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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:epistasisGA.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings epistasisGA_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/epistasisGA.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘epistasisGA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘epistasisGA’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  download from 'https://CRAN.R-project.org/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/bioc/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/bioc/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/annotation/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/annotation/src/contrib/PACKAGES' failed
Warning: unable to access index for repository https://bioconductor.org/packages/3.17/data/experiment/src/contrib:
  download from 'https://bioconductor.org/packages/3.17/data/experiment/src/contrib/PACKAGES' failed
 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: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
* 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 R 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘E_GADGETS.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘GADGETS.Rmd’ using ‘UTF-8’... failed to complete the test
  ‘Including_Maternal_SNPs.Rmd’ using ‘UTF-8’... failed to complete the test
 ERROR
Errors in running code in vignettes:
when running code in ‘E_GADGETS.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.172   0.029   0.196 

... incomplete output.  Crash?
when running code in ‘GADGETS.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.162   0.042   0.198 

... incomplete output.  Crash?
when running code in ‘Including_Maternal_SNPs.Rmd’
  ...
> proc.time()
   user  system elapsed 
  0.182   0.017   0.194 

... incomplete output.  Crash?

* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... ERROR
Rd conversion errors:
Converting parsed Rd's to LaTeX Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error in writeLines(x, con, useBytes = TRUE, ...) : 
  Error writing to connection:  No space left on device
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/epistasisGA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL epistasisGA
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘epistasisGA’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/library/bigmemory/include' -I/usr/local/include    -fPIC  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.0/library/BH/include' -I'/home/biocbuild/R/R-4.3.0/library/bigmemory/include' -I/usr/local/include    -fPIC  -g -O2  -c epistasisGA.cpp -o epistasisGA.o
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  361 |     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
      |                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
      |                                                                 ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  507 |     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
      |                               ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  520 |     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
      |                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  603 |     shared_ptr & operator=( std::auto_ptr<Y> & r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/R/R-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  612 |     shared_ptr & operator=( std::auto_ptr<Y> && r )
      |                                  ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/R/R-4.3.0/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/R/R-4.3.0/library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/R/R-4.3.0/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-4.3.0/library/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  614 |         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10.3.1/bits/locale_conv.h:41,
                 from /usr/include/c++/10.3.1/locale:43,
                 from /usr/include/c++/10.3.1/iomanip:43,
                 from /home/biocbuild/R/R-4.3.0/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/R/R-4.3.0/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/10.3.1/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -L/home/biocbuild/R/R-4.3.0/lib -lRlapack -L/home/biocbuild/R/R-4.3.0/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R-4.3.0/lib -lR
installing to /home/biocbuild/R/R-4.3.0/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)