Alan O'Callaghan
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/BASiCStan |
| git_branch: devel |
| git_last_commit: 118c13a |
| git_last_commit_date: 2024-02-14 09:35:46 -0400 (Wed, 14 Feb 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:20 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 132/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BASiCStan 1.5.1 (landing page) Alan O'Callaghan
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the BASiCStan package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCStan.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: BASiCStan |
| Version: 1.5.1 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:BASiCStan.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings BASiCStan_1.5.1.tar.gz |
| StartedAt: 2024-03-28 02:59:25 -0000 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:06:16 -0000 (Thu, 28 Mar 2024) |
| EllapsedTime: 410.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCStan.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:BASiCStan.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings BASiCStan_1.5.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BASiCStan.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* 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 ‘BASiCStan/DESCRIPTION’ ... OK
* this is package ‘BASiCStan’ version ‘1.5.1’
* 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 ‘BASiCStan’ 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 123.2Mb
sub-directories of 1Mb or more:
libs 123.0Mb
* 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 ... NOTE
Unexported objects imported by ':::' calls:
‘BASiCS:::.BASiCS_MCMC_Start’ ‘BASiCS:::.EmpiricalBayesMu’
‘BASiCS:::.estimateRBFLocations’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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
* 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/BASiCStan.Rcheck/00check.log’
for details.
BASiCStan.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL BASiCStan
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘BASiCStan’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_basics_regression.cc -o stanExports_basics_regression.o
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/apply.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/serialization/array_optimization.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/serialization/array_wrapper.hpp:21,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/serialization/array.hpp:26,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/ublas/storage.hpp:22,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/ublas/vector.hpp:21,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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 stanExports_basics_regression.cc:5:
stanExports_basics_regression.h: In instantiation of ‘void model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1439:36: required from here
stanExports_basics_regression.h:954:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
954 | int pos__ = std::numeric_limits<int>::min();
| ^~~~~
stanExports_basics_regression.h: In instantiation of ‘void model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1449:36: required from here
stanExports_basics_regression.h:954:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:30:89: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
1252 | int ret = stan::services::error_codes::CONFIG;
| ^~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, -1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/core.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:30:89: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun.hpp:163,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/simplex_constrain.hpp: In instantiation of ‘auto stan::math::simplex_constrain(const T&, stan::scalar_type_t<T>&) [with T = Eigen::Map<const Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> >; stan::require_rev_col_vector_t<T>* <anonymous> = 0; stan::scalar_type_t<T> = stan::math::var_value<double>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:569:31: required from ‘auto stan::io::deserializer<T>::read_constrain_simplex(LP&, size_t) [with Ret = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; bool Jacobian = true; LP = stan::math::var_value<double>; stan::require_not_std_vector_t<Ret>* <anonymous> = 0; T = stan::math::var_value<double>; size_t = long unsigned int]’
stanExports_basics_regression.h:666:65: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/simplex_constrain.hpp:94:30: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
94 | for (Eigen::Index k = 0; k < N; ++k) {
| ~~^~~
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/simplex_constrain.hpp: In instantiation of ‘auto stan::math::simplex_constrain(const T&) [with T = Eigen::Map<const Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> >; stan::require_rev_col_vector_t<T>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/deserializer.hpp:571:31: required from ‘auto stan::io::deserializer<T>::read_constrain_simplex(LP&, size_t) [with Ret = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; bool Jacobian = true; LP = stan::math::var_value<double>; stan::require_not_std_vector_t<Ret>* <anonymous> = 0; T = stan::math::var_value<double>; size_t = long unsigned int]’
stanExports_basics_regression.h:666:65: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/simplex_constrain.hpp:40:30: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
40 | for (Eigen::Index k = 0; k < N; ++k) {
| ~~^~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/beta.hpp:1721,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
299 | result_type operator()()
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
543 | std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol)
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/gamma_lpdf.hpp:71:24: required from ‘stan::return_type_t<T, L, U> stan::math::gamma_lpdf(const T_y&, const T_shape&, const T_inv_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_shape = double; T_inv_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression.h:734:56: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::<lambda(double)>; T = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:77:19: required from ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpdf(const T_prob&, const T_prior_size&) [with bool propto = true; T_prob = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_prior_size = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_n, T_prob>* <anonymous> = 0; stan::return_type_t<T1, T2> = stan::math::var_value<double>]’
