<double>, -1, -1>; T5__ = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T6__ = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; stan::require_all_t<stan::is_eigen_matrix_dynamic<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_col_vector<T6__>, stan::is_vt_not_complex<T6__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, typename stan::base_type<T6__, void>::type>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:1248:56:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:23:88:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:559:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  559 |   for (int j = 0; j < col_idx.ns_.size(); ++j) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:830:54:   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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1472:36:   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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1509:20:   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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:1663:93:   required from ‘boost::math::tools::promote_args_t<RT1, RT2, A> 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>; boost::math::tools::promote_args_t<RT1, RT2, A> = double]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/beta.hpp:793:16: 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
  793 |    result_type operator()()
      |                ^~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue_varmat.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing.hpp:13,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/model_header.hpp:13,
                 from stanExports_negBinomial_MPI.h:25,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp: In instantiation of ‘stan::plain_type_t<T> stan::model::rvalue(EigMat&&, const char*, const Idx&, const stan::model::index_multi&) [with EigMat = const Eigen::Matrix<double, -1, -1>&; Idx = stan::model::index_omni; stan::require_eigen_dense_dynamic_t<M>* <anonymous> = 0; stan::require_not_same_t<typename std::decay<_Tp2>::type, stan::model::index_uni>* <anonymous> = 0; stan::plain_type_t<T> = std::decay<const Eigen::Matrix<double, -1, -1>&>::type]’:
stanExports_negBinomial_MPI.h:400:36:   required from ‘std::vector<Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, typename stan::base_type<T6__, void>::type>::type, -1, 1> > model_negBinomial_MPI_namespace::get_reference_parameters_MPI(const int&, const int&, const std::vector<int>&, const std::vector<std::vector<int> >&, const T4__&, const T5__&, const T6__&, std::ostream*) [with T4__ = Eigen::Matrix<double, -1, -1>; T5__ = Eigen::Matrix<double, -1, 1>; T6__ = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; stan::require_all_t<stan::is_eigen_matrix_dynamic<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_col_vector<T6__>, stan::is_vt_not_complex<T6__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, typename stan::base_type<T6__, void>::type>::type = double; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:1248:56:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50:   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_negBinomial_MPI_namespace::model_negBinomial_MPI; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:15:87:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/model/indexing/rvalue.hpp:559:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  559 |   for (int j = 0; j < col_idx.ns_.size(); ++j) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/skew_normal_lpdf.hpp:49:16:   required from ‘stan::return_type_t<T_y0, T_param, T_t0, T_ts> stan::math::skew_normal_lpdf(const T_y&, const T_loc&, const T_scale&, const T_shape&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = stan::math::var_value<double>; T_scale = stan::math::var_value<double>; T_shape = stan::math::var_value<double>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_n, T_N, T_size1, T_size2>* <anonymous> = 0; stan::return_type_t<T_y0, T_param, T_t0, T_ts> = stan::math::var_value<double>]’
stanExports_negBinomial_MPI.h:1224:62:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:23:88:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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]
  153 |   for (size_t i = 0; i < x.size(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:69:15:   required from ‘stan::return_type_t<T, L, U> stan::math::double_exponential_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 = int; T_scale = int; 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, L, U> = stan::math::var_value<double>]’
stanExports_negBinomial_MPI.h:1230:71:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:23:88:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/skew_normal_lpdf.hpp:49:16:   required from ‘stan::return_type_t<T_y0, T_param, T_t0, T_ts> stan::math::skew_normal_lpdf(const T_y&, const T_loc&, const T_scale&, const T_shape&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = double; T_scale = double; T_shape = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_n, T_N, T_size1, T_size2>* <anonymous> = 0; stan::return_type_t<T_y0, T_param, T_t0, T_ts> = double]’
