##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmig.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmig_1.1.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/cellmig.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmig/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmig’ version ‘1.1.7’
* 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 ‘cellmig’ 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 ... INFO
  specified C++17
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      2.1Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gen_partial: no visible binding for global variable ‘delta’
get_dose_response_profile: no visible binding for global variable
  ‘isTip’
get_dose_response_profile: no visible binding for global variable
  ‘label’
get_dose_response_profile: no visible binding for global variable
  ‘dose’
get_dose_response_profile: no visible binding for global variable
  ‘X2.5.’
get_dose_response_profile: no visible binding for global variable
  ‘X97.5.’
get_dose_response_profile: no visible binding for global variable
  ‘plate’
get_pairs: no visible binding for global variable ‘group_x’
get_pairs: no visible binding for global variable ‘group_y’
get_pairs: no visible binding for global variable ‘rho_M’
get_pairs: no visible binding for global variable ‘rho_M_exp’
get_ppc_means: no visible binding for global variable ‘v’
get_ppc_means: no visible binding for global variable ‘X2.5.’
get_ppc_means: no visible binding for global variable ‘X97.5.’
get_ppc_violins: no visible binding for global variable ‘dose’
get_ppc_violins: no visible binding for global variable ‘v’
get_ppc_violins: no visible binding for global variable ‘well’
get_ppc_violins: no visible binding for global variable ‘yhat’
get_violins: no visible binding for global variable ‘dose’
get_violins: no visible binding for global variable ‘rho’
Undefined global functions or variables:
  X2.5. X97.5. delta dose group_x group_y isTip label plate rho rho_M
  rho_M_exp v well yhat
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... 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
cellmig-package           51.447  1.823  35.280
cellmig                   50.571  2.003  35.365
get_dose_response_profile 43.236  1.402  29.880
ppc_violin                10.510  0.878   8.778
get_pairs                  9.220  0.772   7.459
get_violins                9.203  0.777   7.229
ppc_means                  9.164  0.672   7.375
get_groups                 8.958  0.721   7.090
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Chain 1: 
  Chain 1:  Elapsed Time: 0 seconds (Warm-up)
  Chain 1:                0 seconds (Sampling)
  Chain 1:                0 seconds (Total)
  Chain 1: 
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 120 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-profiles.R:66:3'): profiles functions with invalid inputs ────
  Expected `get_dose_response_profile(x = o, groups = groups, exponentiate = TRUE)` to produce warnings.
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 120 ]
  Error:
  ! Test failures.
  Execution halted
* 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: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/cellmig.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘cellmig’ ...
** this is package ‘cellmig’ version ‘1.1.7’
** using staged installation
** libs
specified C++17
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_M.cc -o stanExports_M.o
In file included from stanExports_M.cc:5:
In file included from ./stanExports_M.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_M.cc:5:
In file included from ./stanExports_M.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_M.cc:5:
In file included from ./stanExports_M.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_M.cc:5:
In file included from ./stanExports_M.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_M.cc:5:
In file included from ./stanExports_M.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_M.cc:5:
In file included from ./stanExports_M.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_M.cc:5:
In file included from ./stanExports_M.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_M.cc:5:
In file included from ./stanExports_M.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_M.cc:5:
./stanExports_M.h:737:11: 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_gen_F.cc -o stanExports_gen_F.o
In file included from stanExports_gen_F.cc:5:
In file included from ./stanExports_gen_F.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_gen_F.cc:5:
In file included from ./stanExports_gen_F.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_gen_F.cc:5:
In file included from ./stanExports_gen_F.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_gen_F.cc:5:
In file included from ./stanExports_gen_F.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_gen_F.cc:5:
In file included from ./stanExports_gen_F.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_gen_F.cc:5:
In file included from ./stanExports_gen_F.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_gen_F.cc:5:
In file included from ./stanExports_gen_F.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_gen_F.cc:5:
In file included from ./stanExports_gen_F.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_gen_F.cc:5:
./stanExports_gen_F.h:136:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
./stanExports_gen_F.h:328:20: warning: unused variable 'jacobian__' [-Wunused-variable]
    constexpr bool jacobian__ = false;
                   ^
./stanExports_gen_F.h:497:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
./stanExports_gen_F.h:514:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
      int pos__ = std::numeric_limits<int>::min();
          ^
13 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 cellmig.so RcppExports.o stanExports_M.o stanExports_gen_F.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-cellmig/00new/cellmig/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cellmig)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-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(cellmig)
> test_check("cellmig")

SAMPLING FOR MODEL 'M' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 8.1e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.81 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 500 [  0%]  (Warmup)
Chain 1: Iteration: 200 / 500 [ 40%]  (Warmup)
Chain 1: Iteration: 201 / 500 [ 40%]  (Sampling)
Chain 1: Iteration: 400 / 500 [ 80%]  (Sampling)
Chain 1: Iteration: 500 / 500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.798 seconds (Warm-up)
Chain 1:                0.457 seconds (Sampling)
Chain 1:                1.255 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'M' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0.000244 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 2.44 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 