stanExports_basics_regression.h:736:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::<lambda(double)>; T = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/multi_normal_lpdf.hpp:71:17: required from ‘stan::return_type_t<T, L, U> stan::math::multi_normal_lpdf(const T_y&, const T_loc&, const T_covar&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_covar = Eigen::Matrix<stan::math::var_value<double>, -1, -1>; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression.h:741:63: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-4.4-devel-2024.03.20/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<stan::math::var_value<double>, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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<stan::math::var_value<double>, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/multi_normal_lpdf.hpp:72:18: required from ‘stan::return_type_t<T, L, U> stan::math::multi_normal_lpdf(const T_y&, const T_loc&, const T_covar&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_covar = Eigen::Matrix<stan::math::var_value<double>, -1, -1>; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression.h:741:63: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t<T, L, U> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression.h:744:57: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::ArrayWrapper<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:63:15: required from ‘stan::return_type_t<T, L, U> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression.h:744:57: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > > >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_nonnegative<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_nonnegative.hpp:26:20: required from ‘void stan::math::check_nonnegative(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/lognormal_lpdf.hpp:46:20: required from ‘stan::return_type_t<T, L, U> stan::math::lognormal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<stan::math::var_value<double>, stan::math::var_value<double> >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<stan::math::var_value<double> >, const Eigen::Array<stan::math::var_value<double>, -1, 1, 0, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::CwiseUnaryOp<stan::math::apply_scalar_unary<F, T, typename std::enable_if<stan::is_eigen<typename std::decay<_Tp2>::type>::value, void>::type>::apply<stan::math::sqrt_fun, Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::<lambda(auto:3&&)>, const 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, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression.h:749:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/lognormal_lpdf.hpp:47:15: required from ‘stan::return_type_t<T, L, U> stan::math::lognormal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<stan::math::var_value<double>, stan::math::var_value<double> >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<stan::math::var_value<double> >, const Eigen::Array<stan::math::var_value<double>, -1, 1, 0, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::CwiseUnaryOp<stan::math::apply_scalar_unary<F, T, typename std::enable_if<stan::is_eigen<typename std::decay<_Tp2>::type>::value, void>::type>::apply<stan::math::sqrt_fun, Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::<lambda(auto:3&&)>, const 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, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression.h:749:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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 = true; T_n = std::vector<int>; T_log_location = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_precision = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<int, stan::math::var_value<double> >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<int>, const Eigen::Array<int, -1, 1> >, const Eigen::ArrayWrapper<const 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_basics_regression.h:762:71: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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 = true; T_n = std::vector<int>; T_log_location = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_precision = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<int, stan::math::var_value<double> >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<int>, const Eigen::Array<int, -1, 1> >, const Eigen::ArrayWrapper<const 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_basics_regression.h:762:71: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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_nonnegative<Eigen::ArrayWrapper<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > > >::<lambda(double)>; T = Eigen::ArrayWrapper<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_nonnegative.hpp:26:20: required from ‘void stan::math::check_nonnegative(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<Eigen::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/poisson_lpmf.hpp:45:20: required from ‘stan::return_type_t<T_prob> stan::math::poisson_lpmf(const T_n&, const T_rate&) [with bool propto = true; T_n = std::vector<int>; T_rate = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_n, T_prob>* <anonymous> = 0; stan::return_type_t<T_prob> = stan::math::var_value<double>]’
stanExports_basics_regression.h:775:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<const Eigen::Matrix<int, -1, 1>, 0, Eigen::Stride<0, 0> > > >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/gamma_lpdf.hpp:71:24: required from ‘stan::return_type_t<T, L, U> stan::math::gamma_lpdf(const T_y&, const T_shape&, const T_inv_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_shape = double; T_inv_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = double]’
stanExports_basics_regression.h:734:56: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t<T, L, U> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = double]’
stanExports_basics_regression.h:744:57: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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_nonnegative<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_nonnegative.hpp:26:20: required from ‘void stan::math::check_nonnegative(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/lognormal_lpdf.hpp:46:20: required from ‘stan::return_type_t<T, L, U> stan::math::lognormal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = Eigen::Matrix<double, -1, 1>; T_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::MatrixWrapper<const Eigen::CwiseUnaryOp<Eigen::internal::scalar_sqrt_op<double>, const Eigen::ArrayWrapper<const 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, L, U> = double]’
stanExports_basics_regression.h:749:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/lognormal_lpdf.hpp:47:15: required from ‘stan::return_type_t<T, L, U> stan::math::lognormal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = Eigen::Matrix<double, -1, 1>; T_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::MatrixWrapper<const Eigen::CwiseUnaryOp<Eigen::internal::scalar_sqrt_op<double>, const Eigen::ArrayWrapper<const 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, L, U> = double]’
stanExports_basics_regression.h:749:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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::ArrayWrapper<Eigen::Map<const Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > > >::<lambda(double)>; T = Eigen::ArrayWrapper<Eigen::Map<const Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::ArrayWrapper<Eigen::Map<const Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/gamma_lpdf.hpp:71:24: required from ‘stan::return_type_t<T, L, U> stan::math::gamma_lpdf(const T_y&, const T_shape&, const T_inv_scale&) [with bool propto = false; T_y = std::vector<double>; T_shape = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<int>, const Eigen::Array<int, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > > >; T_inv_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<int>, const Eigen::Array<int, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const 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, L, U> = double]’