stanExports_negBinomial_MPI.h:1224:62:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50:   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_negBinomial_MPI_namespace::model_negBinomial_MPI; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:15:87:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/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<Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > > >::<lambda(double)>; T = Eigen::ArrayWrapper<Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > >; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > >]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:69:15:   required from ‘stan::return_type_t<T, L, U> stan::math::double_exponential_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, 1, -1>; T_loc = int; T_scale = int; 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, L, U> = double]’
stanExports_negBinomial_MPI.h:1230:71:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50:   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_negBinomial_MPI_namespace::model_negBinomial_MPI; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:15:87:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::ArrayWrapper<Eigen::Transpose<const Eigen::Matrix<double, 1, -1> > > >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from stanExports_negBinomial_MPI.cc:5:
stanExports_negBinomial_MPI.h: In instantiation of ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’:
stanExports_negBinomial_MPI.h:242:21:   required from ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) const [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/functor/map_rect_reduce.hpp:68:24:   required from ‘stan::math::matrix_d stan::math::internal::map_rect_reduce<F, double, stan::math::var_value<double> >::operator()(const vector_d&, const vector_d&, const std::vector<double>&, const std::vector<int>&, std::ostream*) const [with F = model_negBinomial_MPI_namespace::lp_reduce_functor__; stan::math::matrix_d = Eigen::Matrix<double, -1, -1>; stan::math::vector_d = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:32:   required from ‘Eigen::Matrix<typename stan::return_type<T_shared_param, T_job_param>::type, -1, 1> stan::math::internal::map_rect_concurrent(const T_shared_param&, const std::vector<Eigen::Matrix<T_job_param, -1, 1> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<int> >&, std::ostream*) [with int call_id = 1; F = model_negBinomial_MPI_namespace::lp_reduce_functor__; T_shared_param = const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >&; T_job_param = stan::math::var_value<double>; stan::require_eigen_col_vector_t<T_rho>* <anonymous> = 0; typename stan::return_type<T_shared_param, T_job_param>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:184:52:   required from ‘Eigen::Matrix<typename stan::return_type<T_shared_param, T_job_param>::type, -1, 1> stan::math::map_rect(const T_shared_param&, const std::vector<Eigen::Matrix<T_job_param, -1, 1> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<int> >&, std::ostream*) [with int call_id = 1; F = model_negBinomial_MPI_namespace::lp_reduce_functor__; T_shared_param = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_job_param = stan::math::var_value<double>; stan::require_eigen_col_vector_t<T_rho>* <anonymous> = 0; typename stan::return_type<T_shared_param, T_job_param>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:1246:70:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:23:88:   required from here
stanExports_negBinomial_MPI.h:438:15: warning: unused variable ‘global_parameters’ [-Wunused-variable]
  438 |   const auto& global_parameters = stan::math::to_ref(global_parameters_arg__);
      |               ^~~~~~~~~~~~~~~~~
stanExports_negBinomial_MPI.h: In instantiation of ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<double, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = double; std::ostream = std::basic_ostream<char>]’:
stanExports_negBinomial_MPI.h:242:21:   required from ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) const [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<double, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/map_rect_reduce.hpp:47:15:   required from ‘stan::math::matrix_d stan::math::internal::map_rect_reduce<F, double, double>::operator()(const vector_d&, const vector_d&, const std::vector<double>&, const std::vector<int>&, std::ostream*) const [with F = model_negBinomial_MPI_namespace::lp_reduce_functor__; stan::math::matrix_d = Eigen::Matrix<double, -1, -1>; stan::math::vector_d = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:32:   required from ‘Eigen::Matrix<typename stan::return_type<T_shared_param, T_job_param>::type, -1, 1> stan::math::internal::map_rect_concurrent(const T_shared_param&, const std::vector<Eigen::Matrix<T_job_param, -1, 1> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<int> >&, std::ostream*) [with int call_id = 1; F = model_negBinomial_MPI_namespace::lp_reduce_functor__; T_shared_param = const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >&; T_job_param = double; stan::require_eigen_col_vector_t<T_rho>* <anonymous> = 0; typename stan::return_type<T_shared_param, T_job_param>::type = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:184:52:   required from ‘Eigen::Matrix<typename stan::return_type<T_shared_param, T_job_param>::type, -1, 1> stan::math::map_rect(const T_shared_param&, const std::vector<Eigen::Matrix<T_job_param, -1, 1> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<int> >&, std::ostream*) [with int call_id = 1; F = model_negBinomial_MPI_namespace::lp_reduce_functor__; T_shared_param = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_job_param = double; stan::require_eigen_col_vector_t<T_rho>* <anonymous> = 0; typename stan::return_type<T_shared_param, T_job_param>::type = double; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:1246:70:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50:   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_negBinomial_MPI_namespace::model_negBinomial_MPI; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:15:87:   required from here
stanExports_negBinomial_MPI.h:438:15: warning: unused variable ‘global_parameters’ [-Wunused-variable]
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:12,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<stan::math::var_value<double>, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<stan::math::var_value<double>, -1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/neg_binomial_2_log_lpmf.hpp:46:15:   required from ‘stan::return_type_t<T_shared_param, T_job_param> stan::math::neg_binomial_2_log_lpmf(const T_n&, const T_log_location&, const T_precision&) [with bool propto = false; T_n = std::vector<int>; T_log_location = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_precision = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; 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_shared_param, T_job_param> = stan::math::var_value<double>]’
stanExports_negBinomial_MPI.h:571:53:   required from ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:242:21:   required from ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) const [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/functor/map_rect_reduce.hpp:68:24:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:184:52:   required from ‘Eigen::Matrix<typename stan::return_type<T_shared_param, T_job_param>::type, -1, 1> stan::math::map_rect(const T_shared_param&, const std::vector<Eigen::Matrix<T_job_param, -1, 1> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<int> >&, std::ostream*) [with int call_id = 1; F = model_negBinomial_MPI_namespace::lp_reduce_functor__; T_shared_param = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_job_param = stan::math::var_value<double>; stan::require_eigen_col_vector_t<T_rho>* <anonymous> = 0; typename stan::return_type<T_shared_param, T_job_param>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:1246:70:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:23:88:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
  153 |   for (size_t i = 0; i < x.size(); i++) {
      |                      ~~^~~~~~~~~~
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_finite<Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_positive_finite.hpp:24:20:   required from ‘void stan::math::check_positive_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/neg_binomial_2_log_lpmf.hpp:47:24:   required from ‘stan::return_type_t<T_shared_param, T_job_param> stan::math::neg_binomial_2_log_lpmf(const T_n&, const T_log_location&, const T_precision&) [with bool propto = false; T_n = std::vector<int>; T_log_location = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_precision = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; 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_shared_param, T_job_param> = stan::math::var_value<double>]’
stanExports_negBinomial_MPI.h:571:53:   required from ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:242:21:   required from ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) const [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/functor/map_rect_reduce.hpp:68:24:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:184:52:   required from ‘Eigen::Matrix<typename stan::return_type<T_shared_param, T_job_param>::type, -1, 1> stan::math::map_rect(const T_shared_param&, const std::vector<Eigen::Matrix<T_job_param, -1, 1> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<int> >&, std::ostream*) [with int call_id = 1; F = model_negBinomial_MPI_namespace::lp_reduce_functor__; T_shared_param = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_job_param = stan::math::var_value<double>; stan::require_eigen_col_vector_t<T_rho>* <anonymous> = 0; typename stan::return_type<T_shared_param, T_job_param>::type = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:1246:70:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:23:88:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<T>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/check_positive_finite.hpp:24:20:   required from ‘void stan::math::check_positive_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/prob/neg_binomial_2_log_lpmf.hpp:47:24:   required from ‘stan::return_type_t<T_shared_param, T_job_param> stan::math::neg_binomial_2_log_lpmf(const T_n&, const T_log_location&, const T_precision&) [with bool propto = false; T_n = std::vector<int>; T_log_location = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::CwiseNullaryOp<stan::model::rvalue<Eigen::Matrix<double, -1, 1>&, 0>::<lambda(auto:703&)> [with auto:703 = Eigen::Matrix<double, -1, 1>]::<lambda(Eigen::Index)>, Eigen::Matrix<double, -1, 1> >, const Eigen::Matrix<double, -1, 1> >; T_precision = Eigen::Matrix<double, -1, 1>; 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_shared_param, T_job_param> = double]’
