Package: MetNet

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetNet_1.0.1.tar.gz

StartedAt: 2019-04-16 01:13:41 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:18:18 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 277.3 seconds

RetCode: 0

Status:  OK

CheckDir: MetNet.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetNet_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MetNet.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetNet’ version ‘1.0.1’
* 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 ‘MetNet’ 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MetNet
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MetNet’ ...
** R
** data
** 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 (MetNet)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> data("x_test", package = "MetNet")
> data("mat_test", package = "MetNet")
> library(stabs)
Loading required package: parallel
> library(rfPermute)
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
> 
> BiocGenerics:::testPackage("MetNet")


Attaching package: 'MetNet'

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

    randomForest

[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
[1] "bayes finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
[1] "bayes finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
[1] "bayes finished."
[1] "clr finished."
[1] "aracne finished."
[1] "pearson finished."
[1] "spearman finished."
[1] "bayes finished."


RUNIT TEST PROTOCOL -- Tue Apr 16 01:18:13 2019 
*********************************************** 
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MetNet RUnit Tests - 14 test functions, 0 errors, 0 failures
Number of test functions: 14 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In ppcor::pcor(t(x), method = method) :
  The inverse of variance-covariance matrix is calculated using Moore-Penrose generalized matrix invers due to its determinant of zero.
2: In sqrt((n - 2 - gp)/(1 - pcor^2)) : NaNs produced
3: In ppcor::spcor(t(x), method = method) :
  The inverse of variance-covariance matrix is calculated using Moore-Penrose generalized matrix invers due to its determinant of zero.
4: In sqrt((n - 2 - gp)/(1 - spcor^2)) : NaNs produced
5: In .aracne(mi, n, eps, 1) : NAs introduced by coercion
> 
> proc.time()
   user  system elapsed 
144.774  97.745 123.658 

name	user	system	elapsed
MetNet-package	1.237	0.010	1.267
addToList	0.016	0.008	0.024
aracne	0.998	0.532	0.452
bayes	0.950	0.263	0.807
clr	1.005	0.658	0.436
combineStructuralStatistical	1.043	0.229	0.928
consensusAdjacency	0.042	0.007	0.049
correlation	0.013	0.006	0.018
createStatisticalAdjacency	0.047	0.007	0.055
createStatisticalAdjacencyList	0.023	0.009	0.033
createStructuralAdjacency	0.009	0.001	0.009
lasso	0.006	0.000	0.007
randomForest	0.003	0.000	0.004
rtCorrection	0.014	0.000	0.016
threeDotsCall	0.000	0.000	0.001