Multiple platform build/check report for BioC 3.9 - CHECK report for martini on tokay2

Package: martini

Version: 1.3.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:martini.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings martini_1.3.1.tar.gz

StartedAt: 2019-04-09 03:58:22 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:03:10 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 287.4 seconds

RetCode: 0

Status: OK

CheckDir: martini.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:martini.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings martini_1.3.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/martini.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'martini/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'martini' version '1.3.1'
* 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 'martini' can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
get_GI_network: no visible binding for global variable 'gene1'
get_GI_network: no visible binding for global variable 'gene2'
get_GM_network: no visible binding for global variable 'gene'
test_cones_modules : <anonymous> : <anonymous>: no visible binding for
  global variable 'snp'
Undefined global functions or variables:
  gene gene1 gene2 snp
* 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 ... OK
* 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/martini/libs/i386/martini.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/martini/libs/x64/martini.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
get_ppi 0.47   0.06    9.83
** 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/martini.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/martini_1.3.1.tar.gz && rm -rf martini.buildbin-libdir && mkdir martini.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=martini.buildbin-libdir martini_1.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL martini_1.3.1.zip && rm martini_1.3.1.tar.gz martini_1.3.1.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2502k  100 2502k    0     0  26.0M      0 --:--:-- --:--:-- --:--:-- 28.0M

install for i386

* installing *source* package 'martini' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/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 RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:61:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include/RcppEigenForward.h:26,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from ../inst/include/martini_RcppExports.h:7,
                 from ../inst/include/martini.h:7,
                 from RcppExports.cpp:4:
RcppExports.cpp: In function 'SEXPREC* _martini_run_scones_try(SEXP, SEXP, SEXP, SEXP)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable 'nprot' [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:29:1: note: in expansion of macro 'BEGIN_RCPP'
 BEGIN_RCPP
 ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable 'stop_sym' [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:29:1: note: in expansion of macro 'BEGIN_RCPP'
 BEGIN_RCPP
 ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/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 evo.cpp -o evo.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/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 run_scones.cpp -o run_scones.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o martini.dll tmp.def RcppExports.o evo.o run_scones.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/usrlib/i386/libgin.a C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/usrlib/i386/libmaxflow.a C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/usrlib/i386/libcephes.a -lz -pthread -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/martini.buildbin-libdir/00LOCK-martini/00new/martini/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 'martini'
    finding HTML links ... done
    arrange_covars                          html  
    calculateE                              html  
    calculateG                              html  
    check_installed                         html  
    encode_gwas                             html  
    evo                                     html  
    get_GI_network                          html  
    get_GM_network                          html  
    get_GS_network                          html  
    get_evo_settings                        html  
    get_ppi                                 html  
    get_snp_modules                         html  
    is_coherent                             html  
    ldweight_edges                          html  
    minigwas                                html  
    minippi                                 html  
    minisnpMapping                          html  
    parse_scones_settings                   html  
    permute_snpMatrix                       html  
    run_scones                              html  
    scones                                  html  
    scones.cv                               html  
    score_fold                              html  
    search_cones                            html  
    simulate_causal_snps                    html  
    simulate_phenotype                      html  
    single_snp_association                  html  
    snp2gene                                html  
    subnet                                  html  
    subvert                                 html  
    test_cones_modules                      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 'martini' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/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 RcppExports.cpp -o RcppExports.o
In file included from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:61:0,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/RcppCommon.h:29,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include/RcppEigenForward.h:26,
                 from C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppEigen/include/RcppEigen.h:25,
                 from ../inst/include/martini_RcppExports.h:7,
                 from ../inst/include/martini.h:7,
                 from RcppExports.cpp:4:
RcppExports.cpp: In function 'SEXPREC* _martini_run_scones_try(SEXP, SEXP, SEXP, SEXP)':
C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/macros/macros.h:32:9: warning: unused variable 'nprot' [-Wunused-variable]
     int nprot = 0;                                                                               \
         ^
RcppExports.cpp:29:1: note: in expansion of macro 'BEGIN_RCPP'
 BEGIN_RCPP
 ^
C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include/Rcpp/macros/macros.h:36:17: warning: unused variable 'stop_sym' [-Wunused-variable]
     static SEXP stop_sym = Rf_install("stop");                                                   \
                 ^
RcppExports.cpp:29:1: note: in expansion of macro 'BEGIN_RCPP'
 BEGIN_RCPP
 ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/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 evo.cpp -o evo.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/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 run_scones.cpp -o run_scones.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o martini.dll tmp.def RcppExports.o evo.o run_scones.o C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/usrlib/x64/libgin.a C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/usrlib/x64/libmaxflow.a C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rgin/usrlib/x64/libcephes.a -lz -pthread -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/martini.buildbin-libdir/martini/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'martini' as martini_1.3.1.zip
* DONE (martini)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'martini' successfully unpacked and MD5 sums checked


