mlm4omics 1.0.1
Irene SL Zeng
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/mlm4omics |
| Branch: RELEASE_3_8 |
| Last Commit: 308441f |
| Last Changed Date: 2019-01-04 13:39:43 -0400 (Fri, 04 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | ERROR | ERROR | skipped | | |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | ERROR | ERROR | skipped | skipped | |
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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/mlm4omics_1.0.1.tar.gz && rm -rf mlm4omics.buildbin-libdir && mkdir mlm4omics.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mlm4omics.buildbin-libdir mlm4omics_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL mlm4omics_1.0.1.zip && rm mlm4omics_1.0.1.tar.gz mlm4omics_1.0.1.zip
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install for i386
* installing *source* package 'mlm4omics' ...
** 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/mlmc_code.stan
Wrote C++ file "stan_files/mlmc_code.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/mlmc_code.cc -o stan_files/mlmc_code.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/mlmc_code.hpp:18,
from stan_files/mlmc_code.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/mlmc_code.hpp:18,
from stan_files/mlmc_code.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/mmlm_code.stan
Wrote C++ file "stan_files/mmlm_code.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/mmlm_code.cc -o stan_files/mmlm_code.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/mmlm_code.hpp:18,
from stan_files/mmlm_code.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/mmlm_code.hpp:18,
from stan_files/mmlm_code.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 mlm4omics.dll tmp.def stan_files/mlmc_code.o stan_files/mmlm_code.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/mmlm_code.cc stan_files/mlmc_code.cc
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/mlm4omics.buildbin-libdir/mlm4omics/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'mlm4omics'
finding HTML links ... done
mlm4omics-package html
mlmc html
mlmm html
pdata html
setinitvalues html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'mlm4omics' ...
** 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/mlmc_code.stan
Wrote C++ file "stan_files/mlmc_code.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/mlmc_code.cc -o stan_files/mlmc_code.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/mlmc_code.hpp:18,
from stan_files/mlmc_code.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/mlmc_code.hpp:18,
from stan_files/mlmc_code.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/mmlm_code.stan
Wrote C++ file "stan_files/mmlm_code.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/mmlm_code.cc -o stan_files/mmlm_code.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/mmlm_code.hpp:18,
from stan_files/mmlm_code.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/mmlm_code.hpp:18,
from stan_files/mmlm_code.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 mlm4omics.dll tmp.def stan_files/mlmc_code.o stan_files/mmlm_code.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/mmlm_code.cc stan_files/mlmc_code.cc
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/mlm4omics.buildbin-libdir/mlm4omics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mlm4omics' as mlm4omics_1.0.1.zip
* DONE (mlm4omics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'mlm4omics' successfully unpacked and MD5 sums checked
In R CMD INSTALL