Package: TRONCO

Version: 2.18.0

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_2.18.0.tar.gz

StartedAt: 2020-04-15 06:18:20 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:23:30 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 310.1 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 --install=check:TRONCO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TRONCO_2.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/TRONCO.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.18.0’
* 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 0.295  0.129  12.590
tronco.kfold.prederr 0.236  0.119  12.013
tronco.bootstrap     0.253  0.091  24.652
* 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’ ...
** 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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 51 (14%)
*** 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 50 (16%)
*** 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 6 edges out of 45 (13%)
*** 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 52 (10%)
*** 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 
 66.672   1.447 162.697 

name	user	system	elapsed
TCGA.multiple.samples	0.019	0.004	0.022
TCGA.remove.multiple.samples	0.029	0.010	0.038
TCGA.shorten.barcodes	0.027	0.006	0.034
annotate.description	0.016	0.007	0.023
annotate.stages	0.013	0.002	0.015
as.adj.matrix	0.016	0.010	0.026
as.alterations	0.006	0.001	0.008
as.bootstrap.scores	0.058	0.004	0.062
as.colors	0.002	0.001	0.003
as.confidence	0.016	0.011	0.027
as.description	0.002	0.001	0.003
as.events	0.003	0.002	0.005
as.events.in.patterns	0.011	0.001	0.012
as.events.in.sample	0.003	0.000	0.004
as.gene	0.006	0.002	0.008
as.genes	0.001	0.000	0.002
as.genes.in.patterns	0.005	0.001	0.005
as.genotypes	0.017	0.007	0.024
as.hypotheses	0.007	0.003	0.009
as.joint.probs	0.015	0.010	0.026
as.kfold.eloss	0.049	0.006	0.055
as.kfold.posterr	0.079	0.008	0.087
as.kfold.prederr	0.113	0.003	0.115
as.marginal.probs	0.004	0.001	0.005
as.models	0.026	0.018	0.043
as.parameters	0.003	0.001	0.005
as.pathway	0.007	0.001	0.008
as.patterns	0.001	0.000	0.002
as.samples	0.002	0.000	0.002
as.selective.advantage.relations	0.222	0.007	0.229
as.stages	0.008	0.002	0.011
as.types	0.001	0.000	0.003
as.types.in.patterns	0.004	0.001	0.006
change.color	0.002	0.001	0.004
consolidate.data	0.048	0.006	0.053
delete.event	0.005	0.001	0.006
delete.gene	0.005	0.001	0.006
delete.hypothesis	0.046	0.019	0.064
delete.model	0.003	0.001	0.004
delete.pattern	0.017	0.006	0.022
delete.samples	0.003	0.001	0.004
delete.type	0.006	0.001	0.007
duplicates	0.010	0.001	0.012
enforce.numeric	0.002	0.000	0.003
enforce.string	0.003	0.000	0.004
events.selection	0.005	0.001	0.006
export.graphml	0.112	0.003	0.116
export.mutex	0.011	0.002	0.013
has.duplicates	0.001	0.001	0.002
has.model	0.001	0.001	0.001
has.stages	0.009	0.001	0.012
import.GISTIC	0.007	0.000	0.008
import.MAF	0.099	0.006	0.108
intersect.datasets	0.001	0.001	0.002
is.compliant	0.002	0.001	0.003
join.events	0.015	0.001	0.016
join.types	0.056	0.008	0.066
keysToNames	0.006	0.001	0.008
nameToKey	0.002	0.001	0.004
nevents	0.001	0.001	0.002
ngenes	0.001	0.000	0.001
nhypotheses	0.001	0.000	0.002
npatterns	0.002	0.001	0.001
nsamples	0.001	0.001	0.002
ntypes	0.001	0.000	0.002
oncoprint.cbio	0.005	0.000	0.007
order.frequency	0.013	0.006	0.020
pheatmap	0.044	0.001	0.045
rank.recurrents	0.004	0.000	0.004
rename.gene	0.002	0.000	0.003
rename.type	0.002	0.000	0.003
samples.selection	0.005	0.001	0.006
trim	0.003	0.001	0.004
tronco.bootstrap	0.253	0.091	24.652
tronco.caprese	0.152	0.004	0.168
tronco.capri	3.431	0.112	3.603
tronco.chowliu	2.153	0.030	2.200
tronco.edmonds	1.944	0.018	1.976
tronco.gabow	2.062	0.018	2.092
tronco.kfold.eloss	0.187	0.033	0.220
tronco.kfold.posterr	0.295	0.129	12.590
tronco.kfold.prederr	0.236	0.119	12.013
tronco.plot	0.175	0.003	0.189
tronco.prim	3.127	0.066	3.216
view	0.003	0.001	0.005
which.samples	0.003	0.001	0.003