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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings epistasisGA_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
* 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 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 ... 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 ... ERROR
Running examples in ‘epistasisGA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: global.test
> ### Title: A function to run a global test of the null hypothesis that
> ###   there are no SNP-disease associations across a range of chromosome
> ###   sizes
> ### Aliases: global.test
> 
> ### ** Examples
> 
> 
> data(case)
> data(dad)
> data(mom)
> case <- as.matrix(case)
> dad <- as.matrix(dad)
> mom <- as.matrix(mom)
> data(snp.annotations)
> set.seed(1400)
> 
> pp.list <- preprocess.genetic.data(case[, 1:10],
+                                father.genetic.data = dad[ , 1:10],
+                                mother.genetic.data = mom[ , 1:10],
+                                ld.block.vec = c(10))
> ## run GA for observed data
> 
> #observed data chromosome size 2
> run.gadgets(pp.list, n.chromosomes = 5, chromosome.size = 2,
+        results.dir = 'tmp_2',
+        cluster.type = 'interactive',
+        registryargs = list(file.dir = 'tmp_reg', seed = 1500),
+        generations = 2, n.islands = 2, island.cluster.size = 1,
+        n.migrations = 0)
No readable configuration file found
Created registry in '/home/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck/tmp_reg' using cluster functions 'Interactive'
Adding 2 jobs ...
Submitting 2 jobs in 1 chunks using cluster functions 'Interactive' ...
>  combined.res2 <- combine.islands('tmp_2', snp.annotations[ 1:10, ],
+                                   pp.list, 2)
>  unlink('tmp_reg', recursive = TRUE)
> 
>  #observed data chromosome size 3
>  run.gadgets(pp.list, n.chromosomes = 5, chromosome.size = 3,
+        results.dir = 'tmp_3',
+        cluster.type = 'interactive',
+        registryargs = list(file.dir = 'tmp_reg', seed = 1500),
+        generations = 2, n.islands = 2, island.cluster.size = 1,
+        n.migrations = 0)
No readable configuration file found
Created registry in '/home/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck/tmp_reg' using cluster functions 'Interactive'
Adding 2 jobs ...
Submitting 2 jobs in 1 chunks using cluster functions 'Interactive' ...
>  combined.res3 <- combine.islands('tmp_3', snp.annotations[ 1:10, ],
+                                   pp.list, 2)
>  unlink('tmp_reg', recursive = TRUE)
> 
> # create three permuted datasets
> set.seed(1400)
> perm.data.list <- permute.dataset(pp.list, "perm_data",
+                                   n.permutations = 3)
> 
> #pre-process permuted data
> case.p1 <- readRDS("perm_data/case.permute1.rds")
> comp.p1 <- readRDS("perm_data/complement.permute1.rds")
> p1.list <- preprocess.genetic.data(case.p1,
+                                    complement.genetic.data = comp.p1,
+                                     ld.block.vec = c(10))
> 
> case.p2 <- readRDS("perm_data/case.permute2.rds")
> comp.p2 <- readRDS("perm_data/complement.permute2.rds")
> p2.list <- preprocess.genetic.data(case.p2,
+                                    complement.genetic.data = comp.p2,
+                                     ld.block.vec = c(10))
> 
> case.p3 <- readRDS("perm_data/case.permute3.rds")
> comp.p3 <- readRDS("perm_data/complement.permute3.rds")
> p3.list <- preprocess.genetic.data(case.p3,
+                                    complement.genetic.data = comp.p3,
+                                    ld.block.vec = c(10))
> 
> #permutation 1, chromosome size 2
> run.gadgets(p1.list, n.chromosomes = 5, chromosome.size = 2,
+        results.dir = 'p1_tmp_2',
+        cluster.type = 'interactive',
+        registryargs = list(file.dir = 'tmp_reg', seed = 1500),
+        generations = 2, n.islands = 2, island.cluster.size = 1,
+        n.migrations = 0)
No readable configuration file found
Created registry in '/home/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck/tmp_reg' using cluster functions 'Interactive'
Adding 2 jobs ...
Submitting 2 jobs in 1 chunks using cluster functions 'Interactive' ...
>  p1.combined.res2 <- combine.islands('p1_tmp_2', snp.annotations[ 1:10, ],
+                                      p1.list, 2)
>  unlink('tmp_reg', recursive = TRUE)
> 
> #permutation 1, chromosome size 3
> run.gadgets(p1.list, n.chromosomes = 5, chromosome.size = 3,
+        results.dir = 'p1_tmp_3',
+        cluster.type = 'interactive',
+        registryargs = list(file.dir = 'tmp_reg', seed = 1500),
+        generations = 2, n.islands = 2, island.cluster.size = 1,
+        n.migrations = 0)
No readable configuration file found
Created registry in '/home/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck/tmp_reg' using cluster functions 'Interactive'
Adding 2 jobs ...
Submitting 2 jobs in 1 chunks using cluster functions 'Interactive' ...
>  p1.combined.res3 <- combine.islands('p1_tmp_3', snp.annotations[ 1:10, ],
+                                      p1.list, 2)
Error in risk.alleles[diff.vecs >= 0] <- alt.alleles[snp.numbers[diff.vecs >=  : 
  NAs are not allowed in subscripted assignments
Calls: combine.islands
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
GxE.test                 13.058 47.000  56.737
compute.graphical.scores 29.032  1.249  20.268
epistasis.test           11.167  0.973  10.243
* 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 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/epistasisGA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL epistasisGA
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘epistasisGA’ ...
** this is package ‘epistasisGA’ version ‘1.10.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/bigmemory/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include' -I'/home/biocbuild/R/R-devel_2025-02-19/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/R/R-devel_2025-02-19/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/R/R-devel_2025-02-19/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 /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/memory:78,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include/armadillo:38,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/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()
      |                               ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/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()
      |                      ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/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 )
      |                                  ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/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 )
      |                                  ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/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/R/R-devel_2025-02-19/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 );
      |                                      ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(testthat)
> library(epistasisGA)
> 
> test_check("epistasisGA")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  3.325   0.166   3.626