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This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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Package 388/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClustIRR 1.6.0  (landing page)
Simo Kitanovski
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/ClustIRR
git_branch: RELEASE_3_21
git_last_commit: b44e437
git_last_commit_date: 2025-04-15 13:21:55 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  

CHECK results for ClustIRR on kjohnson3

To the developers/maintainers of the ClustIRR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClustIRR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ClustIRR
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2025-04-21 18:41:41 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 18:46:39 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 297.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ClustIRR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ClustIRR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClustIRR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClustIRR’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ClustIRR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
* 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_summary: no visible binding for global variable ‘community’
get_beta_scatterplot : get_scatters: no visible binding for global
  variable ‘mean_x’
get_beta_scatterplot : get_scatters: no visible binding for global
  variable ‘mean_y’
get_beta_scatterplot : get_scatters: no visible binding for global
  variable ‘specificity’
get_beta_scatterplot : get_scatters: no visible binding for global
  variable ‘size_x’
get_beta_scatterplot : get_scatters: no visible binding for global
  variable ‘size_y’
get_beta_scatterplot: no visible binding for global variable
  ‘community’
get_beta_violins : get_violins: no visible binding for global variable
  ‘specificity’
get_beta_violins : get_violins: no visible binding for global variable
  ‘size’
get_beta_violins: no visible binding for global variable ‘community’
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..’
Undefined global functions or variables:
  ..count.. community mean_x mean_y size size_x size_y specificity
  x_adj y_adj
* checking Rd files ... NOTE
prepare_Rd: decode_communities.Rd:21-23: Dropping empty section \details
* 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 ... NOTE
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
dco                  59.682  2.248  61.664
get_ag_summary       58.652  2.747  60.817
get_beta_violins     58.670  2.610  60.524
get_beta_scatterplot 58.231  2.560  60.529
detect_communities    4.708  0.620   4.479
decode_communities    4.536  0.521   4.461
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/ClustIRR.Rcheck/00check.log’
for details.

Installation output

ClustIRR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘ClustIRR’ ...
** this is package ‘ClustIRR’ version ‘1.6.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.sdk’


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
5 warnings generated.


clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"../inst/include" -I"/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_dm.cc:5:
In file included from ./stanExports_dm.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_dm.cc:5:
./stanExports_dm.h:501:11: 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/4.5-arm64/Resources/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include' -I/opt/R/arm64/include    -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fPIC  -falign-functions=64 -Wall -g -O2   -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/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:26:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseCore:61:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseCore/TriangularSolver.h:273:13: warning: variable 'count' set but not used [-Wunused-but-set-variable]
      Index count = 0;
            ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/Sparse:29:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/SparseLU:35:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:78:9: warning: variable 'nsuper_et_post' set but not used [-Wunused-but-set-variable]
  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
        ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h:79:9: warning: variable 'nsuper_et' set but not used [-Wunused-but-set-variable]
  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
        ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:47:31: warning: 'rstan::io::r_cout_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:21:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/io/r_ostream.hpp:70:31: warning: 'rstan::io::r_cerr_streambuf::xsputn' hides overloaded virtual function [-Woverloaded-virtual]
      virtual std::streamsize xsputn(const char_type* s, int n) {
                              ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/c++/v1/streambuf:291:24: note: hidden overloaded virtual function 'std::basic_streambuf<char>::xsputn' declared here: type mismatch at 2nd parameter ('streamsize' (aka 'long') vs 'int')
    virtual streamsize xsputn(const char_type* __s, streamsize __n);
                       ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/IterativeSolvers:46:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/IterativeSolvers/IDRS.h:72:10: warning: variable 'replacements' set but not used [-Wunused-but-set-variable]
                        Index replacements = 0;
                              ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:31:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/RcppEigenForward.h:37:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:45:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppEigen/include/unsupported/Eigen/src/SparseExtra/MarketIO.h:246:7: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int count = 0;
      ^
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:43:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/src/stan/io/dump.hpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim.hpp:14:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun.hpp:35:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/fun/binomial_coefficient_log.hpp:13:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/partials_propagator.hpp:8:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:57:1: warning: 'ops_partials_edge' defined as a struct template here but previously declared as a class template; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
struct ops_partials_edge<ViewElt, Op, require_st_arithmetic<Op>> {
^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/StanHeaders/include/stan/math/prim/functor/operands_and_partials.hpp:45:1: note: did you mean struct here?
class ops_partials_edge;
^~~~~
struct
In file included from stanExports_dmh.cc:5:
In file included from ./stanExports_dmh.h:23:
In file included from /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/rstaninc.hpp:4:
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rstan/include/rstan/stan_fit.hpp:1252:9: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
    int ret = stan::services::error_codes::CONFIG;
        ^
In file included from stanExports_dmh.cc:5:
./stanExports_dmh.h:650:11: 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 ClustIRR.so RcppExports.o stanExports_dm.o stanExports_dmh.o -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib -ltbb -ltbbmalloc -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib/ -Wl,-rpath,/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/lib/ -ltbb -ltbbmalloc -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: ignoring duplicate libraries: '-ltbb', '-ltbbmalloc'
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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)

