Package: TRONCO

Version: 2.10.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.10.3.tar.gz

StartedAt: 2018-04-12 10:31:58 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 10:35:59 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 241.1 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.10.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TRONCO.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.10.3’
* 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 ‘TRONCO’ 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
tronco.bootstrap 0.13  0.018  14.779
* 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: OK

* installing *source* package ‘TRONCO’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TRONCO)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.

> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(TRONCO)
> 
> test_check("TRONCO")
*** Checking input events.
*** Inferring a progression model with the following settings.
	Dataset size: n = 40, m = 30.
	Algorithm: CAPRESE with shrinkage coefficient: 0.5.
*** Evaluating LogLik informations.
The reconstruction has been successfully completed in 00h:00m:00s 
*** Checking input events.
*** Inferring a progression model with the following settings.
	Dataset size: n = 40, m = 30.
	Algorithm: Edmonds with "no_reg" regularization	Random seed: NULL.
	Bootstrap iterations (Wilcoxon): 1.
		exhaustive bootstrap: TRUE.
		p-value: 0.05.
		minimum bootstrapped scores: 3.
*** Bootstraping selective advantage scores (prima facie).
	....
	Evaluating "temporal priority" (Wilcoxon, p-value 0.05)
	Evaluating "probability raising" (Wilcoxon, p-value 0.05)
*** Loop detection found loops to break.
	Removed 7 edges out of 52 (13%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s 
*** Checking input events.
*** Inferring a progression model with the following settings.
	Dataset size: n = 40, m = 30.
	Algorithm: Gabow with "no_reg" regularization	Random seed: NULL.
	Bootstrap iterations (Wilcoxon): 1.
		exhaustive bootstrap: TRUE.
		p-value: 0.05.
		minimum bootstrapped scores: 3.
*** Bootstraping selective advantage scores (prima facie).
	...............
	Evaluating "temporal priority" (Wilcoxon, p-value 0.05)
	Evaluating "probability raising" (Wilcoxon, p-value 0.05)
*** Loop detection found loops to break.
	Removed 7 edges out of 51 (14%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s 
*** Checking input events.
*** Inferring a progression model with the following settings.
	Dataset size: n = 40, m = 30.
	Algorithm: Chow Liu with "bic, aic" regularization	Random seed: NULL.
	Bootstrap iterations (Wilcoxon): 1.
		exhaustive bootstrap: TRUE.
		p-value: 0.05.
		minimum bootstrapped scores: 3.
*** Bootstraping selective advantage scores (prima facie).
	........
	Evaluating "temporal priority" (Wilcoxon, p-value 0.05)
	Evaluating "probability raising" (Wilcoxon, p-value 0.05)
*** Loop detection found loops to break.
	Removed 8 edges out of 58 (14%)
*** Performing likelihood-fit with regularization bic .
*** Performing likelihood-fit with regularization aic .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s 
*** Checking input events.
*** Inferring a progression model with the following settings.
	Dataset size: n = 40, m = 30.
	Algorithm: Prim with "no_reg" regularization	Random seed: NULL.
	Bootstrap iterations (Wilcoxon): 1.
		exhaustive bootstrap: TRUE.
		p-value: 0.05.
		minimum bootstrapped scores: 3.
*** Bootstraping selective advantage scores (prima facie).
	.........
	Evaluating "temporal priority" (Wilcoxon, p-value 0.05)
	Evaluating "probability raising" (Wilcoxon, p-value 0.05)
*** Loop detection found loops to break.
	Removed 8 edges out of 49 (16%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 253 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 55.865   0.657 122.192 

name	user	system	elapsed
TCGA.multiple.samples	0.013	0.003	0.015
TCGA.remove.multiple.samples	0.076	0.006	0.082
TCGA.shorten.barcodes	0.012	0.004	0.017
annotate.description	0.013	0.004	0.017
annotate.stages	0.007	0.001	0.008
as.adj.matrix	0.038	0.007	0.044
as.alterations	0.003	0.000	0.004
as.bootstrap.scores	0.136	0.001	0.139
as.colors	0.001	0.000	0.002
as.confidence	0.043	0.007	0.051
as.description	0.001	0.000	0.001
as.events	0.002	0.001	0.003
as.events.in.patterns	0.017	0.001	0.018
as.events.in.sample	0.004	0.000	0.004
as.gene	0.004	0.001	0.005
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.004	0.001	0.004
as.genotypes	0.008	0.003	0.012
as.hypotheses	0.005	0.002	0.006
as.joint.probs	0.021	0.006	0.027
as.kfold.eloss	0.122	0.004	0.127
as.kfold.posterr	0.206	0.009	0.216
as.kfold.prederr	0.105	0.010	0.115
as.marginal.probs	0.014	0.001	0.016
as.models	0.019	0.014	0.033
as.parameters	0.002	0.001	0.003
as.pathway	0.004	0.000	0.005
as.patterns	0.002	0.000	0.002
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.160	0.005	0.167
as.stages	0.022	0.001	0.023
as.types	0.001	0.000	0.002
as.types.in.patterns	0.004	0.000	0.004
change.color	0.002	0.001	0.003
consolidate.data	0.026	0.001	0.026
delete.event	0.004	0.001	0.005
delete.gene	0.005	0.001	0.005
delete.hypothesis	0.073	0.012	0.084
delete.model	0.003	0.001	0.003
delete.pattern	0.012	0.003	0.016
delete.samples	0.011	0.000	0.012
delete.type	0.004	0.001	0.005
duplicates	0.002	0.000	0.002
enforce.numeric	0.002	0.001	0.002
enforce.string	0.003	0.000	0.003
events.selection	0.047	0.000	0.048
export.graphml	0.255	0.005	0.261
export.mutex	0.056	0.002	0.058
has.duplicates	0.002	0.000	0.002
has.model	0.002	0.001	0.002
has.stages	0.005	0.001	0.007
import.GISTIC	0.139	0.001	0.140
import.MAF	0.121	0.002	0.125
intersect.datasets	0.001	0.001	0.002
is.compliant	0.001	0.000	0.002
join.events	0.021	0.000	0.021
join.types	0.088	0.006	0.094
keysToNames	0.006	0.001	0.007
nameToKey	0.002	0.000	0.002
nevents	0.001	0.001	0.002
ngenes	0.001	0.000	0.002
nhypotheses	0.002	0.001	0.002
npatterns	0.001	0.001	0.002
nsamples	0.001	0.000	0.002
ntypes	0.001	0.001	0.002
oncoprint.cbio	0.005	0.001	0.006
order.frequency	0.009	0.004	0.013
pheatmap	0.786	0.004	0.799
rank.recurrents	0.003	0.001	0.003
rename.gene	0.002	0.000	0.002
rename.type	0.017	0.001	0.018
samples.selection	0.003	0.000	0.003
trim	0.002	0.000	0.003
tronco.bootstrap	0.130	0.018	14.779
tronco.caprese	0.218	0.002	0.221
tronco.capri	2.209	0.032	2.242
tronco.chowliu	1.407	0.011	1.420
tronco.edmonds	1.301	0.020	1.323
tronco.gabow	1.123	0.010	1.134
tronco.kfold.eloss	0.258	0.021	0.280
tronco.kfold.posterr	0.375	0.045	4.286
tronco.kfold.prederr	0.108	0.040	3.786
tronco.plot	0.689	0.005	0.694
tronco.prim	1.634	0.024	1.658
view	0.007	0.000	0.008
which.samples	0.002	0.000	0.003