| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-01 07:38:35 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 | ||||
|
To the developers/maintainers of the BASiCStan package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCStan.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 117/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BASiCStan 1.1.0 (landing page) Alan O'Callaghan
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: BASiCStan |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BASiCStan.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BASiCStan_1.1.0.tar.gz |
| StartedAt: 2023-02-27 21:11:46 -0000 (Mon, 27 Feb 2023) |
| EndedAt: 2023-02-27 21:18:37 -0000 (Mon, 27 Feb 2023) |
| EllapsedTime: 410.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BASiCStan.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BASiCStan.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings BASiCStan_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BASiCStan.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘BASiCStan/DESCRIPTION’ ... OK
* this is package ‘BASiCStan’ version ‘1.1.0’
* 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 ‘BASiCStan’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 70.7Mb
sub-directories of 1Mb or more:
libs 70.4Mb
* 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘BASiCS:::.BASiCS_MCMC_Start’ ‘BASiCS:::.EmpiricalBayesMu’
‘BASiCS:::.estimateRBFLocations’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BASiCStan 4.783 0.248 5.033
* 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 ...
‘BASiCStan.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BASiCStan.Rcheck/00check.log’
for details.
BASiCStan.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BASiCStan
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘BASiCStan’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_basics_regression.cc -o stanExports_basics_regression.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_args.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:20,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.17-bioc/R/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>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:278,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpmf(const T_prob&, const T_prior_size&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_prob, T_prior_size>::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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:328,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T4>::value, Eigen::Array<typename stan::partials_return_type<T_alpha>::type, -1, 1>, typename stan::partials_return_type<T_alpha>::type>’ locally defined but not used [-Wunused-local-typedefs]
52 | using T_alpha_val = typename std::conditional_t<
| ^~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:51,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vv_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<stan::math::var, R2, C2, (Eigen::AutoAlign | (((R2 == 1) && (C2 != 1)) ? Eigen::RowMajor : (((C2 == 1) && (R2 != 1)) ? Eigen::ColMajor : Eigen::ColMajor))), R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<stan::math::var, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
27 | using idx_t = typename index_type<matrix_v>::type;
| ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vd_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<double, R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<double, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
64 | using idx_t = typename index_type<matrix_d>::type;
| ^~~~~
In file included from stanExports_basics_regression.cc:5:
stanExports_basics_regression.h: In member function ‘virtual void model_basics_regression_namespace::model_basics_regression::transform_inits(const stan::io::var_context&, std::vector<int>&, std::vector<double>&, std::ostream*) const’:
stanExports_basics_regression.h:431:24: warning: typedef ‘local_scalar_t__’ locally defined but not used [-Wunused-local-typedefs]
431 | typedef double local_scalar_t__;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
74 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’:
stanExports_basics_regression.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1238:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
1238 | int ret = stan::services::error_codes::CONFIG;
| ^~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_basics_regression_namespace::model_basics_regression; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_basics_regression.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:91:22: 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]
91 | if (p_names.size() != draws.cols()) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:109:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
109 | for (size_t i = 0; i < draws.rows(); ++i) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/err/check_cholesky_factor.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:9,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:64:74: 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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:19:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘long int’ [-Wsign-compare]
19 | if (!(y <= high_vec[n])) {
| ~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘void stan::services::get_model_parameters(const Model&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<long unsigned int> >&) [with Model = model_basics_regression_namespace::model_basics_regression]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:105:23: required from ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_basics_regression_namespace::model_basics_regression; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_basics_regression_namespace::model_basics_regression; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_basics_regression.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:41:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
41 | for (int j = 0; j < dimss[i].size(); ++j)
| ~~^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:46,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression.h:20,
from stanExports_basics_regression.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
14 | static void set_zero_all_adjoints() {
| ^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I'/home/biocbuild/bbs-3.17-bioc/R/library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include' -I/usr/local/include -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -g -O2 -Wall -c stanExports_basics_regression_nospikes.cc -o stanExports_basics_regression_nospikes.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-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++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
507 | explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
520 | shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
603 | shared_ptr & operator=( std::auto_ptr<Y> & r )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
612 | shared_ptr & operator=( std::auto_ptr<Y> && r )
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
614 | this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_args.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:20,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.17-bioc/R/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>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_log.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:278,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp: In function ‘stan::return_type_t<T1, T2> stan::math::dirichlet_lpmf(const T_prob&, const T_prior_size&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp:60:9: warning: typedef ‘using T_partials_vec = struct Eigen::Matrix<typename stan::partials_return_type<T_prob, T_prior_size>::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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp:5,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:328,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp:52:9: warning: typedef ‘using T_alpha_val = std::conditional_t<stan::is_vector<T4>::value, Eigen::Array<typename stan::partials_return_type<T_alpha>::type, -1, 1>, typename stan::partials_return_type<T_alpha>::type>’ locally defined but not used [-Wunused-local-typedefs]
