genphen 1.11.23
Simo Kitanovski
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/genphen |
| Branch: master |
| Last Commit: 8b53390 |
| Last Changed Date: 2019-03-15 08:41:52 -0400 (Fri, 15 Mar 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| merida2 | 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://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/genphen_1.11.23.tar.gz && rm -rf genphen.buildbin-libdir && mkdir genphen.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genphen.buildbin-libdir genphen_1.11.23.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL genphen_1.11.23.zip && rm genphen_1.11.23.tar.gz genphen_1.11.23.zip
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install for i386
* installing *source* package 'genphen' ...
** libs
"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/H.stan
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Wrote C++ file "stan_files/H.cc"
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-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-3.9-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
from C:/Users/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
from C:/Users/biocbuild/bbs-3.9-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-3.9-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˜1.9-B/R/bin/i386/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/U.stan
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Wrote C++ file "stan_files/U.cc"
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-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-3.9-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
from C:/Users/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
from C:/Users/biocbuild/bbs-3.9-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-3.9-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˜1.9-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-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-3.9-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/bin/i386 -lR
rm stan_files/U.cc stan_files/H.cc
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/genphen.buildbin-libdir/00LOCK-genphen/00new/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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'genphen' ...
** libs
"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/H.stan
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Wrote C++ file "stan_files/H.cc"
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-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-3.9-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
from C:/Users/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
from C:/Users/biocbuild/bbs-3.9-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-3.9-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˜1.9-B/R/bin/x64/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/U.stan
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Wrote C++ file "stan_files/U.cc"
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-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-3.9-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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-3.9-bioc/R/library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/detail/const_mod.hpp:23,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/linear_congruential.hpp:30,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include/boost/random/additive_combine.hpp:27,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:15,
from C:/Users/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
from C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include/rstan/stan_fit.hpp:34,
from C:/Users/biocbuild/bbs-3.9-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-3.9-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˜1.9-B/R/include" -DNDEBUG -I"../inst/include" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -I"`"C:/Users/BIOCBU˜1/BBS-3˜1.9-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-3.9-bioc/R/library/StanHeaders/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/rstan/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/BH/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-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˜1.9-B/R/bin/x64 -lR
rm stan_files/U.cc stan_files/H.cc
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/genphen.buildbin-libdir/genphen/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genphen' as genphen_1.11.23.zip
* DONE (genphen)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'genphen' successfully unpacked and MD5 sums checked