Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:42 -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 IgGeneUsage package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IgGeneUsage.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 946/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
IgGeneUsage 1.13.1 (landing page) Simo Kitanovski
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: IgGeneUsage |
Version: 1.13.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IgGeneUsage.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings IgGeneUsage_1.13.1.tar.gz |
StartedAt: 2023-02-28 06:06:29 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 06:28:43 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1333.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: IgGeneUsage.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:IgGeneUsage.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings IgGeneUsage_1.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/IgGeneUsage.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 ‘IgGeneUsage/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘IgGeneUsage’ version ‘1.13.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘IgGeneUsage’ 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 40.2Mb sub-directories of 1Mb or more: libs 39.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed LOO 299.181 0.460 300.567 DGU 68.840 0.232 69.078 * 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 ... ‘User_Manual.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/IgGeneUsage.Rcheck/00check.log’ for details.
IgGeneUsage.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL IgGeneUsage ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘IgGeneUsage’ ... ** 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_zibb.cc -o stanExports_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.cc:5: stanExports_zibb.h: In member function ‘virtual void model_zibb_namespace::model_zibb::transform_inits(const stan::io::var_context&, std::vector<int>&, std::vector<double>&, std::ostream*) const’: stanExports_zibb.h:266:24: warning: typedef ‘local_scalar_t__’ locally defined but not used [-Wunused-local-typedefs] 266 | 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_zibb.h:20, from stanExports_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb_namespace::model_zibb; 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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb_namespace::model_zibb; 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_zibb_namespace::model_zibb; 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_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb.h:20, from stanExports_zibb.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_zibb_namespace::model_zibb]’: /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_zibb_namespace::model_zibb; 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_zibb_namespace::model_zibb; 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_zibb.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_zibb.h:20, from stanExports_zibb.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() { | ^~~~~~~~~~~~~~~~~~~~~ In file included from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Core:503, from /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/Dense:1, from /home/biocbuild/bbs-3.17-bioc/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13, from /home/biocbuild/bbs-3.17-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3, from stanExports_zibb.h:20, from stanExports_zibb.cc:5: /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function ‘static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, false>; Lhs = Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>; int LhsMode = 17; Rhs = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, -1, 1> >, const Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, 1, true>, -1, 1, false> >]’: /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:227:7: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 225 | internal::selfadjoint_matrix_vector_product<Scalar, Index, (internal::traits<ActualLhsTypeCleaned>::Flags&RowMajorBit) ? RowMajor : ColMajor, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | ( | ^ 228 | lhs.rows(), // size | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 | actualRhsPtr, // rhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | actualDestPtr, // result info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | actualAlpha // scale factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | ); | ~ /home/biocbuild/bbs-3.17-bioc/R/library/RcppEigen/include/Eigen/src/Core/products/SelfadjointMatrixVector.h:39:24: note: by argument 4 of type ‘const double*’ to ‘static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = long int; int StorageOrder = 0; int UpLo = 1; bool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]’ declared here 39 | EIGEN_DONT_INLINE void selfadjoint_matrix_vector_product<Scalar,Index,StorageOrder,UpLo,ConjugateLhs,ConjugateRhs,Version>::run( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o IgGeneUsage.so RcppExports.o stanExports_zibb.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-IgGeneUsage/00new/IgGeneUsage/libs ** R ** data ** 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 (IgGeneUsage)
IgGeneUsage.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(IgGeneUsage) > > test_check("IgGeneUsage") Tests stan model SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 0.000112 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.12 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 3.46005 seconds (Warm-up) Chain 1: 8.57732 seconds (Sampling) Chain 1: 12.0374 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 9.5e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.95 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 2: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 2: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 2: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 2: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 2: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 2: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 2: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 2: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 2: Iteration: 2500 / 2500 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 3.9688 seconds (Warm-up) Chain 2: 10.3676 seconds (Sampling) Chain 2: 14.3364 seconds (Total) Chain 2: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 8.7e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.87 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 3: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 3: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 3: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 3: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 3: Iteration: 2500 / 2500 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 5.14323 seconds (Warm-up) Chain 3: 19.3821 seconds (Sampling) Chain 3: 24.5253 seconds (Total) Chain 3: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 8.3e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.83 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 5.52407 seconds (Warm-up) Chain 1: 17.8793 seconds (Sampling) Chain 1: 23.4034 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 7.