Package: AMARETTO

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AMARETTO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AMARETTO_1.0.0.tar.gz

StartedAt: 2019-10-16 00:29:04 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:34:52 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 348.9 seconds

RetCode: 0

Status:  OK

CheckDir: AMARETTO.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:AMARETTO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AMARETTO_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/AMARETTO.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 ‘AMARETTO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AMARETTO’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘AMARETTO’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  Apache License (== 2.0) + file LICENSE
'LinkingTo' field is unused: package has no 'src' directory
* 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
Examples with CPU or elapsed time > 5s
                           user system elapsed
AMARETTO_Download        16.051  1.304  19.576
AMARETTO_VisualizeModule  5.363  0.072   5.437
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/AMARETTO.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AMARETTO
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘AMARETTO’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (AMARETTO)

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.

> library(testthat)
> library(AMARETTO)
Loading required package: impute
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: dplyr

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: ComplexHeatmap
Loading required package: grid
========================================
ComplexHeatmap version 2.0.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.
========================================

> 
> test_check("AMARETTO")
	Found 1 CNV driver genes.
	Found 24 MethylMix driver genes.
	Found a total of 24 unique drivers with your selected method.
Running AMARETTO on 80 genes and 45 samples.
	Stopping if less then 0.8 genes reassigned.
	Autoregulation is turned ON.
Elapsed time is 2.642000 seconds
Average nr of regulators per module: 8.600000 
Elapsed time is 0.123000 seconds
Nr of reassignments is: 5 
Elapsed time is 1.535000 seconds
Average nr of regulators per module: 9.400000 
Elapsed time is 0.086000 seconds
Nr of reassignments is: 0 
Elapsed time is 4.389000 seconds
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 43 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 17.609   1.454  19.013 

name	user	system	elapsed
AMARETTO_CreateModuleData	2.521	0.061	2.582
AMARETTO_CreateRegulatorPrograms	2.814	0.138	2.951
AMARETTO_Download	16.051	1.304	19.576
AMARETTO_EvaluateTestSet	2.189	0.034	2.223
AMARETTO_ExportResults	2.240	0.054	2.299
AMARETTO_HTMLreport	0.000	0.000	0.001
AMARETTO_Initialize	0.999	0.020	1.019
AMARETTO_Preprocess	0.000	0.001	0.001
AMARETTO_Run	1.888	0.045	1.933
AMARETTO_VisualizeModule	5.363	0.072	5.437