##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClustIRR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClustIRR_1.9.32.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ClustIRR.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-10 23:21:24 UTC
* using option ‘--no-vignettes’
* checking for file ‘ClustIRR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClustIRR’ version ‘1.9.32’
* 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 ‘ClustIRR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
* used SDK: ‘MacOSX26.2.sdk’
* checking C++ specification ... INFO
  specified C++17
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
get_ag_gene_hits: no visible binding for global variable ‘cells’
get_ag_gene_hits: no visible binding for global variable ‘clones’
get_ag_gene_hits: no visible binding for global variable ‘community’
get_ag_gene_hits: no visible binding for global variable ‘ag’
get_ag_species_hits: no visible binding for global variable ‘cells’
get_ag_species_hits: no visible binding for global variable ‘clones’
get_ag_species_hits: no visible binding for global variable ‘community’
get_ag_species_hits: no visible binding for global variable ‘ag’
get_beta_cprob_ag: no visible binding for global variable ‘b’
get_beta_cprob_ag: no visible binding for global variable ‘p_ag’
get_beta_cprob_ag: no visible binding for global variable ‘p_b’
get_beta_violin_ag: no visible binding for global variable ‘spec’
get_beta_violin_ag: no visible binding for global variable ‘size’
get_cdr3_motifs: no visible binding for global variable ‘clone_size’
get_community_summary : get_estats: no visible binding for global
  variable ‘community’
get_community_summary : get_estats: no visible binding for global
  variable ‘nweight’
get_community_summary : get_estats: no visible binding for global
  variable ‘ncweight’
get_community_summary : get_estats: no visible binding for global
  variable ‘w’
get_community_summary : get_estats: no visible binding for global
  variable ‘n_edges’
get_cosine_similarity: no visible binding for global variable ‘i’
get_cosine_similarity: no visible binding for global variable ‘j’
get_cosine_similarity: no visible binding for global variable ‘CS’
get_honeycombs: no visible binding for global variable ‘x_adj’
get_honeycombs: no visible binding for global variable ‘y_adj’
get_honeycombs: no visible binding for global variable ‘..count..’
get_intergraph_edges : get_ix: no visible binding for global variable
  ‘Var1’
get_intergraph_edges : get_ix: no visible binding for global variable
  ‘Var2’
get_score: no visible binding for global variable ‘from’
get_score: no visible binding for global variable ‘nweight’
get_score_pair: no visible binding for global variable ‘from’
get_score_pair: no visible binding for global variable ‘nweight’
Undefined global functions or variables:
  ..count.. CS Var1 Var2 ag b cells clone_size clones community from i
  j n_edges ncweight nweight p_ag p_b size spec w x_adj y_adj
* 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
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/ClustIRR.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘ClustIRR’ ...
** this is package ‘ClustIRR’ version ‘1.9.32’
** using staged installation
** libs
specified C++17
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++17
using SDK: ‘MacOSX26.2.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/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/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.6/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/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Library/Frameworks/R.framework/Versions/4.6/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]
   79 |   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/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   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/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/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_dm.cc -o stanExports_dm.o
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Library/Frameworks/R.framework/Versions/4.6/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   47 |       virtual std::streamsize xsputn(const char_type* s, int n) {
      |                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/streambuf:343:22: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
  343 |   virtual streamsize xsputn(const char_type* __s, streamsize __n) {
      |                      ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   70 |       virtual std::streamsize xsputn(const char_type* s, int n) {
      |                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/streambuf:343:22: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
  343 |   virtual streamsize xsputn(const char_type* __s, streamsize __n) {
      |                      ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.6/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]
   57 | struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
      | ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
   45 | class ops_partials_edge;
      | ^~~~~
      | struct
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^
In file included from stanExports_dm.cc:5:
./stanExports_dm.h:492:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
  492 |       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/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/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c stanExports_dmh.cc -o stanExports_dmh.o
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  273 |       Index count = 0;
      |             ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.6/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]
   78 |   Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
      |         ^
/Library/Frameworks/R.framework/Versions/4.6/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]
   79 |   Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
      |         ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   47 |       virtual std::streamsize xsputn(const char_type* s, int n) {
      |                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/streambuf:343:22: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
  343 |   virtual streamsize xsputn(const char_type* __s, streamsize __n) {
      |                      ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
   70 |       virtual std::streamsize xsputn(const char_type* s, int n) {
      |                               ^
/Library/Developer/CommandLineTools/SDKs/MacOSX26.sdk/usr/include/c++/v1/streambuf:343:22: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
  343 |   virtual streamsize xsputn(const char_type* __s, streamsize __n) {
      |                      ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
   72 |                         Index replacements = 0;
      |                               ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  246 |   int count = 0;
      |       ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.6/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]
   57 | struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
      | ^
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
   45 | class ops_partials_edge;
      | ^~~~~
      | struct
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.6/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
 1252 |     int ret = stan::services::error_codes::CONFIG;
      |         ^
In file included from stanExports_dmh.cc:5:
./stanExports_dmh.h:660:11: warning: variable 'pos__' set but not used [-Wunused-but-set-variable]
  660 |       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 ClustIRR.so RcppExports.o stanExports_dm.o stanExports_dmh.o -L/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.6/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/Resources/library/00LOCK-ClustIRR/00new/ClustIRR/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 (ClustIRR)

R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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> library(testthat)
> library(ClustIRR)
> library(rBLAST)
Loading required package: Biostrings
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
Loading required package: stats4

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: XVector
Loading required package: Seqinfo

Attaching package: 'Biostrings'

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

    strsplit

> test_check("ClustIRR")
[ FAIL 0 | WARN 0 | SKIP 5 | PASS 0 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• BLAST+ is not installed. (5): 'test-cdr3_na.R:1:1', 'test-get_blosum.R:1:1',
  'test-multi-chain-clustering.R:1:1', 'test-s.R:1:1',
  'test-save_interactive_graph.R:1:1'

[ FAIL 0 | WARN 0 | SKIP 5 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  2.661   0.221   2.792