##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decemedip.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decemedip_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/decemedip.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decemedip/DESCRIPTION’ ... OK
* this is package ‘decemedip’ version ‘0.99.8’
* 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 ‘decemedip’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.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 ... 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 R/sysdata.rda ... 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 ... INFO
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
decemedip 19.827  0.639  21.835
* 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: OK

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decemedip
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘decemedip’ ...
** this is package ‘decemedip’ version ‘0.99.8’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.1.sdk’


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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/4.6-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_decemedip0.cc -o stanExports_decemedip0.o
In file included from stanExports_decemedip0.cc:5:
In file included from ./stanExports_decemedip0.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip0.cc:5:
In file included from ./stanExports_decemedip0.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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_decemedip0.cc:5:
In file included from ./stanExports_decemedip0.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip0.cc:5:
In file included from ./stanExports_decemedip0.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip0.cc:5:
In file included from ./stanExports_decemedip0.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip0.cc:5:
In file included from ./stanExports_decemedip0.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip0.cc:5:
In file included from ./stanExports_decemedip0.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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_decemedip0.cc:5:
In file included from ./stanExports_decemedip0.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip0.cc:5:
./stanExports_decemedip0.h:964:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
10 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/4.6-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/4.6-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_decemedip1.cc -o stanExports_decemedip1.o
In file included from stanExports_decemedip1.cc:5:
In file included from ./stanExports_decemedip1.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip1.cc:5:
In file included from ./stanExports_decemedip1.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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_decemedip1.cc:5:
In file included from ./stanExports_decemedip1.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip1.cc:5:
In file included from ./stanExports_decemedip1.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip1.cc:5:
In file included from ./stanExports_decemedip1.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip1.cc:5:
In file included from ./stanExports_decemedip1.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip1.cc:5:
In file included from ./stanExports_decemedip1.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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_decemedip1.cc:5:
In file included from ./stanExports_decemedip1.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.6-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_decemedip1.cc:5:
./stanExports_decemedip1.h:1077:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
10 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 decemedip.so RcppExports.o stanExports_decemedip0.o stanExports_decemedip1.o -L/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: ignoring duplicate libraries: '-ltbb', '-ltbbmalloc'
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-decemedip/00new/decemedip/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for request: ‘values’ when loading ‘MEDIPS’
** testing if installed package keeps a record of temporary installation path
* DONE (decemedip)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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Platform: aarch64-apple-darwin20

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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(decemedip)
No methods found in package 'IRanges' for request: 'values' when loading 'MEDIPS'
> 
> test_check("decemedip")
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
  6.058   0.278   6.521