Yuan Yin
| Snapshot Date: 2023-10-24 14:05:06 -0400 (Tue, 24 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/decontX |
| git_branch: RELEASE_3_18 |
| git_last_commit: 980f09b |
| git_last_commit_date: 2023-10-24 11:52:30 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-10-25 11:41:22 -0400 (Wed, 25 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4727 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4465 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4476 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 516/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decontX 1.0.0 (landing page) Yuan Yin
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the decontX package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decontX.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: decontX |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:decontX.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings decontX_1.0.0.tar.gz |
| StartedAt: 2023-10-25 09:38:12 -0000 (Wed, 25 Oct 2023) |
| EndedAt: 2023-10-25 09:57:19 -0000 (Wed, 25 Oct 2023) |
| EllapsedTime: 1146.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: decontX.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:decontX.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings decontX_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/decontX.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘decontX/DESCRIPTION’ ... OK
* this is package ‘decontX’ version ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decontX’ can be installed ... OK
* used C compiler: ‘gcc (GCC) 10.3.1’
* 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 53.6Mb
sub-directories of 1Mb or more:
libs 53.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
decontPro 16.226 0.208 16.484
decontX 14.388 0.203 14.652
plotDecontXMarkerPercentage 13.032 0.048 13.103
plotDecontXContamination 12.440 0.056 12.519
plotDecontXMarkerExpression 12.284 0.120 12.428
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘decontPro.Rmd’ using ‘UTF-8’... OK
‘decontX.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/decontX.Rcheck/00check.log’
for details.
decontX.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL decontX
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘decontX’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
using C++ compiler: ‘g++ (GCC) 10.3.1’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c DecontX.cpp -o DecontX.o
DecontX.cpp: In function ‘Eigen::SparseMatrix<double, 0, int> calculateNativeMatrix(const Eigen::MappedSparseMatrix<double>&, const NumericVector&, const NumericMatrix&, const NumericMatrix&, const IntegerVector&, const double&)’:
DecontX.cpp:321:10: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
321 | double x;
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c matrixNorm.cpp -o matrixNorm.o
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -fPIC -g -O2 -Wall -c matrixSums.c -o matrixSums.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c matrixSumsSparse.cpp -o matrixSumsSparse.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -I'/home/biocbuild/R/R-4.3.1/site-library/rstan/include' -I'/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_shrinkage.cc -o stanExports_shrinkage.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
361 | explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_shrinkage.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_shrinkage.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_shrinkage.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_shrinkage.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_shrinkage.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_shrinkage.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_shrinkage.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/callbacks/writer.hpp:4,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/filtered_values.hpp:4,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:23,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:110,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp: In function ‘Eigen::Matrix<typename stan::value_type<T>::type, EigMat::ColsAtCompileTime, EigMat::RowsAtCompileTime> stan::math::generalized_inverse(const EigMat&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/generalized_inverse.hpp:34:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs]
34 | using value_t = value_type_t<EigMat>;
| ^~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:319,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp: In function ‘std::vector<T> stan::math::tail(const std::vector<T>&, size_t)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/tail.hpp:46:9: warning: typedef ‘using idx_t = stan::math::index_type_t<std::vector<T> >’ locally defined but not used [-Wunused-local-typedefs]
46 | using idx_t = index_type_t<std::vector<T>>;
| ^~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/ode_rk45.hpp:9,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor/integrate_ode_rk45.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/functor.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
from /usr/include/c++/10.3.1/locale:43,
from /usr/include/c++/10.3.1/iomanip:43,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/R/R-4.3.1/site-library/Rcpp/include/Rcpp.h:27,
from stanExports_shrinkage.cc:3:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_log.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::bernoulli_logit_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/bernoulli_logit_glm_lpmf.hpp:59:9: warning: typedef ‘using T_y_val = std::conditional_t<stan::is_vector<T2>::value, Eigen::Matrix<typename stan::partials_return_type<T_y>::type, -1, 1>, typename stan::partials_return_type<T_y>::type>’ locally defined but not used [-Wunused-local-typedefs]
