Package: mlm4omics

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mlm4omics.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings mlm4omics_1.2.0.tar.gz

StartedAt: 2019-06-14 05:08:03 -0400 (Fri, 14 Jun 2019)

EndedAt: 2019-06-14 05:10:36 -0400 (Fri, 14 Jun 2019)

EllapsedTime: 153.8 seconds

RetCode: 0

Status:  OK

CheckDir: mlm4omics.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mlm4omics.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings mlm4omics_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/mlm4omics.Rcheck'
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'mlm4omics/DESCRIPTION' ... OK
* this is package 'mlm4omics' version '1.2.0'
* 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 whether package 'mlm4omics' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/mlm4omics.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
* 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-3.9-bioc/R/library/mlm4omics/libs/i386/mlm4omics.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/mlm4omics/libs/x64/mlm4omics.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
mlmc 0.76    0.1   11.63
** running examples for arch 'x64' ... OK
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/mlm4omics.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/mlm4omics_1.2.0.tar.gz && rm -rf mlm4omics.buildbin-libdir && mkdir mlm4omics.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mlm4omics.buildbin-libdir mlm4omics_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL mlm4omics_1.2.0.zip && rm mlm4omics_1.2.0.tar.gz mlm4omics_1.2.0.zip
###
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100 47335  100 47335    0     0   741k      0 --:--:-- --:--:-- --:--:--  840k

install for i386

* installing *source* package 'mlm4omics' ...
** using staged installation
** 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/mlmc_code.stan
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Wrote C++ file "stan_files/mlmc_code.cc"
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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/mlmc_code.cc -o stan_files/mlmc_code.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/mlmc_code.hpp:18,
                 from stan_files/mlmc_code.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/mlmc_code.hpp:18,
                 from stan_files/mlmc_code.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/mmlm_code.stan
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Wrote C++ file "stan_files/mmlm_code.cc"
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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/mmlm_code.cc -o stan_files/mmlm_code.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/mmlm_code.hpp:18,
                 from stan_files/mmlm_code.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/mmlm_code.hpp:18,
                 from stan_files/mmlm_code.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 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˜1.9-B/R/bin/i386 -lR
rm stan_files/mmlm_code.cc stan_files/mlmc_code.cc
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/mlm4omics.buildbin-libdir/00LOCK-mlm4omics/00new/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 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 'mlm4omics' ...
** using non-staged installation
** 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/mlmc_code.stan
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Wrote C++ file "stan_files/mlmc_code.cc"
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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/mlmc_code.cc -o stan_files/mlmc_code.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/mlmc_code.hpp:18,
                 from stan_files/mlmc_code.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/mlmc_code.hpp:18,
                 from stan_files/mlmc_code.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/mmlm_code.stan
Registered S3 methods overwritten by 'ggplot2':
  method         from 
  [.quosures     rlang
  c.quosures     rlang
  print.quosures rlang
Wrote C++ file "stan_files/mmlm_code.cc"
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-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/mmlm_code.cc -o stan_files/mmlm_code.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/mmlm_code.hpp:18,
                 from stan_files/mmlm_code.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/mmlm_code.hpp:18,
                 from stan_files/mmlm_code.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 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˜1.9-B/R/bin/x64 -lR
rm stan_files/mmlm_code.cc stan_files/mlmc_code.cc
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/mlm4omics.buildbin-libdir/mlm4omics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mlm4omics' as mlm4omics_1.2.0.zip
* DONE (mlm4omics)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'mlm4omics' successfully unpacked and MD5 sums checked

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
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(Rcpp)
> library(mlm4omics)
> 
> test_check("mlm4omics")
[1] "errors in data"
[1] "errors in data"
[1] "errors in data"
[1] "errors in data"
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 WARNINGS: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.57    0.28    2.82 

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
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(Rcpp)
> library(mlm4omics)
> 
> test_check("mlm4omics")
[1] "errors in data"
[1] "errors in data"
[1] "errors in data"
[1] "errors in data"
== testthat results  ===========================================================
OK: 3 SKIPPED: 0 WARNINGS: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.64    0.21    2.84