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CHECK report for MetNet on merida1

This page was generated on 2019-04-16 12:11:58 -0400 (Tue, 16 Apr 2019).

Package 947/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MetNet 1.0.1
Thomas Naake
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/MetNet
Branch: RELEASE_3_8
Last Commit: 87f2f49
Last Changed Date: 2019-01-04 13:39:11 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  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: 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

Command output

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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


Installation output

MetNet.Rcheck/00install.out

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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)

Tests output

MetNet.Rcheck/tests/runTests.Rout


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 

Example timings

MetNet.Rcheck/MetNet-Ex.timings

nameusersystemelapsed
MetNet-package1.2370.0101.267
addToList0.0160.0080.024
aracne0.9980.5320.452
bayes0.9500.2630.807
clr1.0050.6580.436
combineStructuralStatistical1.0430.2290.928
consensusAdjacency0.0420.0070.049
correlation0.0130.0060.018
createStatisticalAdjacency0.0470.0070.055
createStatisticalAdjacencyList0.0230.0090.033
createStructuralAdjacency0.0090.0010.009
lasso0.0060.0000.007
randomForest0.0030.0000.004
rtCorrection0.0140.0000.016
threeDotsCall0.0000.0000.001