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CHECK report for martini on tokay1

This page was generated on 2020-04-15 12:29:57 -0400 (Wed, 15 Apr 2020).

Package 954/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
martini 1.6.0
Hector Climente-Gonzalez
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/martini
Branch: RELEASE_3_10
Last Commit: 4f0f2b9
Last Changed Date: 2019-10-29 13:10:59 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: martini
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:martini.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings martini_1.6.0.tar.gz
StartedAt: 2020-04-15 04:27:37 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 04:31:01 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 204.2 seconds
RetCode: 0
Status:  OK  
CheckDir: martini.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:martini.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings martini_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/martini.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.6.0'
* 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 '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-3.10-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-3.10-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
** 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-3.10-bioc/meat/martini.Rcheck/00check.log'
for details.

Installation output

martini.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/martini_1.6.0.tar.gz && rm -rf martini.buildbin-libdir && mkdir martini.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=martini.buildbin-libdir martini_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL martini_1.6.0.zip && rm martini_1.6.0.tar.gz martini_1.6.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2502k  100 2502k    0     0  32.7M      0 --:--:-- --:--:-- --:--:-- 34.4M

install for i386

* installing *source* package 'martini' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c evo.cpp -o evo.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c run_scones.cpp -o run_scones.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o martini.dll tmp.def RcppExports.o evo.o run_scones.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/usrlib/i386/libgin.a C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/usrlib/i386/libmaxflow.a C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/usrlib/i386/libcephes.a -lz -pthread -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c evo.cpp -o evo.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -DAS_GINLIB -DAS_RGINLIB -fopenmp -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppEigen/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c run_scones.cpp -o run_scones.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o martini.dll tmp.def RcppExports.o evo.o run_scones.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/usrlib/x64/libgin.a C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/usrlib/x64/libmaxflow.a C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rgin/usrlib/x64/libcephes.a -lz -pthread -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/martini.buildbin-libdir/martini/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'martini' as martini_1.6.0.zip
* DONE (martini)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'martini' successfully unpacked and MD5 sums checked

Tests output

martini.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0 sec

Searching ConES with eta = 3 and lambda = 2.5

Finished in 0 sec

Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0 sec

Searching ConES with eta = 1 and lambda = 2

Finished in 0 sec

Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.015 sec

Searching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033

Finished in 0 sec

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 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.013 sec

Searching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033

Finished in 0 sec

eta = 1.360181e-32 
lambda = 1.360181e-33 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.002 sec

Searching ConES with eta = 1 and lambda = 2

Finished in 0 sec

eta = 1 
lambda = 2 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.012 sec

Searching ConES with eta = 1.36018e-032 and lambda = 1.36018e-033

Finished in 0 sec

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: 221 | SKIPPED: 3 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  18.37    1.35   56.26

martini.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(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")
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0 sec

Searching ConES with eta = 3 and lambda = 2.5

Finished in 0 sec

Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0 sec

Searching ConES with eta = 1 and lambda = 2

Finished in 0 sec

Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.014 sec

Searching ConES with eta = 1e-006 and lambda = 1e-007

Finished in 0 sec

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 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.013 sec

Searching ConES with eta = 1e-006 and lambda = 1e-007

Finished in 0 sec

eta = 1e-06 
lambda = 1e-07 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.001 sec

Searching ConES with eta = 1 and lambda = 2

Finished in 0 sec

eta = 1 
lambda = 2 
Computing univariate association.
Selecting the best hyperparameters...
Running models.
Finding best model.
Finished in 0.013 sec

Searching ConES with eta = 1e-006 and lambda = 1e-007

Finished in 0 sec

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: 221 | SKIPPED: 3 | WARNINGS: 5 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  22.25    1.07   43.89

Example timings

martini.Rcheck/examples_i386/martini-Ex.timings

nameusersystemelapsed
check_installed000
encode_gwas0.020.000.01
get_GI_network0.060.000.06
get_GM_network0.020.000.02
get_GS_network000
get_evo_settings000
get_ppi0.500.090.77
get_snp_modules0.480.020.50
is_coherent000
ldweight_edges0.080.000.08
minigwas0.000.010.01
minippi000
minisnpMapping0.010.000.02
parse_scones_settings000
scones0.020.020.03
scones.cv0.220.130.34
search_cones0.090.000.10
simulate_causal_snps0.050.000.05
simulate_phenotype0.030.000.03
subnet0.030.000.03
subvert0.030.000.03
test_cones_modules0.170.000.17

martini.Rcheck/examples_x64/martini-Ex.timings

nameusersystemelapsed
check_installed000
encode_gwas0.020.000.02
get_GI_network0.010.000.09
get_GM_network0.030.000.03
get_GS_network000
get_evo_settings000
get_ppi0.580.060.84
get_snp_modules0.480.000.64
is_coherent0.020.000.02
ldweight_edges0.040.000.04
minigwas000
minippi000
minisnpMapping0.000.020.01
parse_scones_settings000
scones0.030.010.05
scones.cv0.200.020.22
search_cones0.100.010.12
simulate_causal_snps0.060.000.07
simulate_phenotype0.050.000.04
subnet0.050.000.05
subvert0.050.000.04
test_cones_modules0.180.000.19