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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(martini)
> library(igraph)

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("martini")
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.016 sec
[0m
[0;34mSearching ConES with eta = 3 and lambda = 2.5
[0m
[0;33mFinished in 0 sec
[0m
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 0 sec
[0m
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.031 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 sec
[0m
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
                       99 52.7071225004667 28.0610178008001 14.9395505324702
99                   -Inf             -Inf             -Inf             -Inf
52.7071225004667 90.00000         90.00000         90.00000         90.00000
28.0610178008001 90.00000         90.00000         90.00000         90.00000
14.9395505324702 90.00000         90.00000         90.00000         90.00000
7.95374464663453 90.00000         90.00000         90.00000         90.00000
4.23453528714745 90.00000         90.00000         90.00000         90.00000
2.2544461627498  90.00000         90.00000         90.00000         90.00000
1.20025626334102 88.69231         88.69231         88.69231         88.69231
0.63901064549361     -Inf             -Inf             -Inf             -Inf
0.34020618556701     -Inf             -Inf             -Inf             -Inf
                 7.95374464663453 4.23453528714745 2.2544461627498
99                           -Inf             -Inf            -Inf
52.7071225004667         90.00000         90.00000        90.00000
28.0610178008001         90.00000         90.00000        90.00000
14.9395505324702         90.00000         90.00000        90.00000
7.95374464663453         90.00000         90.00000        90.00000
4.23453528714745         90.00000         90.00000        90.00000
2.2544461627498          90.00000         90.00000        90.00000
1.20025626334102         88.69231         88.69231        88.69231
0.63901064549361             -Inf             -Inf            -Inf
0.34020618556701             -Inf             -Inf            -Inf
                 1.20025626334102 0.63901064549361 0.34020618556701
99                           -Inf             -Inf             -Inf
52.7071225004667         90.00000         90.00000         90.00000
28.0610178008001         90.00000         90.00000         90.00000
14.9395505324702         90.00000         90.00000         90.00000
7.95374464663453         90.00000         90.00000         90.00000
4.23453528714745         90.00000         90.00000         90.00000
2.2544461627498          90.00000         90.00000         90.00000
1.20025626334102         88.69231         88.69231         88.69231
0.63901064549361             -Inf             -Inf             -Inf
0.34020618556701             -Inf             -Inf             -Inf
Selected parameters:
eta = 52.70712 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     0
0 -Inf
Selected parameters:
eta = 0 
lambda = 0 
Grid of consistency scores (etas x lambdas):
                         0 0.222222222222222 0.444444444444445
0                     -Inf              -Inf              -Inf
0.222222222222222     -Inf              -Inf              -Inf
0.444444444444445     -Inf              -Inf              -Inf
0.666666666666667     -Inf              -Inf              -Inf
0.888888888888889     -Inf              -Inf              -Inf
1.11111111111111  88.69231          88.69231          88.69231
1.33333333333333  88.69231          88.69231          88.69231
1.55555555555556  88.69231          88.69231          88.69231
1.77777777777778  88.69231          88.69231          88.69231
2                 88.69231          88.69231          88.69231
                  0.666666666666667 0.888888888888889 1.11111111111111
0                              -Inf              -Inf             -Inf
0.222222222222222              -Inf              -Inf             -Inf
0.444444444444445              -Inf              -Inf             -Inf
0.666666666666667              -Inf              -Inf             -Inf
0.888888888888889              -Inf              -Inf             -Inf
1.11111111111111           88.69231          88.69231         88.69231
1.33333333333333           88.69231          88.69231         88.69231
1.55555555555556           88.69231          88.69231         88.69231
1.77777777777778           88.69231          88.69231         88.69231
2                          88.69231          88.69231         88.69231
                  1.33333333333333 1.55555555555556 1.77777777777778        2
0                             -Inf             -Inf             -Inf     -Inf
0.222222222222222             -Inf             -Inf             -Inf     -Inf
0.444444444444445             -Inf             -Inf             -Inf     -Inf
0.666666666666667             -Inf             -Inf             -Inf     -Inf
0.888888888888889             -Inf             -Inf             -Inf     -Inf
1.11111111111111          88.69231         88.69231         88.69231 88.69231
1.33333333333333          88.69231         88.69231         88.69231 88.69231
1.55555555555556          88.69231         88.69231         88.69231 88.69231
1.77777777777778          88.69231         88.69231         88.69231 88.69231
2                         88.69231         88.69231         88.69231 88.69231
Selected parameters:
eta = 1.111111 
lambda = 0 
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.016 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 sec
[0m
eta = 1.360181e-32 
lambda = 1.360181e-33 
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 0 sec
[0m
eta = 1 
lambda = 2 
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.015 sec
[0m
[0;34mSearching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033
[0m
[0;33mFinished in 0 sec
[0m
eta = 1.360181e-32 
lambda = 1.360181e-33 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
== testthat results  ===========================================================
OK: 226 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  17.92    1.51   91.07


