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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings epistasisGA_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/epistasisGA.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘epistasisGA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epistasisGA’ version ‘1.13.0’
* 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 ‘epistasisGA’ can be installed ... WARNING
Found the following significant warnings:
  epistasisGA.cpp:970:26: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  epistasisGA.cpp:970:63: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  epistasisGA.cpp:1045:77: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  epistasisGA.cpp:1399:64: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.23-bioc/meat/epistasisGA.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking 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 ... OK
* 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
network.plot             29.471  0.962  23.311
compute.graphical.scores 27.569  1.208  18.989
GxE.test                 24.559  2.650  28.941
epistasis.test            9.656  1.130   9.286
global.test               8.811  1.647   8.910
GADGETS                   8.417  1.037  14.381
preprocess.genetic.data   5.892  0.961   7.705
run.gadgets               5.301  0.892   6.186
permute.dataset           5.099  0.880   6.492
combine.islands           4.747  1.181   5.266
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/epistasisGA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL epistasisGA
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘epistasisGA’ ...
** this is package ‘epistasisGA’ version ‘1.13.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/bigmemory/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/bigmemory/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c epistasisGA.cpp -o epistasisGA.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:326:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/13/memory:78,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo:38,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
                 from epistasisGA.cpp:1:
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  354 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  365 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  423 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  430 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  432 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
/usr/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
epistasisGA.cpp: In function ‘Rcpp::List chrom_fitness_score(Rcpp::IntegerMatrix, Rcpp::IntegerMatrix, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::IntegerVector, int, int, double, double, bool)’:
epistasisGA.cpp:970:26: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  970 |          !arma::is_finite(n_case_high_risk) | !arma::is_finite(n_comp_high_risk)){
      |           ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo:518:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
epistasisGA.cpp:970:63: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  970 |          !arma::is_finite(n_case_high_risk) | !arma::is_finite(n_comp_high_risk)){
      |                                                ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
epistasisGA.cpp:1045:77: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
 1045 |     if ( (fitness_score <= 0) | R_isnancpp(fitness_score) | !arma::is_finite(fitness_score) ){
      |                                                              ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
epistasisGA.cpp: In function ‘Rcpp::List GxE_fitness_score_mvlm(Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, arma::uvec, arma::vec, arma::vec, arma::vec, bool, Rcpp::NumericVector, int, int, bool)’:
epistasisGA.cpp:1115:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1115 |         for (int i = 0; i < exposure_mat.n_rows; i++){
      |                         ~~^~~~~~~~~~~~~~~~~~~~~
epistasisGA.cpp:1212:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
 1212 |         for (int i = 1; i < beta_full.n_rows; i++){
      |                         ~~^~~~~~~~~~~~~~~~~~
epistasisGA.cpp:1399:64: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<eT>::result*) [with eT = double; typename arma_scalar_only<eT>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
 1399 |             if ( (s <= 0) | (R_isnancpp(s)) | (!arma::is_finite(s)) | any(H_Einv_diag <= 0)){
      |                                                 ~~~~~~~~~~~~~~~^~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
  167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
      | ^~~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-epistasisGA/00new/epistasisGA/libs
** R
** data
** 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 (epistasisGA)

R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(epistasisGA)
> 
> test_check("epistasisGA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  8.907   0.710   9.632