Tests output

ClustIRR.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 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(ClustIRR)
> test_check("ClustIRR")


Analyze database: 100.0% (100.0)                    
  Index database: 100.0% (100.0)                    
    Read queries: 100.0% (1986.0 Bytes)                    
    Read queries: 100.0% (1986.0 Bytes)                    
 Search database: 100.0% (100.0)                    
      Write hits: 100.0% (183.0)                    


Analyze database: 100.0% (100.0)                    
  Index database: 100.0% (100.0)                    
    Read queries: 100.0% (1946.0 Bytes)                    
    Read queries: 100.0% (1946.0 Bytes)                    
 Search database: 100.0% (100.0)                    
      Write hits: 100.0% (159.0)                    


Analyze database: 100.0% (99.0)                    
  Index database: 100.0% (99.0)                    
    Read queries: 100.0% (1965.0 Bytes)                    
    Read queries: 100.0% (1965.0 Bytes)                    
 Search database: 100.0% (99.0)                    
      Write hits: 100.0% (182.0)                    


Analyze database: 100.0% (100.0)                    
  Index database: 100.0% (100.0)                    
    Read queries: 100.0% (1946.0 Bytes)                    
    Read queries: 100.0% (1946.0 Bytes)                    
 Search database: 100.0% (100.0)                    
      Write hits: 100.0% (159.0)                    


Analyze database: 100.0% (1.0)                    
  Index database: 100.0% (1.0)                    
    Read queries: 100.0% (19.0 Bytes)                    
 Search database: 100.0% (1.0)                    
      Write hits: 100.0% (1.0)                    


Analyze database: 100.0% (1.0)                    
  Index database: 100.0% (1.0)                    
    Read queries: 100.0% (18.0 Bytes)                    
 Search database: 100.0% (1.0)                    
      Write hits: 100.0% (1.0)                    


Analyze database: 100.0% (99.0)                    
  Index database: 100.0% (99.0)                    
    Read queries: 100.0% (1965.0 Bytes)                    
    Read queries: 100.0% (1965.0 Bytes)                    
 Search database: 100.0% (99.0)                    
      Write hits: 100.0% (182.0)                    


Analyze database: 100.0% (99.0)                    
  Index database: 100.0% (99.0)                    
    Read queries: 100.0% (1926.0 Bytes)                    
    Read queries: 100.0% (1926.0 Bytes)                    
 Search database: 100.0% (99.0)                    
      Write hits: 100.0% (150.0)                    


[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
  2.834   0.329   4.628

Example timings

ClustIRR.Rcheck/ClustIRR-Ex.timings

nameusersystemelapsed
BLOSUM620.0010.0020.003
CDR3ab0.0220.0010.025
clust_irr-class0.3050.0250.360
clustirr0.2580.0210.316
dco59.682 2.24861.664
decode_communities4.5360.5214.461
detect_communities4.7080.6204.479
get_ag_summary58.652 2.74760.817
get_beta_scatterplot58.231 2.56060.529
get_beta_violins58.670 2.61060.524
get_honeycombs2.0040.3953.289
mcpas0.0290.0010.030
plot_graph0.2380.0360.297
tcr3d0.0010.0010.001
vdjdb0.0830.0010.085