59 | using T_y_val =
| ^~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_log.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:31,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_lpdf(const T_y&, const T_scale_succ&, const T_scale_fail&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_lpdf.hpp:50:9: warning: typedef ‘using T_partials_matrix = class Eigen::Matrix<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
50 | using T_partials_matrix = Eigen::Matrix<T_partials_return, Eigen::Dynamic, 1>;
| ^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_log.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:37,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::beta_proportion_lpdf(const T_y&, const T_loc&, const T_prec&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/beta_proportion_lpdf.hpp:55:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
55 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_log.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:63,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::cauchy_lpdf(const T_y&, const T_loc&, const T_scale&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/cauchy_lpdf.hpp:45:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
45 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_log.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:74,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpdf(const T_prob&, const T_prior_size&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/dirichlet_lpdf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_n, T_prob>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
60 | using T_partials_vec = typename Eigen::Matrix<T_partials_return, -1, 1>;
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_log.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:91,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::double_exponential_lpdf(const T_y&, const T_loc&, const T_scale&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/double_exponential_lpdf.hpp:44:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
44 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:111,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp: In function ‘stan::return_type_t<T_x, T_sigma, T_l> stan::math::frechet_cdf(const T_y&, const T_shape&, const T_scale&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/frechet_cdf.hpp:30:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_y, T_scale_succ, T_scale_fail>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
30 | using T_partials_array = Eigen::Array<T_partials_return, Eigen::Dynamic, 1>;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_log.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:245,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp: In function ‘stan::return_type_t<T_shared_param, T_job_param> stan::math::ordered_logistic_lpmf(const T_y&, const T_loc&, const T_cut&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/ordered_logistic_lpmf.hpp:76:9: warning: typedef ‘using T_partials_array = class Eigen::Array<typename stan::partials_return_type<T_loc, T_cut>::type, -1, 1>’ locally defined but not used [-Wunused-local-typedefs]
76 | using T_partials_array = Eigen::Array<T_partials_return, -1, 1>;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_log.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob.hpp:277,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp: In function ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::poisson_log_glm_lpmf(const T_y&, const T_x&, const T_alpha&, const T_beta&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/poisson_log_glm_lpmf.hpp:62:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T_prob>::value, Eigen::Array<typename stan::partials_return_type<T_cut>::type, -1, 1>, typename stan::partials_return_type<T_cut>::type>’ locally defined but not used [-Wunused-local-typedefs]
62 | using T_alpha_val = typename std::conditional_t<
| ^~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:32,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp: In lambda function:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_decompose.hpp:83:11: warning: typedef ‘using Block_ = class Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>’ locally defined but not used [-Wunused-local-typedefs]
83 | using Block_ = Eigen::Block<Eigen::MatrixXd>;
| ^~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:34,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp: In function ‘stan::math::var_value<Eigen::Matrix<double, -1, -1> > stan::math::cholesky_factor_constrain(const T&, int, int)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/cholesky_factor_constrain.hpp:32:9: warning: typedef ‘using T_scalar = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs]
32 | using T_scalar = value_type_t<T>;
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:71,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp: In function ‘auto stan::math::generalized_inverse(const VarMat&)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/generalized_inverse.hpp:64:9: warning: typedef ‘using value_t = stan::value_type_t<T>’ locally defined but not used [-Wunused-local-typedefs]
64 | using value_t = value_type_t<VarMat>;
| ^~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing.hpp:8,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:15,
