Package: TRONCO

Version: 2.15.2

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_2.15.2.tar.gz

StartedAt: 2019-04-09 04:15:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:20:12 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 306.4 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_2.15.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘2.15.2’
* 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 0.321  0.139  11.919
tronco.kfold.prederr 0.264  0.134  11.650
tronco.bootstrap     0.269  0.103  22.652
* 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’ ...
** 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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 6 edges out of 50 (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 6 edges out of 50 (12%)
*** 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 52 (10%)
*** 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 11 edges out of 56 (20%)
*** 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 
 66.701   1.724 162.487 

name	user	system	elapsed
TCGA.multiple.samples	0.015	0.004	0.019
TCGA.remove.multiple.samples	0.023	0.007	0.031
TCGA.shorten.barcodes	0.019	0.005	0.024
annotate.description	0.021	0.008	0.030
annotate.stages	0.017	0.001	0.019
as.adj.matrix	0.017	0.010	0.027
as.alterations	0.006	0.001	0.007
as.bootstrap.scores	0.074	0.004	0.078
as.colors	0.001	0.001	0.003
as.confidence	0.018	0.012	0.030
as.description	0.002	0.002	0.003
as.events	0.003	0.002	0.006
as.events.in.patterns	0.012	0.001	0.014
as.events.in.sample	0.004	0.001	0.004
as.gene	0.004	0.002	0.006
as.genes	0.003	0.001	0.003
as.genes.in.patterns	0.006	0.002	0.010
as.genotypes	0.017	0.007	0.023
as.hypotheses	0.007	0.003	0.009
as.joint.probs	0.015	0.009	0.025
as.kfold.eloss	0.052	0.006	0.057
as.kfold.posterr	0.093	0.008	0.101
as.kfold.prederr	0.130	0.002	0.135
as.marginal.probs	0.004	0.001	0.005
as.models	0.031	0.023	0.054
as.parameters	0.003	0.002	0.005
as.pathway	0.008	0.001	0.009
as.patterns	0.002	0.001	0.003
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.222	0.007	0.233
as.stages	0.013	0.003	0.015
as.types	0.002	0.001	0.003
as.types.in.patterns	0.006	0.001	0.007
change.color	0.001	0.000	0.002
consolidate.data	0.049	0.009	0.058
delete.event	0.007	0.002	0.008
delete.gene	0.008	0.002	0.009
delete.hypothesis	0.056	0.022	0.079
delete.model	0.005	0.002	0.006
delete.pattern	0.024	0.009	0.034
delete.samples	0.005	0.001	0.007
delete.type	0.010	0.002	0.012
duplicates	0.003	0.001	0.004
enforce.numeric	0.003	0.001	0.004
enforce.string	0.003	0.001	0.003
events.selection	0.005	0.001	0.006
export.graphml	0.135	0.003	0.142
export.mutex	0.008	0.002	0.010
has.duplicates	0.002	0.001	0.002
has.model	0.002	0.001	0.002
has.stages	0.007	0.001	0.008
import.GISTIC	0.005	0.001	0.005
import.MAF	0.087	0.004	0.093
intersect.datasets	0.001	0.001	0.003
is.compliant	0.002	0.000	0.003
join.events	0.016	0.001	0.016
join.types	0.069	0.011	0.081
keysToNames	0.008	0.002	0.010
nameToKey	0.003	0.001	0.005
nevents	0.002	0.000	0.003
ngenes	0.002	0.001	0.003
nhypotheses	0.002	0.001	0.003
npatterns	0.002	0.001	0.003
nsamples	0.002	0.001	0.003
ntypes	0.002	0.001	0.003
oncoprint.cbio	0.008	0.002	0.011
order.frequency	0.011	0.006	0.016
pheatmap	0.063	0.001	0.065
rank.recurrents	0.004	0.001	0.004
rename.gene	0.002	0.000	0.003
rename.type	0.002	0.000	0.003
samples.selection	0.003	0.000	0.004
trim	0.005	0.001	0.006
tronco.bootstrap	0.269	0.103	22.652
tronco.caprese	0.219	0.006	0.232
tronco.capri	2.883	0.094	3.001
tronco.chowliu	2.104	0.029	2.148
tronco.edmonds	2.085	0.027	2.135
tronco.gabow	2.518	0.028	2.563
tronco.kfold.eloss	0.197	0.031	0.233
tronco.kfold.posterr	0.321	0.139	11.919
tronco.kfold.prederr	0.264	0.134	11.650
tronco.plot	0.181	0.003	0.198
tronco.prim	3.122	0.062	3.201
view	0.006	0.001	0.007
which.samples	0.004	0.000	0.005