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
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.

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Type 'contributors()' for more information and
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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(martini)
> library(igraph)

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("martini")
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0 sec
[0m
[0;34mSearching ConES with eta = 3 and lambda = 2.5
[0m
[0;33mFinished in 0 sec
[0m
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 0 sec
[0m
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.016 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 sec
[0m
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
                       99 52.7071225004667 28.0610178008001 14.9395505324702
99                   -Inf             -Inf             -Inf             -Inf
52.7071225004667 90.00000         90.00000         90.00000         90.00000
28.0610178008001 90.00000         90.00000         90.00000         90.00000
14.9395505324702 90.00000         90.00000         90.00000         90.00000
7.95374464663453 90.00000         90.00000         90.00000         90.00000
4.23453528714745 90.00000         90.00000         90.00000         90.00000
2.2544461627498  90.00000         90.00000         90.00000         90.00000
1.20025626334102 88.69231         88.69231         88.69231         88.69231
0.63901064549361     -Inf             -Inf             -Inf             -Inf
0.34020618556701     -Inf             -Inf             -Inf             -Inf
                 7.95374464663453 4.23453528714745 2.2544461627498
99                           -Inf             -Inf            -Inf
52.7071225004667         90.00000         90.00000        90.00000
28.0610178008001         90.00000         90.00000        90.00000
14.9395505324702         90.00000         90.00000        90.00000
7.95374464663453         90.00000         90.00000        90.00000
4.23453528714745         90.00000         90.00000        90.00000
2.2544461627498          90.00000         90.00000        90.00000
1.20025626334102         88.69231         88.69231        88.69231
0.63901064549361             -Inf             -Inf            -Inf
0.34020618556701             -Inf             -Inf            -Inf
                 1.20025626334102 0.63901064549361 0.34020618556701
99                           -Inf             -Inf             -Inf
52.7071225004667         90.00000         90.00000         90.00000
28.0610178008001         90.00000         90.00000         90.00000
14.9395505324702         90.00000         90.00000         90.00000
7.95374464663453         90.00000         90.00000         90.00000
4.23453528714745         90.00000         90.00000         90.00000
2.2544461627498          90.00000         90.00000         90.00000
1.20025626334102         88.69231         88.69231         88.69231
0.63901064549361             -Inf             -Inf             -Inf
0.34020618556701             -Inf             -Inf             -Inf
Selected parameters:
eta = 52.70712 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     0
0 -Inf
Selected parameters:
eta = 0 
lambda = 0 
Grid of consistency scores (etas x lambdas):
                         0 0.222222222222222 0.444444444444445
0                     -Inf              -Inf              -Inf
0.222222222222222     -Inf              -Inf              -Inf
0.444444444444445     -Inf              -Inf              -Inf
0.666666666666667     -Inf              -Inf              -Inf
0.888888888888889     -Inf              -Inf              -Inf
1.11111111111111  88.69231          88.69231          88.69231
1.33333333333333  88.69231          88.69231          88.69231
1.55555555555556  88.69231          88.69231          88.69231
1.77777777777778  88.69231          88.69231          88.69231
2                 88.69231          88.69231          88.69231
                  0.666666666666667 0.888888888888889 1.11111111111111
0                              -Inf              -Inf             -Inf
0.222222222222222              -Inf              -Inf             -Inf
0.444444444444445              -Inf              -Inf             -Inf
0.666666666666667              -Inf              -Inf             -Inf
0.888888888888889              -Inf              -Inf             -Inf
1.11111111111111           88.69231          88.69231         88.69231
1.33333333333333           88.69231          88.69231         88.69231
1.55555555555556           88.69231          88.69231         88.69231
1.77777777777778           88.69231          88.69231         88.69231
2                          88.69231          88.69231         88.69231
                  1.33333333333333 1.55555555555556 1.77777777777778        2
0                             -Inf             -Inf             -Inf     -Inf
0.222222222222222             -Inf             -Inf             -Inf     -Inf
0.444444444444445             -Inf             -Inf             -Inf     -Inf
0.666666666666667             -Inf             -Inf             -Inf     -Inf
0.888888888888889             -Inf             -Inf             -Inf     -Inf
1.11111111111111          88.69231         88.69231         88.69231 88.69231
1.33333333333333          88.69231         88.69231         88.69231 88.69231
1.55555555555556          88.69231         88.69231         88.69231 88.69231
1.77777777777778          88.69231         88.69231         88.69231 88.69231
2                         88.69231         88.69231         88.69231 88.69231
Selected parameters:
eta = 1.111111 
lambda = 0 
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.016 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 sec
[0m
eta = 1e-06 
lambda = 1e-07 
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0 sec
[0m
[0;34mSearching ConES with eta = 1 and lambda = 2
[0m
[0;33mFinished in 0 sec
[0m
eta = 1 
lambda = 2 
[0;32mComputing univariate association.[0m
[0;34mSelecting the best hyperparameters...[0m
[0;32mRunning models.[0m
[0;32mFinding best model.[0m
[0;33mFinished in 0.015 sec
[0m
[0;34mSearching ConES with eta = 1e-006 and lambda = 1e-007
[0m
[0;33mFinished in 0 sec
[0m
eta = 1e-06 
lambda = 1e-07 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
Grid of consistency scores (etas x lambdas):
     99   99   99   99   99   99   99   99   99   99
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
99 -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf -Inf
Selected parameters:
eta = 99 
lambda = 99 
== testthat results  ===========================================================
OK: 226 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  16.78    0.81   73.59