stanExports_negBinomial_MPI.h:571:53:   required from ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<double, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = double; std::ostream = std::basic_ostream<char>]’
stanExports_negBinomial_MPI.h:242:21:   required from ‘Eigen::Matrix<typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type, -1, 1> model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()(const T0__&, const T1__&, const std::vector<T_l>&, const std::vector<int>&, std::ostream*) const [with T0__ = Eigen::Matrix<double, -1, 1>; T1__ = Eigen::Matrix<double, -1, 1>; T2__ = double; stan::require_all_t<stan::is_col_vector<T>, stan::is_vt_not_complex<T4__>, stan::is_col_vector<Col>, stan::is_vt_not_complex<T0__>, stan::is_stan_scalar<T1__> >* <anonymous> = 0; typename boost::math::tools::promote_args<typename stan::base_type<T>::type, typename stan::base_type<T0__, void>::type, T2__>::type = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/functor/map_rect_reduce.hpp:47:15:   required from ‘stan::math::matrix_d stan::math::internal::map_rect_reduce<F, double, double>::operator()(const vector_d&, const vector_d&, const std::vector<double>&, const std::vector<int>&, std::ostream*) const [with F = model_negBinomial_MPI_namespace::lp_reduce_functor__; stan::math::matrix_d = Eigen::Matrix<double, -1, -1>; stan::math::vector_d = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:32:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
stanExports_negBinomial_MPI.h:1246:70:   required from ‘stan::scalar_type_t<T2> model_negBinomial_MPI_namespace::model_negBinomial_MPI::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_negBinomial_MPI.h:1849:47:   required from ‘T_ model_negBinomial_MPI_namespace::model_negBinomial_MPI::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-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:56:50:   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_negBinomial_MPI_namespace::model_negBinomial_MPI; bool jacobian = false]’
/home/biocbuild/R/R-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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-beta-2024-04-15_r86425/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_negBinomial_MPI_namespace::model_negBinomial_MPI; 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_negBinomial_MPI.cc:15:87:   required from here
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:153:24: 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-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp: In function ‘typename boost::math::tools::promote_args<Real, typename Seq::value_type>::type boost::math::hypergeometric_pFq(const Seq&, const Seq&, const Real&, Real*, const Policy&) [with Seq = std::vector<double>; Real = 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-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:61:44: 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
   61 |          std::pair<value_type, value_type> r = boost::math::detail::hypergeometric_pFq_checked_series_impl(aj, bj, value_type(z), pol, boost::math::detail::iteration_terminator(boost::math::policies::get_max_series_iterations<forwarding_policy>()), scale);
      |                                            ^
In file included from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/gamma.hpp:18,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/stan/math/prim.hpp:14,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/stan_fit.hpp:43,
                 from /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/rstan/include/rstan/rstaninc.hpp:4,
                 from stanExports_negBinomial_MPI.h:23,
                 from stanExports_negBinomial_MPI.cc:5:
/home/biocbuild/R/R-beta-2024-04-15_r86425/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<double>; U = double]’:
/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: 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
  217 |    value_type v = g();
      |               ^
/home/biocbuild/R/R-beta-2024-04-15_r86425/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-beta-2024-04-15_r86425/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
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o ppcseq.so RcppExports.o stanExports_negBinomial_MPI.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-ppcseq/00new/ppcseq/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ppcseq)


