Package: mlm4omics

Version: 0.99.22

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:mlm4omics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings mlm4omics_0.99.22.tar.gz

StartedAt: 2018-10-07 02:17:53 -0400 (Sun, 07 Oct 2018)

EndedAt: 2018-10-07 02:18:44 -0400 (Sun, 07 Oct 2018)

EllapsedTime: 51.3 seconds

RetCode: 0

Status:  OK

CheckDir: mlm4omics.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:mlm4omics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings mlm4omics_0.99.22.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/mlm4omics.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mlm4omics/DESCRIPTION’ ... OK
* this is package ‘mlm4omics’ version ‘0.99.22’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘mlm4omics’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 48.6Mb
  sub-directories of 1Mb or more:
    libs  48.3Mb
* 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/mlm4omics.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL mlm4omics
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘mlm4omics’ ...
** libs
"/home/biocbuild/bbs-3.8-bioc/R/bin/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"
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"`"/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c stan_files/mmlm_code.cc -o stan_files/mmlm_code.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:36,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/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:
/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:65:18: warning: ‘stan::math::NEGATIVE_EPSILON’ defined but not used [-Wunused-variable]
     const double NEGATIVE_EPSILON
                  ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/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:
/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:17: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
     static void set_zero_all_adjoints() {
                 ^
"/home/biocbuild/bbs-3.8-bioc/R/bin/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"
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"`"/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c stan_files/mlmc_code.cc -o stan_files/mlmc_code.o
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:36,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/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:
/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:65:18: warning: ‘stan::math::NEGATIVE_EPSILON’ defined but not used [-Wunused-variable]
     const double NEGATIVE_EPSILON
                  ^
In file included from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core.hpp:44:0,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/log_prob_grad.hpp:4,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/model/test_gradients.hpp:7,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/src/stan/services/diagnose/diagnose.hpp:10,
                 from /home/biocbuild/bbs-3.8-bioc/R/library/rstan/include/rstan/stan_fit.hpp:35,
                 from /home/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:
/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_adjoints.hpp:14:17: warning: ‘void stan::math::set_zero_all_adjoints()’ defined but not used [-Wunused-function]
     static void set_zero_all_adjoints() {
                 ^
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"../inst/include" -I"`"/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript" --vanilla -e "cat(system.file('include', 'src', package = 'StanHeaders'))"`" -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -I"/home/biocbuild/bbs-3.8-bioc/R/library/StanHeaders/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/rstan/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/BH/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o mlm4omics.so stan_files/mmlm_code.o stan_files/mlmc_code.o init.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
rm stan_files/mlmc_code.cc stan_files/mmlm_code.cc
installing to /home/biocbuild/bbs-3.8-bioc/R/library/mlm4omics/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mlm4omics)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  2.040   0.076   2.108 

name	user	system	elapsed
mlmc	0.452	0.004	0.456
mlmm	0.744	0.012	0.759
setinitvalues	0.004	0.000	0.004