##############################################################################
##############################################################################
###
### 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ppcseq.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ppcseq/DESCRIPTION’ ... OK
* this is package ‘ppcseq’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ppcseq’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
* 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 ... INFO
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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ppcseq.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ppcseq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ppcseq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.sdk’


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/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/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
5 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/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/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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 ('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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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 ('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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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/4.5-arm64/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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-arm64/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();
          ^
./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>, Eigen::Matrix<double, -1, 1>, double, nullptr>' requested here
    return lp_reduce(global_parameters, local_parameters, real_data,
           ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/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>, Eigen::Matrix<double, -1, 1>, double, nullptr>' requested here
    return F()(shared_params, job_specific_params, x_r, x_i, msgs).transpose();
           ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/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/4.5-arm64/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>> &, 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>>, 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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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>, Eigen::Matrix<stan::math::var_value<double>, -1, 1>, double, nullptr>' requested here
    return lp_reduce(global_parameters, local_parameters, real_data,
           ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/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>, Eigen::Matrix<stan::math::var_value<double>, -1, 1>, 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/4.5-arm64/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/4.5-arm64/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>> &, 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>>, 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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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/4.5-arm64/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)
                                                                                      ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ppcseq.so RcppExports.o stanExports_negBinomial_MPI.o -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: ignoring duplicate libraries: '-ltbb', '-ltbbmalloc'
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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Platform: aarch64-apple-darwin20

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> 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 
  1.619   0.119   1.555