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.73 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 2: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 2: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 2: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 2: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 2: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 2: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 2: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 2: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 2: Iteration: 2500 / 2500 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 5.37378 seconds (Warm-up) Chain 2: 17.8487 seconds (Sampling) Chain 2: 23.2225 seconds (Total) Chain 2: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 6.9e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 3: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 3: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 3: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 3: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 3: Iteration: 2500 / 2500 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 5.21058 seconds (Warm-up) Chain 3: 29.8834 seconds (Sampling) Chain 3: 35.094 seconds (Total) Chain 3: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 8.7e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.87 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 4.95057 seconds (Warm-up) Chain 1: 26.8816 seconds (Sampling) Chain 1: 31.8322 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 7.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.79 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 2: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 2: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 2: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 2: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 2: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 2: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 2: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 2: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 2: Iteration: 2500 / 2500 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 5.21336 seconds (Warm-up) Chain 2: 17.8881 seconds (Sampling) Chain 2: 23.1015 seconds (Total) Chain 2: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 7.2e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds. Chain 3: Adjust your expectations accordingly! 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Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 5.51842 seconds (Warm-up) Chain 1: 18.0342 seconds (Sampling) Chain 1: 23.5527 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 7.8e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.78 seconds. Chain 2: Adjust your expectations accordingly! 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Chain 3: Chain 3: Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 3: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 3: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 3: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 3: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 3: Iteration: 2500 / 2500 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 4.3999 seconds (Warm-up) Chain 3: 17.9695 seconds (Sampling) Chain 3: 22.3694 seconds (Total) Chain 3: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 8.2e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.82 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 5.98593 seconds (Warm-up) Chain 1: 17.9941 seconds (Sampling) Chain 1: 23.98 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 7.1e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.71 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 2: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 2: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 2: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 2: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 2: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 2: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 2: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 2: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 2: Iteration: 2500 / 2500 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 4.06501 seconds (Warm-up) Chain 2: 12.2778 seconds (Sampling) Chain 2: 16.3428 seconds (Total) Chain 2: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 7.3e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.73 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 3: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 3: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 3: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 3: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 3: Iteration: 2500 / 2500 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 4.17391 seconds (Warm-up) Chain 3: 26.32 seconds (Sampling) Chain 3: 30.4939 seconds (Total) Chain 3: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 8.4e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.84 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 4.94175 seconds (Warm-up) Chain 1: 17.8172 seconds (Sampling) Chain 1: 22.7589 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 6.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 2: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 2: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 2: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 2: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 2: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 2: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 2: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 2: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 2: Iteration: 2500 / 2500 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 4.60676 seconds (Warm-up) Chain 2: 18.2703 seconds (Sampling) Chain 2: 22.877 seconds (Total) Chain 2: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 6.7e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.67 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 3: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 3: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 3: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 3: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 3: Iteration: 2500 / 2500 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 3.87695 seconds (Warm-up) Chain 3: 17.8798 seconds (Sampling) Chain 3: 21.7567 seconds (Total) Chain 3: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 8.8e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.88 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 4.65347 seconds (Warm-up) Chain 1: 18.6485 seconds (Sampling) Chain 1: 23.3019 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 6.