Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1582/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ppcseq 1.14.0 (landing page) Stefano Mangiola
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the ppcseq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ppcseq.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: ppcseq |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ppcseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ppcseq_1.14.0.tar.gz |
StartedAt: 2024-11-20 01:18:05 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 01:23:22 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 317.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ppcseq.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ppcseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ppcseq_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ppcseq.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ppcseq/DESCRIPTION’ ... OK * this is package ‘ppcseq’ version ‘1.14.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ppcseq’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... OK Not all R platforms support C++17 * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE add_partition: no visible binding for global variable ‘.’ add_scaled_counts_bulk.calcNormFactor: no visible binding for global variable ‘transcript’ add_scaled_counts_bulk.get_low_expressed: no visible binding for global variable ‘transcript’ check_if_within_posterior: no visible binding for global variable ‘.lower’ check_if_within_posterior: no visible binding for global variable ‘.upper’ check_if_within_posterior: no visible binding for global variable ‘ppc’ do_inference: no visible binding for global variable ‘idx_MPI’ do_inference: no visible binding for global variable ‘read_count_MPI_row’ do_inference: no visible binding for global variable ‘.’ do_inference: no visible binding for global variable ‘symbol MPI row’ draws_to_tibble_x: no visible binding for global variable ‘.’ draws_to_tibble_x: no visible binding for global variable ‘dummy’ draws_to_tibble_x: no visible binding for global variable ‘.variable’ draws_to_tibble_x: no visible binding for global variable ‘.chain’ draws_to_tibble_x: no visible binding for global variable ‘.iteration’ draws_to_tibble_x: no visible binding for global variable ‘.draw’ draws_to_tibble_x: no visible binding for global variable ‘.value’ draws_to_tibble_x_y: no visible binding for global variable ‘.’ draws_to_tibble_x_y: no visible binding for global variable ‘dummy’ draws_to_tibble_x_y: no visible binding for global variable ‘.variable’ draws_to_tibble_x_y: no visible binding for global variable ‘.chain’ draws_to_tibble_x_y: no visible binding for global variable ‘.iteration’ draws_to_tibble_x_y: no visible binding for global variable ‘.draw’ draws_to_tibble_x_y: no visible binding for global variable ‘.value’ find_optimal_number_of_chains: no visible binding for global variable ‘tot’ find_optimal_number_of_chains: no visible binding for global variable ‘chains’ fit_to_counts_rng: no visible binding for global variable ‘.variable’ fit_to_counts_rng: no visible binding for global variable ‘S’ fit_to_counts_rng: no visible binding for global variable ‘G’ fit_to_counts_rng: no visible binding for global variable ‘.’ fit_to_counts_rng_approximated: no visible binding for global variable ‘.’ fit_to_counts_rng_approximated: no visible binding for global variable ‘S’ fit_to_counts_rng_approximated: no visible binding for global variable ‘G’ fit_to_counts_rng_approximated: no visible binding for global variable ‘CI’ format_for_MPI: no visible binding for global variable ‘.’ format_for_MPI: no visible binding for global variable ‘G’ format_for_MPI: no visible binding for global variable ‘idx_MPI’ format_input: no visible binding for global variable ‘.’ format_results: no visible binding for global variable ‘sample_wise_data’ get_scaled_counts_bulk: no visible binding for global variable ‘med’ get_scaled_counts_bulk: no visible binding for global variable ‘tot_filt’ get_scaled_counts_bulk: no visible binding for global variable ‘nf’ get_scaled_counts_bulk: no visible binding for global variable ‘.’ get_scaled_counts_bulk: no visible binding for global variable ‘tot’ identify_outliers: no visible binding for global variable ‘.’ identify_outliers: no visible binding for global variable ‘do_check___’ identify_outliers: no visible binding for global variable ‘multiplier’ identify_outliers: no visible binding for global variable ‘exposure_rate’ identify_outliers: no visible binding for global variable ‘write_on_disk’ identify_outliers: no visible binding for global variable ‘.variable’ identify_outliers: no visible binding for global variable ‘S’ identify_outliers: no visible binding for global variable ‘G’ identify_outliers: no visible binding for global variable ‘.lower’ identify_outliers: no visible binding for global variable ‘.upper’ identify_outliers_1_step: no visible binding for global variable ‘.’ identify_outliers_1_step: no visible global function definition for ‘scale_abundance’ identify_outliers_1_step: no visible binding for global variable ‘TMM’ identify_outliers_1_step: no visible binding for global variable ‘multiplier’ identify_outliers_1_step: no visible binding for global variable ‘l’ identify_outliers_1_step: no visible binding for global variable ‘l %>% sd’ identify_outliers_1_step: no visible binding for global variable ‘cc’ identify_outliers_1_step: no visible binding for global variable ‘write_on_disk’ identify_outliers_1_step: no visible binding for global variable ‘.variable’ identify_outliers_1_step: no visible binding for global variable ‘S’ identify_outliers_1_step: no visible binding for global variable ‘G’ identify_outliers_1_step: no visible binding for global variable ‘.lower’ identify_outliers_1_step: no visible binding for global variable ‘.upper’ identify_outliers_1_step: no visible binding for global variable ‘ppc’ identify_outliers_1_step: no visible binding for global variable ‘exposure_rate’ inits_fx: no visible binding for global variable ‘res_discovery’ inits_fx: no visible binding for global variable ‘.variable’ inits_fx: no visible binding for global variable ‘S’ inits_fx: no visible binding for global variable ‘G’ inits_fx: no visible binding for global variable ‘init’ merge_results: no visible binding for global variable ‘.variable’ merge_results: no visible binding for global variable ‘S’ merge_results: no visible binding for global variable ‘G’ merge_results: no visible binding for global variable ‘slope’ merge_results: no visible binding for global variable ‘exposure_rate’ merge_results: no visible binding for global variable ‘multiplier’ merge_results: no visible binding for global variable ‘.lower’ merge_results: no visible binding for global variable ‘.upper’ merge_results: no visible binding for global variable ‘ppc’ plot_credible_intervals: no visible binding for global variable ‘sample_wise_data’ produce_plots: no visible binding for global variable ‘.upper’ select_to_check_and_house_keeping: no visible binding for global variable ‘.’ summary_to_tibble: no visible binding for global variable ‘.’ Undefined global functions or variables: . .chain .draw .iteration .lower .upper .value .variable CI G S TMM cc chains do_check___ dummy exposure_rate idx_MPI init l l %>% sd med multiplier nf ppc read_count_MPI_row res_discovery sample_wise_data scale_abundance slope symbol MPI row tot tot_filt transcript write_on_disk Consider adding importFrom("base", "row") importFrom("stats", "sd") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ppcseq.Rcheck/00check.log’ for details.
ppcseq.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ppcseq ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ppcseq’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include' -I/opt/R/x86_64/include -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fPIC -falign-functions=64 -Wall -g -O2 -c stanExports_negBinomial_MPI.cc -o stanExports_negBinomial_MPI.o In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:21: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual] virtual std::streamsize xsputn(const char_type* s, int n) { ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('std::streamsize' (aka 'long') vs 'int') virtual streamsize xsputn(const char_type* __s, streamsize __n); ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> { ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here? class ops_partials_edge; ^~~~~ struct In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable] int ret = stan::services::error_codes::CONFIG; ^ In file included from stanExports_negBinomial_MPI.cc:5: ./stanExports_negBinomial_MPI.h:1422:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable] int pos__ = std::numeric_limits<int>::min(); ^ In file included from stanExports_negBinomial_MPI.cc:5: In file included from ./stanExports_negBinomial_MPI.h:23: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/rstaninc.hpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:43: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:46: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/choose.hpp:7: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/binomial.