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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings epistasisGA_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epistasisGA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epistasisGA’ version ‘1.10.0’
* 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:391:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  epistasisGA.cpp:970:17: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  epistasisGA.cpp:970:54: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  epistasisGA.cpp:1045:68: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  epistasisGA.cpp:1382:55: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
  epistasisGA.cpp:1952:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
  epistasisGA.cpp:2511:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
  epistasisGA.cpp:2736:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) GADGETS.Rd:158: Lost braces
   158 | the cluster. See code{run.gadgets} for additional 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 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 ... 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
compute.graphical.scores 31.741  2.726  23.203
network.plot             30.866  2.219  22.360
GxE.test                 12.069  0.886  11.907
epistasis.test           10.964  1.476  10.879
global.test               9.495  2.208   9.898
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL epistasisGA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘epistasisGA’ ...
** this is package ‘epistasisGA’ version ‘1.10.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/bigmemory/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/bigmemory/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c epistasisGA.cpp -o epistasisGA.o
epistasisGA.cpp:391:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
      if ((x(this_row , this_col) == 1) & (y(this_row, this_col) == 1)){
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                        &&
epistasisGA.cpp:391:11: note: cast one or both operands to int to silence this warning
epistasisGA.cpp:970:17: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
         !arma::is_finite(n_case_high_risk) | !arma::is_finite(n_comp_high_risk)){
                ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
[[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
  ^
epistasisGA.cpp:970:54: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
         !arma::is_finite(n_case_high_risk) | !arma::is_finite(n_comp_high_risk)){
                                                     ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
[[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
  ^
epistasisGA.cpp:1045:68: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
    if ( (fitness_score <= 0) | R_isnancpp(fitness_score) | !arma::is_finite(fitness_score) ){
                                                                   ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
[[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
  ^
epistasisGA.cpp:1382:55: warning: 'is_finite<double>' is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
            if ( (s <= 0) | (R_isnancpp(s)) | (!arma::is_finite(s)) | any(H_Einv_diag <= 0)){
                                                      ^
/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:164:3: note: 'is_finite<double>' has been explicitly marked deprecated here
[[deprecated("change arma::is_finite(val) to std::isfinite(val)")]]
  ^
epistasisGA.cpp:1952:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
        if ( (mutated_snps.length() != unique(mutated_snps).length()) | (sum(in(mutated_snps, target_chrom)) > 0) ){
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                      ||
epistasisGA.cpp:1952:14: note: cast one or both operands to int to silence this warning
epistasisGA.cpp:2511:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
    if ((is_true(any(mom_snps_l))) & (is_true(any(child_snps_l)))){
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   &&
epistasisGA.cpp:2511:9: note: cast one or both operands to int to silence this warning
epistasisGA.cpp:2736:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
      if (null_mean_vec_.isNotNull() & null_se_vec_.isNotNull()){
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                     &&
epistasisGA.cpp:2736:11: note: cast one or both operands to int to silence this warning
8 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 epistasisGA.so RcppExports.o epistasisGA.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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 version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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.

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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(epistasisGA)
> 
> test_check("epistasisGA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  3.673   0.335   3.995