stanExports_basics_regression.h:755:56: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<const Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > > >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > > >; T_precision = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<int>, const Eigen::Array<int, -1, 1> >, const Eigen::ArrayWrapper<const 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_basics_regression.h:762:71: required from ‘stan::scalar_type_t<T2> model_basics_regression_namespace::model_basics_regression::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_basics_regression.h:1412:47: required from ‘T_ model_basics_regression_namespace::model_basics_regression::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_namespace::model_basics_regression; 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_basics_regression.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:23,
from stanExports_basics_regression.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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 -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include' -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_basics_regression_nospikes.cc -o stanExports_basics_regression_nospikes.o
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/apply.hpp:24,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/serialization/array_optimization.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/serialization/array_wrapper.hpp:21,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/serialization/array.hpp:26,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/ublas/storage.hpp:22,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/ublas/vector.hpp:21,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:23,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/cov_exp_quad.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun.hpp:41,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/gp_exp_quad_cov.hpp: In lambda function:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/util/initialize.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:75: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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 stanExports_basics_regression_nospikes.cc:5:
stanExports_basics_regression_nospikes.h: In instantiation of ‘void model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:1025:36: required from here
stanExports_basics_regression_nospikes.h:695:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
695 | int pos__ = std::numeric_limits<int>::min();
| ^~~~~
stanExports_basics_regression_nospikes.h: In instantiation of ‘void model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:1035:36: required from here
stanExports_basics_regression_nospikes.h:695:11: warning: variable ‘pos__’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:30:89: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
1252 | int ret = stan::services::error_codes::CONFIG;
| ^~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, -1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/meta.hpp:70,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/invalid_argument.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/core/init_threadpool_tbb.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/core.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:10,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:75: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:30:89: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/hypergeometric_pFq.hpp:11,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/rev/fun/inv_inc_beta.hpp:77:76: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_inc_beta.hpp:37:46: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/beta.hpp:1721,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:60: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
299 | result_type operator()()
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:260,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
543 | std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol)
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:46,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:29:56: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::<lambda(double)>; T = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/multi_normal_lpdf.hpp:71:17: required from ‘stan::return_type_t<T, L, U> stan::math::multi_normal_lpdf(const T_y&, const T_loc&, const T_covar&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_covar = Eigen::Matrix<stan::math::var_value<double>, -1, -1>; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression_nospikes.h:548:63: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare]
153 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-4.4-devel-2024.03.20/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<stan::math::var_value<double>, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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<stan::math::var_value<double>, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/multi_normal_lpdf.hpp:72:18: required from ‘stan::return_type_t<T, L, U> stan::math::multi_normal_lpdf(const T_y&, const T_loc&, const T_covar&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_covar = Eigen::Matrix<stan::math::var_value<double>, -1, -1>; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression_nospikes.h:548:63: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t<T, L, U> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression_nospikes.h:551:57: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::ArrayWrapper<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:63:15: required from ‘stan::return_type_t<T, L, U> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression_nospikes.h:551:57: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > > >::Index’ {aka ‘long int’} [-Wsign-compare]