from stanExports_shrinkage.h:25,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp: In function ‘void stan::model::assign(Mat1&&, const stan::model::cons_index_list<stan::model::index_multi, stan::model::cons_index_list<stan::model::index_multi, stan::model::nil_index_list> >&, const Mat2&, const char*, int)’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/indexing/lvalue_varmat.hpp:349:9: warning: typedef ‘using pair_type = struct std::pair<int, std::vector<int, stan::math::arena_allocator<int> > >’ locally defined but not used [-Wunused-local-typedefs]
349 | using pair_type = std::pair<int, arena_vec>;
| ^~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:96:75: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
73 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp: In instantiation of ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:73:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_shrinkage_namespace::model_shrinkage; 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_shrinkage.cc:30:89: required from here
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
1252 | int ret = stan::services::error_codes::CONFIG;
| ^~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:47:58: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
158 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Matrix<double, -1, -1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, -1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<(((!(Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit)) && (! T::IsVectorAtCompileTime)) && (!(Eigen::internal::traits<_Rhs>::Flags & Eigen::RowMajorBit)))>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/variational/families/normal_fullrank.hpp:74:66: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:222:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
222 | for (size_t i = 0; i < x.rows(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:223:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
223 | for (size_t j = 0; j < x.cols(); j++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_finite<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_finite.hpp:29:20: required from ‘void stan::math::check_finite(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:21:70: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
158 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_positive<Eigen::Matrix<double, -1, 1> >::<lambda(double)>; T = Eigen::Matrix<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_positive.hpp:29:20: required from ‘void stan::math::check_positive(const char*, const char*, const T_y&) [with T_y = Eigen::Matrix<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/util/validate_diag_inv_metric.hpp:22:74: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Matrix<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:68,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_shrinkage_namespace::model_shrinkage; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1253:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_shrinkage_namespace::model_shrinkage; 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_shrinkage.cc:30:89: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:89:22: warning: comparison of integer expressions of different signedness: ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
89 | if (p_names.size() != draws.cols()) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:107:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
107 | for (size_t i = 0; i < draws.rows(); ++i) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_cholesky_factor.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp: In instantiation of ‘static void stan::math::internal::less_or_equal<T_y, T_high, is_vec>::check(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int; bool is_vec = false]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:74:74: required from ‘void stan::math::check_less_or_equal(const char*, const char*, const T_y&, const T_high&) [with T_y = long unsigned int; T_high = long int]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:78:36: required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/array_var_context.hpp:117:75: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_less_or_equal.hpp:23:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘std::decay_t<long int>’ {aka ‘long int’} [-Wsign-compare]
23 | if (!(y <= high_vec[n])) {
| ~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun.hpp:144,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:8,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:49,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/simplex_constrain.hpp: In instantiation of ‘auto stan::math::simplex_constrain(const T&) [with T = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; stan::require_rev_col_vector_t<T>* <anonymous> = 0]’:
stanExports_shrinkage.h:382:42: required from ‘stan::scalar_type_t<T2> model_shrinkage_namespace::model_shrinkage::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_shrinkage.h:1106:49: required from ‘T__ model_shrinkage_namespace::model_shrinkage::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_shrinkage_namespace::model_shrinkage; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_shrinkage_namespace::model_shrinkage; 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_shrinkage.cc:23:88: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/rev/fun/simplex_constrain.hpp:42:30: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
42 | for (Eigen::Index k = 0; k < N; ++k) {
| ~~^~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/model_header.hpp:8,
from stanExports_shrinkage.h:25,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp: In instantiation of ‘T stan::io::reader<T>::scalar() [with T = double]’:
stanExports_shrinkage.h:662:26: required from ‘void model_shrinkage_namespace::model_shrinkage::write_array_impl(RNG&, VecR&, VecI&, VecVar&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; VecR = std::vector<double>; VecI = std::vector<int>; VecVar = std::vector<double>; stan::require_vector_like_vt<std::is_floating_point, VecR>* <anonymous> = 0; stan::require_vector_like_vt<std::is_integral, VecI>* <anonymous> = 0; stan::require_std_vector_vt<std::is_floating_point, VecVar>* <anonymous> = 0; std::ostream = std::basic_ostream<char>]’
stanExports_shrinkage.h:1094:23: required from ‘void model_shrinkage_namespace::model_shrinkage::write_array(RNG&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with RNG = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1105:23: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::constrain_pars(SEXP) [with Model = model_shrinkage_namespace::model_shrinkage; 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_shrinkage.cc:26:89: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp:139:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Map<const Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare]
139 | if (pos_ >= data_r_.size()) {
| ~~~~~^~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp: In instantiation of ‘T stan::io::reader<T>::scalar() [with T = stan::math::var_value<double>]’:
stanExports_shrinkage.h:491:26: required from ‘stan::scalar_type_t<T2> model_shrinkage_namespace::model_shrinkage::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_shrinkage.h:1106:49: required from ‘T__ model_shrinkage_namespace::model_shrinkage::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_shrinkage_namespace::model_shrinkage; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_shrinkage_namespace::model_shrinkage; 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_shrinkage.cc:23:88: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/reader.hpp:139:14: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Map<const Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 0, Eigen::Stride<0, 0> > >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:2128:35: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/gamma_p.hpp:76:55: required from here
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
299 | result_type operator()()
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:240,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp: In instantiation of ‘std::pair<_FIter, _FIter> boost::math::detail::owens_t_T1_accelerated(T, T, const Policy&) [with T = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:874:46: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&, const std::integral_constant<int, 65>&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:979:36: required from ‘RealType boost::math::detail::owens_t_dispatch(RealType, RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1000:38: required from ‘RealType boost::math::detail::owens_t(RealType, RealType, const Policy&) [with RealType = long double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1072:86: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2, const Policy&) [with T1 = double; T2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:1078:24: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::owens_t(T1, T2) [with T1 = double; T2 = double; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/owens_t.hpp:58:77: required from here
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/owens_t.hpp:543:26: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
543 | std::pair<T, T> owens_t_T1_accelerated(T h, T a, const Policy& pol)
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/binomial.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t<T>::result_type boost::math::detail::ibeta_fraction2_t<T>::operator()() [with T = double; boost::math::detail::ibeta_fraction2_t<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:729:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1367:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1404:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:1543:93: required from ‘typename boost::math::tools::promote_args<RT1, RT2, A>::type boost::math::ibeta(RT1, RT2, RT3, const Policy&) [with RT1 = double; RT2 = double; RT3 = double; Policy = boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2, A>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/inc_beta.hpp:28:56: required from here
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/beta.hpp:692:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
692 | result_type operator()()
| ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_2F1_converges.hpp:5,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err.hpp:4,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:12,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::Array<double, -1, 1> >::<lambda(double)>; T = Eigen::Array<double, -1, 1>; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::Array<double, -1, 1>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:69:16: required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = true; T_y = Eigen::Matrix<stan::math::var_value<double>, -1, 1>; T_loc = stan::math::var_value<double>; T_scale = stan::math::var_value<double>; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = stan::math::var_value<double>]’