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ppcseq)
Loading required package: rstan
Loading required package: StanHeaders

rstan version 2.32.6 (Stan version 2.32.2)

For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions,
change `threads_per_chain` option:
rstan_options(threads_per_chain = 1)

> 
> test_check("ppcseq")
No group or design set. Assuming all samples belong to one group.
executing do_inference
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000661 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.61 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1:    100       -14049.484             1.000            1.000
Chain 1:    200        -9132.662             0.769            1.000
Chain 1:    300        -7560.287             0.582            0.538
Chain 1:    400        -7474.963             0.439            0.538
Chain 1:    500        -7468.604             0.352            0.208
Chain 1:    600        -7461.625             0.293            0.208
Chain 1:    700        -7455.197             0.251            0.011
Chain 1:    800        -7455.154             0.220            0.011
Chain 1:    900        -7458.146             0.196            0.001   MEDIAN ELBO CONVERGED
Chain 1: 
Chain 1: Drawing a sample of size 1000 from the approximate posterior... 
Chain 1: COMPLETED.
executing check_if_within_posterior
executing save_generated_quantities_in_case
executing fit_to_counts_rng
executing do_inference
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000689 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.89 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1:    100       -12432.546             1.000            1.000
Chain 1:    200        -8537.182             0.728            1.000
Chain 1:    300        -7495.970             0.532            0.456
Chain 1:    400        -7445.807             0.400            0.456
Chain 1:    500        -7442.564             0.320            0.139
Chain 1:    600        -7441.820             0.267            0.139
Chain 1:    700        -7442.090             0.229            0.007
Chain 1:    800        -7448.039             0.200            0.007
Chain 1:    900        -7436.408             0.178            0.002   MEDIAN ELBO CONVERGED
Chain 1: 
Chain 1: Drawing a sample of size 1000 from the approximate posterior... 
Chain 1: COMPLETED.
executing check_if_within_posterior
executing save_generated_quantities_in_case
executing fit_to_counts_rng_approximated
No group or design set. Assuming all samples belong to one group.
executing do_inference
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000629 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.29 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Iteration: 250 / 250 [100%]  (Adaptation)
Chain 1: Success! Found best value [eta = 0.1].
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1:    100      -233511.069             1.000            1.000
Chain 1:    200       -80610.963             1.448            1.897
Chain 1:    300       -39162.001             1.318            1.058
Chain 1:    400       -23324.214             1.159            1.058
Chain 1:    500       -16690.430             1.006            1.000
Chain 1:    600       -13889.910             0.872            1.000
Chain 1:    700       -12694.152             0.761            0.679
Chain 1:    800       -11956.912             0.674            0.679
Chain 1:    900       -11526.925             0.603            0.397
Chain 1:   1000       -11213.533             0.545            0.397
Chain 1:   1100       -10955.443             0.498            0.202
Chain 1:   1200       -10733.197             0.458            0.202
Chain 1:   1300       -10533.866             0.424            0.094
Chain 1:   1400       -10333.905             0.395            0.094
Chain 1:   1500       -10143.803             0.370            0.062
Chain 1:   1600        -9965.686             0.348            0.062
Chain 1:   1700        -9803.621             0.329            0.037
Chain 1:   1800        -9649.838             0.311            0.037
Chain 1:   1900        -9501.285             0.296            0.028
Chain 1:   2000        -9367.818             0.282            0.028
Chain 1:   2100        -9243.003             0.269            0.024
Chain 1:   2200        -9128.132             0.257            0.024
Chain 1:   2300        -9015.800             0.247            0.021
Chain 1:   2400        -8907.463             0.237            0.021
Chain 1:   2500        -8809.591             0.228            0.019
Chain 1:   2600        -8715.650             0.220            0.019
