Package: MetNet

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2019-10-16 04:33:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:45:42 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 710.0 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MetNet.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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/3.6/Resources/library’
* installing *source* package ‘MetNet’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MetNet)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 -- Wed Oct 16 04:45:30 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 
452.809 559.549 500.634 

name	user	system	elapsed
MetNet-package	1.467	0.022	1.497
addToList	0.027	0.023	0.050
aracne	1.172	0.644	0.577
bayes	0.746	0.019	0.764
clr	1.372	0.833	0.632
combineStructuralStatistical	0.916	0.017	0.932
consensusAdjacency	0.025	0.008	0.033
correlation	0.011	0.008	0.018
createStatisticalAdjacency	0.030	0.015	0.044
createStatisticalAdjacencyList	0.035	0.024	0.059
createStructuralAdjacency	0.010	0.001	0.011
lasso	0.009	0.001	0.010
randomForest	0.005	0.001	0.006
rtCorrection	0.018	0.002	0.019
threeDotsCall	0.001	0.000	0.001