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/beta.hpp:1721: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:29:15: warning: unused variable 'x_extrema' [-Wunused-variable] const T x_extrema = 1 / (1 + a); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:304:7: note: in instantiation of member function 'boost::math::detail::temme_root_finder<double>::temme_root_finder' requested here temme_root_finder<T>(-lu, alpha), x, lower, upper, policies::digits<T, Policy>() / 2); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:615:20: note: in instantiation of function template specialization 'boost::math::detail::temme_method_2_ibeta_inverse<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here x = temme_method_2_ibeta_inverse(a, b, p, r, theta, pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:992:17: note: in instantiation of function template specialization 'boost::math::detail::ibeta_inv_imp<double, boost::math::policies::policy<boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_float<false>, boost::math::policies::promote_double<false>>>' requested here rx = detail::ibeta_inv_imp( ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include/boost/math/special_functions/detail/ibeta_inverse.hpp:1023:11: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return ibeta_inv(a, b, p, static_cast<result_type*>(nullptr), pol); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/fun/inv_inc_beta.hpp:32:23: note: in instantiation of function template specialization 'boost::math::ibeta_inv<double, double, double, boost::math::policies::policy<boost::math::policies::overflow_error<boost::math::policies::errno_on_error>, boost::math::policies::pole_error<boost::math::policies::errno_on_error>, boost::math::policies::promote_double<false>, boost::math::policies::digits2<0>>>' requested here return boost::math::ibeta_inv(a, b, p, boost_policy_t<>()); ^ In file included from stanExports_negBinomial_MPI.cc:5: ./stanExports_negBinomial_MPI.h:438:15: warning: unused variable 'global_parameters' [-Wunused-variable] const auto& global_parameters = stan::math::to_ref(global_parameters_arg__); ^ ./stanExports_negBinomial_MPI.h:242:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce<Eigen::Matrix<double, -1, 1, 0>, Eigen::Matrix<double, -1, 1, 0>, double, nullptr>' requested here return lp_reduce(global_parameters, local_parameters, real_data, ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect_reduce.hpp:47:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()<Eigen::Matrix<double, -1, 1, 0>, Eigen::Matrix<double, -1, 1, 0>, double, nullptr>' requested here return F()(shared_params, job_specific_params, x_r, x_i, msgs).transpose(); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:23: note: in instantiation of member function 'stan::math::internal::map_rect_reduce<model_negBinomial_MPI_namespace::lp_reduce_functor__, double, double>::operator()' requested here job_output[i] = ReduceF()(shared_params_dbl, value_of(job_params[i]), ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:183:20: note: in instantiation of function template specialization 'stan::math::internal::map_rect_concurrent<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, const Eigen::Map<Eigen::Matrix<double, -1, 1, 0>, 0> &, double, nullptr>' requested here return internal::map_rect_concurrent<call_id, F, T_shared_param_ref, ^ ./stanExports_negBinomial_MPI.h:1246:38: note: in instantiation of function template specialization 'stan::math::map_rect<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, Eigen::Map<Eigen::Matrix<double, -1, 1, 0>, 0>, double, nullptr>' requested here stan::math::map_rect<1, lp_reduce_functor__>( ^ ./stanExports_negBinomial_MPI.h:1849:12: note: (skipping 1 context in backtrace; use -ftemplate-backtrace-limit=0 to see all) return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:129:33: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::model_negBinomial_MPI::log_prob<false, true, double>' requested here log_prob = model.template log_prob<false, Jacobian>(unconstrained, ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_negBinomial_MPI_namespace::model_negBinomial_MPI, stan::io::var_context, 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>>>' requested here std::vector<double> cont_vector = util::initialize( ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_negBinomial_MPI_namespace::model_negBinomial_MPI>' requested here return_code = stan::services::diagnose::diagnose(model, ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_negBinomial_MPI_namespace::model_negBinomial_MPI, 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>>>' requested here ret = command(args, model_, holder, names_oi_tidx_, ^ stanExports_negBinomial_MPI.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_negBinomial_MPI_namespace::model_negBinomial_MPI, 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>>>::call_sampler' requested here .