name	user	system	elapsed
check_installed	0	0	0
encode_gwas	0.00	0.02	0.01
get_GI_network	0.03	0.01	0.04
get_GM_network	0.02	0.00	0.02
get_GS_network	0	0	0
get_evo_settings	0	0	0
get_ppi	0.47	0.06	9.83
get_snp_modules	0.27	0.02	0.28
is_coherent	0	0	0
ldweight_edges	0.05	0.02	0.07
minigwas	0.18	0.01	0.20
minippi	0.00	0.02	0.02
minisnpMapping	0	0	0
parse_scones_settings	0	0	0
scones	0.05	0.00	0.04
scones.cv	0.23	0.07	0.31
search_cones	0.11	0.00	0.11
simulate_causal_snps	0.05	0.00	0.05
simulate_phenotype	0.06	0.00	0.06
subnet	0.05	0.00	0.05
subvert	0.03	0.00	0.03
test_cones_modules	0.17	0.00	0.17

name	user	system	elapsed
check_installed	0	0	0
encode_gwas	0.00	0.02	0.01
get_GI_network	0.07	0.00	0.06
get_GM_network	0.01	0.00	0.02
get_GS_network	0.02	0.00	0.02
get_evo_settings	0	0	0
get_ppi	0.37	0.08	0.64
get_snp_modules	0.41	0.00	1.22
is_coherent	0	0	0
ldweight_edges	0.11	0.00	0.10
minigwas	0.03	0.00	0.04
minippi	0.00	0.01	0.01
minisnpMapping	0	0	0
parse_scones_settings	0	0	0
scones	0.05	0.00	0.05
scones.cv	0.25	0.02	0.26
search_cones	0.14	0.02	0.43
simulate_causal_snps	0.07	0.00	0.07
simulate_phenotype	0.07	0.01	0.08
subnet	0.06	0.00	0.06
subvert	0.05	0.02	0.07
test_cones_modules	0.23	0.00	0.23

CHECK report for martini on tokay2

Summary

Command output

Installation output

Tests output

Example timings