genphen 1.10.3
Simo Kitanovski
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### 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