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler) ^ In file included from stanExports_negBinomial_MPI.cc:5: ./stanExports_negBinomial_MPI.h:438:15: warning: unused variable 'global_parameters' [-Wunused-variable] const auto& global_parameters = stan::math::to_ref(global_parameters_arg__); ^ ./stanExports_negBinomial_MPI.h:242:12: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce<Eigen::Matrix<double, -1, 1, 0>, Eigen::Matrix<stan::math::var_value<double>, -1, 1, 0>, double, nullptr>' requested here return lp_reduce(global_parameters, local_parameters, real_data, ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_reduce.hpp:68:21: note: in instantiation of function template specialization 'model_negBinomial_MPI_namespace::lp_reduce_functor__::operator()<Eigen::Matrix<double, -1, 1, 0>, Eigen::Matrix<stan::math::var_value<double>, -1, 1, 0>, double, nullptr>' requested here vector_v fx_v = F()(shared_params, job_specific_params_v, x_r, x_i, msgs); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/rev/functor/map_rect_concurrent.hpp:41:23: note: in instantiation of member function 'stan::math::internal::map_rect_reduce<model_negBinomial_MPI_namespace::lp_reduce_functor__, double, stan::math::var_value<double>>::operator()' requested here job_output[i] = ReduceF()(shared_params_dbl, value_of(job_params[i]), ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/stan/math/prim/functor/map_rect.hpp:183:20: note: in instantiation of function template specialization 'stan::math::internal::map_rect_concurrent<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, const Eigen::Map<Eigen::Matrix<double, -1, 1, 0>, 0> &, stan::math::var_value<double>, nullptr>' requested here return internal::map_rect_concurrent<call_id, F, T_shared_param_ref, ^ ./stanExports_negBinomial_MPI.h:1246:38: note: in instantiation of function template specialization 'stan::math::map_rect<1, model_negBinomial_MPI_namespace::lp_reduce_functor__, Eigen::Map<Eigen::Matrix<double, -1, 1, 0>, 0>, stan::math::var_value<double>, nullptr>' requested here stan::math::map_rect<1, lp_reduce_functor__>( ^ ./stanExports_negBinomial_MPI.h:1849:12: note: (skipping 2 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all) return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream); ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/services/util/initialize.hpp:167:31: note: in instantiation of function template specialization 'stan::model::log_prob_grad<true, true, model_negBinomial_MPI_namespace::model_negBinomial_MPI>' requested here log_prob = stan::model::log_prob_grad<true, Jacobian>( ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:49:43: note: in instantiation of function template specialization 'stan::services::util::initialize<true, model_negBinomial_MPI_namespace::model_negBinomial_MPI, stan::io::var_context, 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>>>' requested here std::vector<double> cont_vector = util::initialize( ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:481:45: note: in instantiation of function template specialization 'stan::services::diagnose::diagnose<model_negBinomial_MPI_namespace::model_negBinomial_MPI>' requested here return_code = stan::services::diagnose::diagnose(model, ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rstan/include/rstan/stan_fit.hpp:1215:11: note: in instantiation of function template specialization 'rstan::(anonymous namespace)::command<model_negBinomial_MPI_namespace::model_negBinomial_MPI, 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>>>' requested here ret = command(args, model_, holder, names_oi_tidx_, ^ stanExports_negBinomial_MPI.cc:15:87: note: in instantiation of member function 'rstan::stan_fit<model_negBinomial_MPI_namespace::model_negBinomial_MPI, 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>>>::call_sampler' requested here .method("call_sampler", &rstan::stan_fit<stan_model, boost::random::ecuyer1988> ::call_sampler) ^ 8 warnings generated. clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ppcseq.so RcppExports.o stanExports_negBinomial_MPI.o -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-ppcseq/00new/ppcseq/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ppcseq)
ppcseq.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(ppcseq) Loading required package: rstan Loading required package: StanHeaders rstan version 2.32.6 (Stan version 2.32.2) For execution on a local, multicore CPU with excess RAM we recommend calling options(mc.cores = parallel::detectCores()). To avoid recompilation of unchanged Stan programs, we recommend calling rstan_options(auto_write = TRUE) For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions, change `threads_per_chain` option: rstan_options(threads_per_chain = 1) > > test_check("ppcseq") [1] "tests for windows are temporarily disabled" [ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 3.552 0.319 3.638
ppcseq.Rcheck/ppcseq-Ex.timings
name | user | system | elapsed | |
identify_outliers | 0.030 | 0.007 | 0.037 | |
plot_credible_intervals | 0.015 | 0.003 | 0.018 | |