Package: TRONCO

Version: 2.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TRONCO_2.12.0.tar.gz

StartedAt: 2018-10-17 00:31:43 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:36:36 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 292.7 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 --install=check:TRONCO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TRONCO_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/TRONCO.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.12.0’
* 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 ‘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 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
tronco.kfold.posterr 0.351  0.151  11.613
tronco.kfold.prederr 0.263  0.135  11.561
tronco.bootstrap     0.280  0.102  21.599
* 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

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

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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 8 edges out of 52 (15%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s 
*** 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 8 edges out of 46 (17%)
*** 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 6 edges out of 55 (11%)
*** 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:03s 
*** 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 53 (15%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 253 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 61.293   1.485 147.957 

name	user	system	elapsed
TCGA.multiple.samples	0.017	0.003	0.021
TCGA.remove.multiple.samples	0.020	0.006	0.025
TCGA.shorten.barcodes	0.015	0.005	0.020
annotate.description	0.024	0.006	0.029
annotate.stages	0.010	0.001	0.011
as.adj.matrix	0.020	0.012	0.033
as.alterations	0.005	0.000	0.006
as.bootstrap.scores	0.059	0.003	0.063
as.colors	0.003	0.001	0.004
as.confidence	0.015	0.009	0.024
as.description	0.002	0.001	0.003
as.events	0.003	0.001	0.005
as.events.in.patterns	0.013	0.001	0.014
as.events.in.sample	0.008	0.002	0.009
as.gene	0.005	0.001	0.006
as.genes	0.002	0.001	0.004
as.genes.in.patterns	0.004	0.000	0.005
as.genotypes	0.016	0.006	0.022
as.hypotheses	0.006	0.002	0.008
as.joint.probs	0.018	0.010	0.029
as.kfold.eloss	0.046	0.005	0.052
as.kfold.posterr	0.086	0.006	0.094
as.kfold.prederr	0.122	0.002	0.128
as.marginal.probs	0.004	0.002	0.006
as.models	0.026	0.018	0.045
as.parameters	0.005	0.001	0.006
as.pathway	0.121	0.001	0.125
as.patterns	0.004	0.001	0.005
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.111	0.008	0.120
as.stages	0.009	0.002	0.011
as.types	0.003	0.001	0.003
as.types.in.patterns	0.005	0.001	0.006
change.color	0.002	0.001	0.003
consolidate.data	0.051	0.009	0.060
delete.event	0.008	0.002	0.010
delete.gene	0.008	0.002	0.010
delete.hypothesis	0.051	0.022	0.074
delete.model	0.004	0.001	0.004
delete.pattern	0.024	0.009	0.033
delete.samples	0.005	0.001	0.006
delete.type	0.008	0.001	0.010
duplicates	0.003	0.001	0.005
enforce.numeric	0.005	0.001	0.006
enforce.string	0.005	0.001	0.006
events.selection	0.008	0.002	0.009
export.graphml	0.146	0.005	0.150
export.mutex	0.013	0.002	0.016
has.duplicates	0.004	0.001	0.004
has.model	0.002	0.001	0.003
has.stages	0.012	0.002	0.014
import.GISTIC	0.009	0.000	0.009
import.MAF	0.105	0.003	0.108
intersect.datasets	0.003	0.001	0.004
is.compliant	0.004	0.001	0.005
join.events	0.008	0.002	0.010
join.types	0.082	0.012	0.095
keysToNames	0.009	0.002	0.010
nameToKey	0.005	0.001	0.006
nevents	0.003	0.001	0.004
ngenes	0.003	0.001	0.004
nhypotheses	0.004	0.001	0.004
npatterns	0.002	0.001	0.004
nsamples	0.003	0.001	0.004
ntypes	0.004	0.001	0.005
oncoprint.cbio	0.011	0.002	0.012
order.frequency	0.019	0.010	0.030
pheatmap	0.075	0.001	0.079
rank.recurrents	0.004	0.000	0.004
rename.gene	0.003	0.000	0.003
rename.type	0.004	0.002	0.006
samples.selection	0.006	0.001	0.007
trim	0.006	0.001	0.006
tronco.bootstrap	0.280	0.102	21.599
tronco.caprese	0.214	0.007	0.238
tronco.capri	2.683	0.104	2.822
tronco.chowliu	1.920	0.021	1.948
tronco.edmonds	1.727	0.016	1.755
tronco.gabow	2.062	0.031	2.120
tronco.kfold.eloss	0.213	0.035	0.250
tronco.kfold.posterr	0.351	0.151	11.613
tronco.kfold.prederr	0.263	0.135	11.561
tronco.plot	0.174	0.004	0.187
tronco.prim	3.267	0.069	3.375
view	0.007	0.001	0.008
which.samples	0.005	0.001	0.006