52 | using T_alpha_val = typename std::conditional_t<
| ^~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
from /home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:34,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:336,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/locale_conv.h:41,
from /usr/include/c++/11/locale:43,
from /usr/include/c++/11/iomanip:43,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from /home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27,
from stanExports_basics_regression_nospikes.cc:3:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:51,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vv_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<stan::math::var, R2, C2, (Eigen::AutoAlign | (((R2 == 1) && (C2 != 1)) ? Eigen::RowMajor : (((C2 == 1) && (R2 != 1)) ? Eigen::ColMajor : Eigen::ColMajor))), R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:27:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<stan::math::var, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
27 | using idx_t = typename index_type<matrix_v>::type;
| ^~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp: In static member function ‘static double stan::math::internal::squared_distance_vd_vari::var_squared_distance(const Eigen::Matrix<stan::math::var, R, C>&, const Eigen::Matrix<double, R2, C2>&)’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: typedef ‘using idx_t = using type = Eigen::EigenBase<Eigen::Matrix<double, -1, -1> >::Index’ locally defined but not used [-Wunused-local-typedefs]
64 | using idx_t = typename index_type<matrix_d>::type;
| ^~~~~
In file included from stanExports_basics_regression_nospikes.cc:5:
stanExports_basics_regression_nospikes.h: In member function ‘virtual void model_basics_regression_nospikes_namespace::model_basics_regression_nospikes::transform_inits(const stan::io::var_context&, std::vector<int>&, std::vector<double>&, std::ostream*) const’:
stanExports_basics_regression_nospikes.h:342:24: warning: typedef ‘local_scalar_t__’ locally defined but not used [-Wunused-local-typedefs]
342 | typedef double local_scalar_t__;
| ^~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:97:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
74 | for (int i = 0; i < dims.size(); i++) {
| ~~^~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:74:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<long unsigned int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp: In instantiation of ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_basics_regression_nospikes_namespace::model_basics_regression_nospikes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’:
stanExports_basics_regression_nospikes.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1238:9: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable]
1238 | int ret = stan::services::error_codes::CONFIG;
| ^~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_basics_regression_nospikes_namespace::model_basics_regression_nospikes; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’:
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_basics_regression_nospikes_namespace::model_basics_regression_nospikes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_basics_regression_nospikes.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:91:22: 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]
91 | if (p_names.size() != draws.cols()) {
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:109:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
109 | for (size_t i = 0; i < draws.rows(); ++i) {
| ~~^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/err/check_cholesky_factor.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:9,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/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/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:64:74: 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/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:79:36: required from ‘std::vector<long unsigned int> stan::io::array_var_context::validate_dims(const std::vector<std::__cxx11::basic_string<char> >&, T, const std::vector<std::vector<long unsigned int> >&) [with T = long int]’
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/io/array_var_context.hpp:118:48: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/scal/err/check_less_or_equal.hpp:19:15: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘long int’ [-Wsign-compare]
19 | if (!(y <= high_vec[n])) {
| ~~~^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:52,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp: In instantiation of ‘void stan::services::get_model_parameters(const Model&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<long unsigned int> >&) [with Model = model_basics_regression_nospikes_namespace::model_basics_regression_nospikes]’:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:105:23: required from ‘int stan::services::standalone_generate(const Model&, const MatrixXd&, unsigned int, stan::callbacks::interrupt&, stan::callbacks::logger&, stan::callbacks::writer&) [with Model = model_basics_regression_nospikes_namespace::model_basics_regression_nospikes; Eigen::MatrixXd = Eigen::Matrix<double, -1, -1>]’
/home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:1239:46: required from ‘SEXPREC* rstan::stan_fit<Model, RNG_t>::standalone_gqs(SEXP, SEXP) [with Model = model_basics_regression_nospikes_namespace::model_basics_regression_nospikes; RNG_t = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; SEXP = SEXPREC*]’
stanExports_basics_regression_nospikes.cc:30:89: required from here
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/sample/standalone_gqs.hpp:41:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long unsigned int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
41 | for (int j = 0; j < dimss[i].size(); ++j)
| ~~^~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:46,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:6,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:4,
from stanExports_basics_regression_nospikes.h:20,
from stanExports_basics_regression_nospikes.cc:5:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp: At global scope:
/home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
14 | static void set_zero_all_adjoints() {
| ^~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o BASiCStan.so RcppExports.o stanExports_basics_regression.o stanExports_basics_regression_nospikes.o -L/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/lib/ -Wl,-rpath,/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-BASiCStan/00new/BASiCStan/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BASiCStan)
BASiCStan.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(BASiCStan)
Loading required package: BASiCS
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Welcome to 'BASiCS'. If you used 'BASiCS' before its release in
Bioconductor, please visit:
https://github.com/catavallejos/BASiCS/wiki.
Loading required package: rstan
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.21.8, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
>
> test_check("BASiCStan")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
>
> proc.time()
user system elapsed
124.867 1.695 126.550
BASiCStan.Rcheck/BASiCStan-Ex.timings
| name | user | system | elapsed | |
| BASiCStan | 4.783 | 0.248 | 5.033 | |
| Stan2BASiCS | 2.489 | 0.056 | 2.545 | |