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/gamma_lpdf.hpp:71:24: required from ‘stan::return_type_t<T, L, U> stan::math::gamma_lpdf(const T_y&, const T_shape&, const T_inv_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_shape = double; T_inv_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression_nospikes.h:553:56: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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_nonnegative<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_nonnegative.hpp:26:20: required from ‘void stan::math::check_nonnegative(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/lognormal_lpdf.hpp:46:20: required from ‘stan::return_type_t<T, L, U> stan::math::lognormal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<stan::math::var_value<double>, stan::math::var_value<double> >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<stan::math::var_value<double> >, const Eigen::Array<stan::math::var_value<double>, -1, 1, 0, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::CwiseUnaryOp<stan::math::apply_scalar_unary<F, T, typename std::enable_if<stan::is_eigen<typename std::decay<_Tp2>::type>::value, void>::type>::apply<stan::math::sqrt_fun, Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::<lambda(auto:3&&)>, const 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, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression_nospikes.h:556:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/lognormal_lpdf.hpp:47:15: required from ‘stan::return_type_t<T, L, U> stan::math::lognormal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<stan::math::var_value<double>, stan::math::var_value<double> >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<stan::math::var_value<double> >, const Eigen::Array<stan::math::var_value<double>, -1, 1, 0, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::CwiseUnaryOp<stan::math::apply_scalar_unary<F, T, typename std::enable_if<stan::is_eigen<typename std::decay<_Tp2>::type>::value, void>::type>::apply<stan::math::sqrt_fun, Eigen::Matrix<stan::math::var_value<double>, -1, 1> >::<lambda(auto:3&&)>, const 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, L, U> = stan::math::var_value<double>]’
stanExports_basics_regression_nospikes.h:556:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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 = true; T_n = std::vector<int>; T_log_location = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_precision = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<int, stan::math::var_value<double> >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<int>, const Eigen::Array<int, -1, 1> >, const Eigen::ArrayWrapper<const 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_basics_regression_nospikes.h:562:71: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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 = true; T_n = std::vector<int>; T_log_location = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_precision = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<int, stan::math::var_value<double> >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<int>, const Eigen::Array<int, -1, 1> >, const Eigen::ArrayWrapper<const 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_basics_regression_nospikes.h:562:71: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T_ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:23:88: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:62:16: required from ‘stan::return_type_t<T, L, U> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = double]’
stanExports_basics_regression_nospikes.h:551:57: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/gamma_lpdf.hpp:71:24: required from ‘stan::return_type_t<T, L, U> stan::math::gamma_lpdf(const T_y&, const T_shape&, const T_inv_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_shape = double; T_inv_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T, L, U> = double]’
stanExports_basics_regression_nospikes.h:553:56: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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_nonnegative<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_nonnegative.hpp:26:20: required from ‘void stan::math::check_nonnegative(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/lognormal_lpdf.hpp:46:20: required from ‘stan::return_type_t<T, L, U> stan::math::lognormal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = Eigen::Matrix<double, -1, 1>; T_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::MatrixWrapper<const Eigen::CwiseUnaryOp<Eigen::internal::scalar_sqrt_op<double>, const Eigen::ArrayWrapper<const 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, L, U> = double]’
stanExports_basics_regression_nospikes.h:556:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/prob/lognormal_lpdf.hpp:47:15: required from ‘stan::return_type_t<T, L, U> stan::math::lognormal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = Eigen::Matrix<double, -1, 1>; T_scale = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::MatrixWrapper<const Eigen::CwiseUnaryOp<Eigen::internal::scalar_sqrt_op<double>, const Eigen::ArrayWrapper<const 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, L, U> = double]’
stanExports_basics_regression_nospikes.h:556:60: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > > >; T_precision = Eigen::MatrixWrapper<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<int, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<int>, const Eigen::Array<int, -1, 1> >, const Eigen::ArrayWrapper<const 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_basics_regression_nospikes.h:562:71: required from ‘stan::scalar_type_t<T2> model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::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_basics_regression_nospikes.h:998:47: required from ‘T_ model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T_ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; bool jacobian = false]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.4-devel-2024.03.20/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_basics_regression_nospikes_namespace::model_basics_regression_nospikes; 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_basics_regression_nospikes.cc:15:87: required from here
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_pFq.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/hypergeometric_2F1.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/grad_2F1.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:129,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim/fun.hpp:31,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/StanHeaders/include/src/stan/io/dump.hpp:7,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:23,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’:
/home/biocbuild/R/R-4.4-devel-2024.03.20/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-4.4-devel-2024.03.20/lib -L/usr/local/lib -o BASiCStan.so RcppExports.o stanExports_basics_regression.o stanExports_basics_regression_nospikes.o -L/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/R/R-4.4-devel-2024.03.20/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/00LOCK-BASiCStan/00new/BASiCStan/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BASiCStan)
BASiCStan.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
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
'citation()' on how to cite R or R packages in publications.
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(BASiCStan)
Loading required package: BASiCS
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
Bioconductor, please visit:
https://github.com/catavallejos/BASiCS/wiki.
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("BASiCStan")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
>
> proc.time()
user system elapsed
86.950 2.378 89.506
BASiCStan.Rcheck/BASiCStan-Ex.timings
| name | user | system | elapsed | |
| BASiCStan | 3.839 | 0.172 | 4.026 | |
| Stan2BASiCS | 2.416 | 0.055 | 2.477 | |