stanExports_shrinkage.h:522:34: required from ‘stan::scalar_type_t<T2> model_shrinkage_namespace::model_shrinkage::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_shrinkage.h:1106:49: required from ‘T__ model_shrinkage_namespace::model_shrinkage::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = true; bool jacobian__ = true; T__ = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:40:79: required from ‘double stan::model::log_prob_grad(const M&, std::vector<double>&, std::vector<int>&, std::vector<double>&, std::ostream*) [with bool propto = true; bool jacobian_adjust_transform = true; M = model_shrinkage_namespace::model_shrinkage; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1183:49: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::grad_log_prob(SEXP, SEXP) [with Model = model_shrinkage_namespace::model_shrinkage; 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_shrinkage.cc:23:88: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::Array<double, -1, 1> >::Index’ {aka ‘long int’} [-Wsign-compare]
158 | for (size_t i = 0; i < x.size(); i++) {
| ~~^~~~~~~~~~
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp: In instantiation of ‘void stan::math::elementwise_check(const F&, const char*, const char*, const T&, const char*, const Indexings& ...) [with F = stan::math::check_not_nan<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::<lambda(double)>; T = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >; Indexings = {}; stan::require_eigen_t<S>* <anonymous> = 0; std::enable_if_t<((Eigen::internal::traits<_Rhs>::Flags & Eigen::LinearAccessBit) || T::IsVectorAtCompileTime)>* <anonymous> = 0]’:
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/check_not_nan.hpp:28:20: required from ‘void stan::math::check_not_nan(const char*, const char*, const T_y&) [with T_y = Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> >]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/prob/normal_lpdf.hpp:69:16: required from ‘stan::return_type_t<T_x, T_alpha, T_beta> stan::math::normal_lpdf(const T_y&, const T_loc&, const T_scale&) [with bool propto = false; T_y = Eigen::Matrix<double, -1, 1>; T_loc = double; T_scale = double; stan::require_all_not_nonscalar_prim_or_rev_kernel_expression_t<T_y, T_scale_succ, T_scale_fail>* <anonymous> = 0; stan::return_type_t<T_x, T_alpha, T_beta> = double]’
stanExports_shrinkage.h:522:34: required from ‘stan::scalar_type_t<T2> model_shrinkage_namespace::model_shrinkage::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_shrinkage.h:1106:49: required from ‘T__ model_shrinkage_namespace::model_shrinkage::log_prob(std::vector<T_l>&, std::vector<int>&, std::ostream*) const [with bool propto__ = false; bool jacobian__ = false; T__ = double; std::ostream = std::basic_ostream<char>]’
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/services/optimize/newton.hpp:55:47: required from ‘int stan::services::optimize::newton(Model&, const stan::io::var_context&, unsigned int, unsigned int, double, int, bool, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&, stan::callbacks::writer&) [with Model = model_shrinkage_namespace::model_shrinkage]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:502:41: required from ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::__cxx11::basic_string<char> >&, RNG_t&) [with Model = model_shrinkage_namespace::model_shrinkage; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Rcpp::List = Rcpp::Vector<19>]’
/home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:1215:18: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::call_sampler(SEXP) [with Model = model_shrinkage_namespace::model_shrinkage; 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_shrinkage.cc:15:87: required from here
/home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/err/elementwise_check.hpp:158:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase<Eigen::ArrayWrapper<const Eigen::Matrix<double, -1, 1> > >::Index’ {aka ‘long int’} [-Wsign-compare]
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:18,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/detail/bessel_jy.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/bessel.hpp:20,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun/bessel_first_kind.hpp:6,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim/fun.hpp:28,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/stan/math/prim.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/StanHeaders/include/src/stan/io/dump.hpp:10,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/stan_fit.hpp:43,
from /home/biocbuild/R/R-4.3.1/site-library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_shrinkage.h:23,
from stanExports_shrinkage.cc:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<long double>; U = long double]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair<long double, long double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
217 | value_type v = g();
| ^
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o decontX.so DecontX.o RcppExports.o matrixNorm.o matrixSums.o matrixSumsSparse.o stanExports_shrinkage.o -L/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/R/R-4.3.1/site-library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-decontX/00new/decontX/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 (decontX)
decontX.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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
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Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(decontX)
>
> test_check("decontX")
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:13 2023 .. Analyzing all cells
Wed Oct 25 09:45:13 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:13 2023 .... Generating UMAP
Wed Oct 25 09:45:20 2023 .... Estimating contamination
Wed Oct 25 09:45:20 2023 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 6.361033 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:20 2023 .. Analyzing cells in batch '1'