SAMPLING FOR MODEL 'M' NOW (CHAIN 2).
Chain 1: Iteration:   1 / 900 [  0%]  (Warmup)
Chain 2: 
Chain 2: Gradient evaluation took 0.000278 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 2.78 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2: 
Chain 2: 
Chain 2: Iteration:   1 / 900 [  0%]  (Warmup)
Chain 2: Iteration: 200 / 900 [ 22%]  (Warmup)
Chain 2: Iteration: 201 / 900 [ 22%]  (Sampling)
Chain 1: Iteration: 200 / 900 [ 22%]  (Warmup)
Chain 1: Iteration: 201 / 900 [ 22%]  (Sampling)
Chain 1: Iteration: 400 / 900 [ 44%]  (Sampling)
Chain 2: Iteration: 400 / 900 [ 44%]  (Sampling)
Chain 1: Iteration: 600 / 900 [ 66%]  (Sampling)
Chain 1: Iteration: 800 / 900 [ 88%]  (Sampling)
Chain 2: Iteration: 600 / 900 [ 66%]  (Sampling)
Chain 1: Iteration: 900 / 900 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 2.58 seconds (Warm-up)
Chain 1:                2.666 seconds (Sampling)
Chain 1:                5.246 seconds (Total)
Chain 1: 
Chain 2: Iteration: 800 / 900 [ 88%]  (Sampling)
Chain 2: Iteration: 900 / 900 [100%]  (Sampling)
Chain 2: 
Chain 2:  Elapsed Time: 2.421 seconds (Warm-up)
Chain 2:                4.382 seconds (Sampling)
Chain 2:                6.803 seconds (Total)
Chain 2: 

SAMPLING FOR MODEL 'M' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 9.2e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.92 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 500 [  0%]  (Warmup)
Chain 1: Iteration: 200 / 500 [ 40%]  (Warmup)
Chain 1: Iteration: 201 / 500 [ 40%]  (Sampling)
Chain 1: Iteration: 400 / 500 [ 80%]  (Sampling)
Chain 1: Iteration: 500 / 500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 1.087 seconds (Warm-up)
Chain 1:                0.449 seconds (Sampling)
Chain 1:                1.536 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'M' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 6.5e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.65 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 500 [  0%]  (Warmup)
Chain 1: Iteration: 200 / 500 [ 40%]  (Warmup)
Chain 1: Iteration: 201 / 500 [ 40%]  (Sampling)
Chain 1: Iteration: 400 / 500 [ 80%]  (Sampling)
Chain 1: Iteration: 500 / 500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.862 seconds (Warm-up)
Chain 1:                0.828 seconds (Sampling)
Chain 1:                1.69 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'M' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 5.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.56 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 500 [  0%]  (Warmup)
Chain 1: Iteration: 200 / 500 [ 40%]  (Warmup)
Chain 1: Iteration: 201 / 500 [ 40%]  (Sampling)
Chain 1: Iteration: 400 / 500 [ 80%]  (Sampling)
Chain 1: Iteration: 500 / 500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.923 seconds (Warm-up)
Chain 1:                0.754 seconds (Sampling)
Chain 1:                1.677 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'M' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 5.6e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.56 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 500 [  0%]  (Warmup)
Chain 1: Iteration: 200 / 500 [ 40%]  (Warmup)
Chain 1: Iteration: 201 / 500 [ 40%]  (Sampling)
Chain 1: Iteration: 400 / 500 [ 80%]  (Sampling)
Chain 1: Iteration: 500 / 500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 0.729 seconds (Warm-up)
Chain 1:                0.435 seconds (Sampling)
Chain 1:                1.164 seconds (Total)
Chain 1: 

SAMPLING FOR MODEL 'M' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 8.7e-05 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.87 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 500 [  0%]  (Warmup)
Chain 1: Iteration: 200 / 500 [ 40%]  (Warmup)
Chain 1: Iteration: 201 / 500 [ 40%]  (Sampling)
Chain 1: Iteration: 400 / 500 [ 80%]  (Sampling)
Chain 1: Iteration: 500 / 500 [100%]  (Sampling)
Chain 1: 
Chain 1:  Elapsed Time: 1.701 seconds (Warm-up)
Chain 1:                1.22 seconds (Sampling)
Chain 1:                2.921 seconds (Total)
Chain 1: 
Saving _problems/test-profiles-68.R
Chain 1: 
Chain 1:  Elapsed Time: 0 seconds (Warm-up)
Chain 1:                0 seconds (Sampling)
Chain 1:                0 seconds (Total)
Chain 1: 
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 120 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-profiles.R:66:3'): profiles functions with invalid inputs ────
Expected `get_dose_response_profile(x = o, groups = groups, exponentiate = TRUE)` to produce warnings.

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 120 ]
Error:
! Test failures.
Execution halted