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This page was generated on 2023-04-12 10:55:36 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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INSTALL results for epistasisGA on nebbiolo2


To the developers/maintainers of the epistasisGA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epistasisGA.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 640/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epistasisGA 1.1.4  (landing page)
Michael Nodzenski
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/epistasisGA
git_branch: devel
git_last_commit: e497130
git_last_commit_date: 2023-01-10 13:44:57 -0400 (Tue, 10 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: epistasisGA
Version: 1.1.4
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL epistasisGA
StartedAt: 2023-04-12 01:54:05 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 01:55:34 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 89.2 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL epistasisGA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘epistasisGA’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c epistasisGA.cpp -o epistasisGA.o
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/lexical_cast.hpp:30,
                 from epistasisGA.cpp:2:
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/site-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++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/site-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++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/site-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++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/site-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++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/site-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++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-bioc/R/site-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++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /home/biocbuild/bbs-3.17-bioc/R/site-library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/bigmemory/include/bigmemory/BigMatrix.h:10,
                 from epistasisGA.cpp:7:
/home/biocbuild/bbs-3.17-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-3.17-bioc/R/site-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++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include/RcppCommon.h:53,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:25,
                 from /home/biocbuild/bbs-3.17-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from epistasisGA.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o epistasisGA.so RcppExports.o epistasisGA.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.17-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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)