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 2: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 2: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 2: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 2: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 2: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 2: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 2: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 2: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 2: Iteration: 2500 / 2500 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 5.46928 seconds (Warm-up) Chain 2: 17.9286 seconds (Sampling) Chain 2: 23.3979 seconds (Total) Chain 2: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 7.1e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.71 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 3: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 3: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 3: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 3: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 3: Iteration: 2500 / 2500 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 4.39146 seconds (Warm-up) Chain 3: 17.8455 seconds (Sampling) Chain 3: 22.2369 seconds (Total) Chain 3: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 8.7e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.87 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 5.66455 seconds (Warm-up) Chain 1: 32.8425 seconds (Sampling) Chain 1: 38.507 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 7.3e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.73 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 2: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 2: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 2: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 2: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 2: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 2: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 2: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 2: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 2: Iteration: 2500 / 2500 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 5.08448 seconds (Warm-up) Chain 2: 18.1282 seconds (Sampling) Chain 2: 23.2127 seconds (Total) Chain 2: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 7e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.7 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 3: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 3: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 3: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 3: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 3: Iteration: 2500 / 2500 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 4.83145 seconds (Warm-up) Chain 3: 16.7079 seconds (Sampling) Chain 3: 21.5393 seconds (Total) Chain 3: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 1). Chain 1: Chain 1: Gradient evaluation took 8.5e-05 seconds Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.85 seconds. Chain 1: Adjust your expectations accordingly! Chain 1: Chain 1: Chain 1: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 1: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 1: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 1: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 1: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 1: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 1: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 1: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 1: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 1: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 1: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 1: Iteration: 2500 / 2500 [100%] (Sampling) Chain 1: Chain 1: Elapsed Time: 4.74421 seconds (Warm-up) Chain 1: 11.3351 seconds (Sampling) Chain 1: 16.0793 seconds (Total) Chain 1: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 2). Chain 2: Chain 2: Gradient evaluation took 6.9e-05 seconds Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.69 seconds. Chain 2: Adjust your expectations accordingly! Chain 2: Chain 2: Chain 2: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 2: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 2: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 2: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 2: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 2: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 2: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 2: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 2: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 2: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 2: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 2: Iteration: 2500 / 2500 [100%] (Sampling) Chain 2: Chain 2: Elapsed Time: 5.23784 seconds (Warm-up) Chain 2: 17.9918 seconds (Sampling) Chain 2: 23.2296 seconds (Total) Chain 2: SAMPLING FOR MODEL 'zibb' NOW (CHAIN 3). Chain 3: Chain 3: Gradient evaluation took 7.2e-05 seconds Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds. Chain 3: Adjust your expectations accordingly! Chain 3: Chain 3: Chain 3: Iteration: 1 / 2500 [ 0%] (Warmup) Chain 3: Iteration: 250 / 2500 [ 10%] (Warmup) Chain 3: Iteration: 500 / 2500 [ 20%] (Warmup) Chain 3: Iteration: 501 / 2500 [ 20%] (Sampling) Chain 3: Iteration: 750 / 2500 [ 30%] (Sampling) Chain 3: Iteration: 1000 / 2500 [ 40%] (Sampling) Chain 3: Iteration: 1250 / 2500 [ 50%] (Sampling) Chain 3: Iteration: 1500 / 2500 [ 60%] (Sampling) Chain 3: Iteration: 1750 / 2500 [ 70%] (Sampling) Chain 3: Iteration: 2000 / 2500 [ 80%] (Sampling) Chain 3: Iteration: 2250 / 2500 [ 90%] (Sampling) Chain 3: Iteration: 2500 / 2500 [100%] (Sampling) Chain 3: Chain 3: Elapsed Time: 5.93582 seconds (Warm-up) Chain 3: 18.0298 seconds (Sampling) Chain 3: 23.9656 seconds (Total) Chain 3: [ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ] > > proc.time() user system elapsed 664.024 1.282 666.079
IgGeneUsage.Rcheck/IgGeneUsage-Ex.timings
name | user | system | elapsed | |
DGU | 68.840 | 0.232 | 69.078 | |
IGHV_Epitopes | 0.002 | 0.001 | 0.003 | |
IGHV_HCV | 0.006 | 0.000 | 0.006 | |
Ig | 0.003 | 0.000 | 0.003 | |
Ig_SE | 0.047 | 0.003 | 0.051 | |
LOO | 299.181 | 0.460 | 300.567 | |
d_zibb | 0.004 | 0.000 | 0.004 | |