Chain 1:   2700        -8618.326             0.212            0.019
Chain 1:   2800        -8544.820             0.205            0.019
Chain 1:   2900        -8460.305             0.198            0.019
Chain 1:   3000        -8391.394             0.192            0.019
Chain 1:   3100        -8317.178             0.186            0.018
Chain 1:   3200        -8260.977             0.180            0.018
Chain 1:   3300        -8197.455             0.175            0.017
Chain 1:   3400        -8139.590             0.170            0.017
Chain 1:   3500        -8088.434             0.165            0.016
Chain 1:   3600        -8038.015             0.161            0.016
Chain 1:   3700        -7990.096             0.157            0.016
Chain 1:   3800        -7949.841             0.153            0.016
Chain 1:   3900        -7912.003             0.149            0.014
Chain 1:   4000        -7871.242             0.145            0.014
Chain 1:   4100        -7837.458             0.142            0.014
Chain 1:   4200        -7803.903             0.139            0.014
Chain 1:   4300        -7774.146             0.135            0.013
Chain 1:   4400        -7746.905             0.132            0.013
Chain 1:   4500        -7721.746             0.130            0.012
Chain 1:   4600        -7697.564             0.127            0.012
Chain 1:   4700        -7673.688             0.124            0.012
Chain 1:   4800        -7652.251             0.122            0.012
Chain 1:   4900        -7631.401             0.119            0.011
Chain 1:   5000        -7616.304             0.117            0.011
Chain 1:   5100        -7603.106             0.097            0.011
Chain 1:   5200        -7584.836             0.059            0.011
Chain 1:   5300        -7576.728             0.038            0.010
Chain 1:   5400        -7557.379             0.024            0.009
Chain 1:   5500        -7546.554             0.016            0.009
Chain 1:   5600        -7535.271             0.012            0.008
Chain 1:   5700        -7527.545             0.011            0.008
Chain 1:   5800        -7517.838             0.009            0.007
Chain 1:   5900        -7510.478             0.009            0.007
Chain 1:   6000        -7503.408             0.008            0.006
Chain 1:   6100        -7498.016             0.008            0.006
Chain 1:   6200        -7494.069             0.007            0.006
Chain 1:   6300        -7489.474             0.007            0.005
Chain 1:   6400        -7482.040             0.006            0.005
Chain 1:   6500        -7477.808             0.006            0.005   MEDIAN ELBO CONVERGED
Chain 1: 
Chain 1: Drawing a sample of size 1000 from the approximate posterior... 
Chain 1: COMPLETED.
executing check_if_within_posterior
executing save_generated_quantities_in_case
executing fit_to_counts_rng
executing do_inference
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: Rejecting initial value:
Chain 1:   Log probability evaluates to log(0), i.e. negative infinity.
Chain 1:   Stan can't start sampling from this initial value.
Chain 1: Rejecting initial value:
Chain 1:   Log probability evaluates to log(0), i.e. negative infinity.
Chain 1:   Stan can't start sampling from this initial value.
Chain 1: 
Chain 1: Gradient evaluation took 0.000648 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 6.48 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1:    100       -12390.732             1.000            1.000
Chain 1:    200        -8559.362             0.724            1.000
Chain 1:    300        -7519.501             0.529            0.448
Chain 1:    400        -7463.799             0.398            0.448
Chain 1:    500        -7443.486             0.319            0.138
Chain 1:    600        -7443.838             0.266            0.138
Chain 1:    700        -7446.515             0.228            0.007
Chain 1:    800        -7442.419             0.200            0.007
Chain 1:    900        -7436.570             0.178            0.003   MEDIAN ELBO CONVERGED
Chain 1: 
Chain 1: Drawing a sample of size 10500 from the approximate posterior... 
Chain 1: COMPLETED.
executing check_if_within_posterior
executing save_generated_quantities_in_case
executing fit_to_counts_rng
[ FAIL 0 | WARN 91 | SKIP 0 | PASS 2 ]

[ FAIL 0 | WARN 91 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
 99.198   1.376 100.750

name	user	system	elapsed
identify_outliers	25.602	0.395	26.057
plot_credible_intervals	24.480	0.207	24.738

CHECK results for ppcseq on kunpeng2

Summary

Command output

Installation output

Tests output

Example timings