Package: TRONCO

Version: 2.16.2

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_2.16.2.tar.gz

StartedAt: 2019-10-16 07:34:32 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:41:19 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 406.6 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_2.16.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TRONCO.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 ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.16.2’
* 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 0.472  0.274  17.822
tronco.kfold.prederr 0.367  0.252  17.291
tronco.bootstrap     0.352  0.185  32.065
* 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/3.6/Resources/library’
* installing *source* package ‘TRONCO’ ...
** 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 (TRONCO)

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.

> 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 6 edges out of 49 (12%)
*** 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 10 edges out of 50 (20%)
*** Performing likelihood-fit with regularization: no_reg .
*** 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: 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 5 edges out of 56 (9%)
*** 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 5 edges out of 53 (9%)
*** 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: 225 | SKIPPED: 0 | WARNINGS: 28 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 78.056   3.431 206.497 

name	user	system	elapsed
TCGA.multiple.samples	0.022	0.006	0.028
TCGA.remove.multiple.samples	0.042	0.022	0.063
TCGA.shorten.barcodes	0.031	0.019	0.051
annotate.description	0.032	0.022	0.053
annotate.stages	0.026	0.006	0.032
as.adj.matrix	0.027	0.025	0.051
as.alterations	0.008	0.003	0.011
as.bootstrap.scores	0.089	0.011	0.099
as.colors	0.003	0.003	0.005
as.confidence	0.032	0.032	0.063
as.description	0.002	0.002	0.004
as.events	0.005	0.004	0.008
as.events.in.patterns	0.015	0.002	0.017
as.events.in.sample	0.008	0.002	0.011
as.gene	0.007	0.003	0.011
as.genes	0.002	0.002	0.005
as.genes.in.patterns	0.008	0.002	0.010
as.genotypes	0.024	0.014	0.037
as.hypotheses	0.011	0.008	0.019
as.joint.probs	0.027	0.026	0.053
as.kfold.eloss	0.071	0.015	0.087
as.kfold.posterr	0.106	0.017	0.125
as.kfold.prederr	0.174	0.008	0.193
as.marginal.probs	0.008	0.004	0.011
as.models	0.049	0.050	0.103
as.parameters	0.005	0.003	0.007
as.pathway	0.011	0.003	0.014
as.patterns	0.003	0.001	0.005
as.samples	0.003	0.002	0.004
as.selective.advantage.relations	0.319	0.017	0.337
as.stages	0.018	0.007	0.025
as.types	0.003	0.002	0.005
as.types.in.patterns	0.010	0.004	0.014
change.color	0.005	0.003	0.008
consolidate.data	0.083	0.013	0.097
delete.event	0.009	0.003	0.011
delete.gene	0.010	0.002	0.012
delete.hypothesis	0.093	0.055	0.148
delete.model	0.006	0.003	0.008
delete.pattern	0.038	0.022	0.060
delete.samples	0.007	0.002	0.010
delete.type	0.011	0.005	0.017
duplicates	0.003	0.002	0.005
enforce.numeric	0.004	0.002	0.005
enforce.string	0.006	0.003	0.009
events.selection	0.009	0.003	0.012
export.graphml	0.164	0.012	0.175
export.mutex	0.016	0.005	0.021
has.duplicates	0.002	0.003	0.005
has.model	0.003	0.002	0.005
has.stages	0.014	0.004	0.019
import.GISTIC	0.010	0.001	0.010
import.MAF	0.117	0.011	0.128
intersect.datasets	0.002	0.002	0.003
is.compliant	0.003	0.002	0.004
join.events	0.007	0.002	0.009
join.types	0.114	0.020	0.135
keysToNames	0.011	0.004	0.016
nameToKey	0.004	0.002	0.006
nevents	0.002	0.002	0.004
ngenes	0.002	0.002	0.004
nhypotheses	0.002	0.002	0.004
npatterns	0.002	0.002	0.003
nsamples	0.002	0.002	0.004
ntypes	0.002	0.001	0.004
oncoprint.cbio	0.011	0.003	0.020
order.frequency	0.022	0.019	0.041
pheatmap	0.083	0.002	0.086
rank.recurrents	0.006	0.002	0.007
rename.gene	0.003	0.001	0.005
rename.type	0.002	0.001	0.003
samples.selection	0.005	0.001	0.007
trim	0.006	0.002	0.008
tronco.bootstrap	0.352	0.185	32.065
tronco.caprese	0.241	0.010	0.270
tronco.capri	3.980	0.252	4.240
tronco.chowliu	2.844	0.078	2.973
tronco.edmonds	2.394	0.044	2.437
tronco.gabow	2.411	0.047	2.457
tronco.kfold.eloss	0.296	0.075	0.371
tronco.kfold.posterr	0.472	0.274	17.822
tronco.kfold.prederr	0.367	0.252	17.291
tronco.plot	0.257	0.010	0.267
tronco.prim	3.817	0.154	3.972
view	0.007	0.002	0.010
which.samples	0.006	0.002	0.008