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CHECK report for genphen on malbec1

This page was generated on 2019-04-16 11:51:58 -0400 (Tue, 16 Apr 2019).

Package 634/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genphen 1.10.3
Simo Kitanovski
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/genphen
Branch: RELEASE_3_8
Last Commit: 4224c97
Last Changed Date: 2019-03-11 12:57:15 -0400 (Mon, 11 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: genphen
Version: 1.10.3
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:genphen.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings genphen_1.10.3.tar.gz
StartedAt: 2019-04-16 00:15:39 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:18:41 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 181.6 seconds
RetCode: 0
Status:  OK 
CheckDir: genphen.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:genphen.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings genphen_1.10.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/genphen.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genphen/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genphen’ version ‘1.10.3’
* 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 ‘genphen’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 41.0Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
* 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 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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
runGenphen 39.94  0.348   57.25
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/genphen.Rcheck/00check.log’
for details.

Installation output

genphen.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL genphen
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘genphen’ ...
** libs
"/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/H.stan
Wrote C++ file "stan_files/H.cc"


g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c stan_files/H.cc -o stan_files/H.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/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-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp: At global scope:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:44,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:325,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/H.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/H.hpp:18,
                 from stan_files/H.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
 static void set_zero_all_adjoints() {
             ^
"/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/U.stan
Wrote C++ file "stan_files/U.cc"


g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c stan_files/U.cc -o stan_files/U.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/shared_ptr.hpp:17:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/time_clock.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time_types.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/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-3.8-bioc/R/library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp: At global scope:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/pending/integer_log2.hpp:7:89: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/invocation/detail/that_ptr.hpp:13:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/invocation/invoke.hpp:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/adapter/fused.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/functional/generation/make_fused.hpp:13,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/fusion/include/make_fused.hpp:11,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/resize.hpp:28,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/state_wrapper.hpp:26,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint/util/ublas_wrapper.hpp:33,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/numeric/odeint.hpp:25,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp:17,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/arr.hpp:44,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/mat.hpp:325,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:12,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template<class T> T * get_pointer(std::auto_ptr<T> const& p)
                                        ^
In file included from /usr/include/c++/5/bits/locale_conv.h:41:0,
                 from /usr/include/c++/5/locale:43,
                 from /usr/include/c++/5/iomanip:43,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/RcppCommon.h:52,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include/Rcpp.h:27,
                 from stan_files/U.cc:1:
/usr/include/c++/5/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/rstaninc.hpp:3,
                 from stan_files/U.hpp:18,
                 from stan_files/U.cc:3:
/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:13: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
 static void set_zero_all_adjoints() {
             ^


g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2 -Wall -c init.cpp -o init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o genphen.so stan_files/H.o stan_files/U.o init.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
rm stan_files/H.cc stan_files/U.cc
installing to /home/biocbuild/bbs-3.8-bioc/R/library/genphen/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genphen)

Tests output

genphen.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

R is a collaborative project with many contributors.
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(genphen)
Loading required package: Rcpp
> 
> test_check("genphen")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 21 SKIPPED: 0 FAILED: 0
> 
> # Once you’re set up the workflow is simple:
> # 1. Modify your code or tests.
> # 2. Test your package with Ctrl/Cmd + Shift + T or devtools::test().
> # 3. Repeat until all tests pass.
> 
> 
> # library(testthat)
> # devtools::test()
> 
> proc.time()
   user  system elapsed 
  5.172   0.164   5.350

Example timings

genphen.Rcheck/genphen-Ex.timings

nameusersystemelapsed
dichotomous.phenotype.saap0.0120.0000.012
genotype.saap0.0040.0000.007
genotype.saap.msa0.0000.0000.002
genotype.snp0.0040.0000.003
genotype.snp.msa0.0040.0000.002
phenotype.saap0.0000.0000.001
phenotype.snp0.0000.0000.001
runDiagnostics2.2320.1600.982
runGenphen39.940 0.34857.250
runPhyloBiasCheck1.6120.0001.616