Package: genphen

Version: 1.10.3

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genphen.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings genphen_1.10.3.tar.gz

StartedAt: 2019-04-13 02:35:25 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 02:45:59 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 633.9 seconds

RetCode: 0

Status:  OK

CheckDir: genphen.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:genphen.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings genphen_1.10.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/genphen.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'genphen' can be installed ... OK
* 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 ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/genphen/libs/i386/genphen.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
runGenphen 0.74    0.1  239.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
runGenphen 1.38   0.19   63.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/genphen.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/genphen_1.10.3.tar.gz && rm -rf genphen.buildbin-libdir && mkdir genphen.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genphen.buildbin-libdir genphen_1.10.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL genphen_1.10.3.zip && rm genphen_1.10.3.tar.gz genphen_1.10.3.zip
###
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install for i386

* installing *source* package 'genphen' ...
** libs
"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/H.stan
Wrote C++ file "stan_files/H.cc"
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'boost_not_in_BH', package = 'rstan'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_NO_CXX11_RVALUE_REFERENCES -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c stan_files/H.cc -o stan_files/H.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
                 from C:/Users/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:
C:/Users/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.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                                                         ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
                 from C:/Users/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:
C:/Users/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() {
             ^
"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/U.stan
Wrote C++ file "stan_files/U.cc"
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'boost_not_in_BH', package = 'rstan'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_NO_CXX11_RVALUE_REFERENCES -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c stan_files/U.cc -o stan_files/U.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
                 from C:/Users/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:
C:/Users/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.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                                                         ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
                 from C:/Users/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:
C:/Users/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() {
             ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'boost_not_in_BH', package = 'rstan'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_NO_CXX11_RVALUE_REFERENCES -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o genphen.dll tmp.def stan_files/H.o stan_files/U.o init.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
rm stan_files/U.cc stan_files/H.cc
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/genphen.buildbin-libdir/genphen/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'genphen'
    finding HTML links ... done
    dichotomous.phenotype.saap              html  
    genotype.saap                           html  
    genotype.saap.msa                       html  
    genotype.snp                            html  
    genotype.snp.msa                        html  
    phenotype.saap                          html  
    phenotype.snp                           html  
    runDiagnostics                          html  
    runGenphen                              html  
    runPhyloBiasCheck                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'genphen' ...
** libs
"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/H.stan
Wrote C++ file "stan_files/H.cc"
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'boost_not_in_BH', package = 'rstan'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_NO_CXX11_RVALUE_REFERENCES -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c stan_files/H.cc -o stan_files/H.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
                 from C:/Users/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:
C:/Users/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.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                                                         ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
                 from C:/Users/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:
C:/Users/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() {
             ^
"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/U.stan
Wrote C++ file "stan_files/U.cc"
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'boost_not_in_BH', package = 'rstan'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_NO_CXX11_RVALUE_REFERENCES -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c stan_files/U.cc -o stan_files/U.o
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
                 from C:/Users/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:
C:/Users/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.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                                                         ^
In file included from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
                 from C:/Users/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:
C:/Users/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() {
             ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'boost_not_in_BH', package = 'rstan'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_NO_CXX11_RVALUE_REFERENCES -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o genphen.dll tmp.def stan_files/H.o stan_files/U.o init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
rm stan_files/U.cc stan_files/H.cc
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/genphen.buildbin-libdir/genphen/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genphen' as genphen_1.10.3.zip
* DONE (genphen)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'genphen' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
   4.35    0.25    4.59 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   4.28    0.29    4.57