Wed Oct 25 09:45:20 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:20 2023 .... Generating UMAP
Wed Oct 25 09:45:24 2023 .... Estimating contamination
Wed Oct 25 09:45:24 2023 .. Calculating final decontaminated matrix
Wed Oct 25 09:45:24 2023 .. Analyzing cells in batch '2'
Wed Oct 25 09:45:24 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:24 2023 .... Generating UMAP
Wed Oct 25 09:45:29 2023 .... Estimating contamination
Wed Oct 25 09:45:29 2023 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 9.178657 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:29 2023 .. Analyzing all cells
Wed Oct 25 09:45:29 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:29 2023 .... Generating UMAP and estimating cell types
Wed Oct 25 09:45:34 2023 .... Estimating contamination
Wed Oct 25 09:45:34 2023 ...... Completed iteration: 9 | converge: 0.0009154
Wed Oct 25 09:45:34 2023 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 4.570288 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:34 2023 .. Analyzing all cells
Wed Oct 25 09:45:34 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:34 2023 .... Generating UMAP and estimating cell types
Wed Oct 25 09:45:39 2023 .... Estimating contamination
Wed Oct 25 09:45:39 2023 ...... Completed iteration: 10 | converge: 0.02021
Wed Oct 25 09:45:39 2023 ...... Completed iteration: 20 | converge: 0.00284
Wed Oct 25 09:45:39 2023 ...... Completed iteration: 30 | converge: 0.0009675
Wed Oct 25 09:45:39 2023 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 4.78218 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:39 2023 .. Analyzing all cells
Wed Oct 25 09:45:39 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:39 2023 .... Generating UMAP and estimating cell types
Wed Oct 25 09:45:44 2023 .... Estimating contamination
Wed Oct 25 09:45:44 2023 ...... Completed iteration: 9 | converge: 0.0009154
Wed Oct 25 09:45:44 2023 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 4.666927 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:45 2023 .. Analyzing all cells
Wed Oct 25 09:45:45 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:45 2023 .... Generating UMAP and estimating cell types
Wed Oct 25 09:45:50 2023 .... Estimating contamination
Wed Oct 25 09:45:50 2023 ...... Completed iteration: 9 | converge: 0.0008168
Wed Oct 25 09:45:50 2023 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 4.781918 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:50 2023 .. Analyzing all cells
Wed Oct 25 09:45:50 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:50 2023 .... Generating UMAP and estimating cell types
Wed Oct 25 09:45:55 2023 .... Estimating contamination
Wed Oct 25 09:45:55 2023 ...... Completed iteration: 10 | converge: 0.02021
Wed Oct 25 09:45:55 2023 ...... Completed iteration: 20 | converge: 0.00284
Wed Oct 25 09:45:55 2023 ...... Completed iteration: 30 | converge: 0.0009675
Wed Oct 25 09:45:55 2023 .. Calculating final decontaminated matrix
--------------------------------------------------
Completed DecontX. Total time: 4.817682 secs
--------------------------------------------------
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:55 2023 .. Analyzing all cells
Wed Oct 25 09:45:55 2023 .... Converting to sparse matrix
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:55 2023 .. Analyzing all cells
Wed Oct 25 09:45:55 2023 .... Converting to sparse matrix
--------------------------------------------------
Starting DecontX
--------------------------------------------------
Wed Oct 25 09:45:55 2023 .. Analyzing all cells
Wed Oct 25 09:45:55 2023 .... Converting to sparse matrix
Wed Oct 25 09:45:55 2023 .... Generating UMAP
Wed Oct 25 09:46:00 2023 .... Generating UMAP
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1: This procedure has not been thoroughly tested and may be unstable
Chain 1: or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1:
Chain 1:
Chain 1:
Chain 1: Gradient evaluation took 0.002618 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 26.18 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: Begin eta adaptation.
Chain 1: Iteration: 1 / 250 [ 0%] (Adaptation)
Chain 1: Iteration: 50 / 250 [ 20%] (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%] (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%] (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%] (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1:
Chain 1: Begin stochastic gradient ascent.
Chain 1: iter ELBO delta_ELBO_mean delta_ELBO_med notes
Chain 1: 100 -8039.760 1.000 1.000
Chain 1: 200 -5731.482 0.701 1.000
Chain 1: 300 -5570.966 0.477 0.403
Chain 1: 400 -5510.810 0.361 0.403
Chain 1: 500 -5480.807 0.290 0.029
Chain 1: 600 -5451.166 0.242 0.029
Chain 1: 700 -5416.328 0.209 0.011
Chain 1: 800 -5401.248 0.183 0.011
Chain 1: 900 -5395.230 0.163 0.006 MEDIAN ELBO CONVERGED
Chain 1:
Chain 1: Drawing a sample of size 1000 from the approximate posterior...
Chain 1: COMPLETED.
[ FAIL 0 | WARN 13 | SKIP 2 | PASS 19 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): 'test-decon.R:27:1', 'test-decon.R:48:1'
[ FAIL 0 | WARN 13 | SKIP 2 | PASS 19 ]
>
> proc.time()
user system elapsed
87.421 1.401 89.044
decontX.Rcheck/decontX-Ex.timings
| name | user | system | elapsed | |
| decontPro | 16.226 | 0.208 | 16.484 | |
| decontX | 14.388 | 0.203 | 14.652 | |
| plotBoxByCluster | 0.884 | 0.000 | 0.886 | |
| plotDecontXContamination | 12.440 | 0.056 | 12.519 | |
| plotDecontXMarkerExpression | 12.284 | 0.120 | 12.428 | |
| plotDecontXMarkerPercentage | 13.032 | 0.048 | 13.103 | |
| plotDensity | 0.816 | 0.008 | 0.825 | |
| retrieveFeatureIndex | 0.001 | 0.000 | 0.001 | |
| simulateContamination | 0.023 | 0.000 | 0.024 | |