Package: TRONCO

Version: 2.16.2

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TRONCO_2.16.2.tar.gz

StartedAt: 2019-10-16 05:35:31 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:39:31 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 239.9 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings TRONCO_2.16.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TRONCO.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.259  0.349   9.609
tronco.kfold.prederr 0.177  0.358   9.300
tronco.bootstrap     0.218  0.256  18.325
* 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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL TRONCO
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 9 edges out of 51 (18%)
*** 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 4 edges out of 45 (9%)
*** 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 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: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 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:02s 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 225 | SKIPPED: 0 | WARNINGS: 28 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 45.107   2.286 118.612 

name	user	system	elapsed
TCGA.multiple.samples	0.02	0.00	0.02
TCGA.remove.multiple.samples	0.027	0.000	0.027
TCGA.shorten.barcodes	0.015	0.004	0.019
annotate.description	0.017	0.000	0.017
annotate.stages	0.02	0.00	0.02
as.adj.matrix	0.011	0.007	0.016
as.alterations	0.005	0.000	0.006
as.bootstrap.scores	0.057	0.000	0.056
as.colors	0.002	0.000	0.001
as.confidence	0.007	0.012	0.019
as.description	0.000	0.002	0.002
as.events	0.001	0.001	0.003
as.events.in.patterns	0.011	0.000	0.011
as.events.in.sample	0.005	0.000	0.005
as.gene	0.005	0.000	0.005
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.005	0.000	0.005
as.genotypes	0.005	0.008	0.013
as.hypotheses	0.006	0.000	0.006
as.joint.probs	0.003	0.012	0.015
as.kfold.eloss	0.064	0.004	0.068
as.kfold.posterr	0.093	0.004	0.098
as.kfold.prederr	0.138	0.000	0.139
as.marginal.probs	0.005	0.000	0.005
as.models	0.021	0.012	0.033
as.parameters	0.003	0.000	0.003
as.pathway	0.007	0.000	0.007
as.patterns	0.002	0.000	0.002
as.samples	0.002	0.000	0.001
as.selective.advantage.relations	0.238	0.004	0.244
as.stages	0.009	0.000	0.009
as.types	0.002	0.001	0.001
as.types.in.patterns	0.002	0.002	0.005
change.color	0.003	0.000	0.002
consolidate.data	0.044	0.004	0.048
delete.event	0.002	0.004	0.007
delete.gene	0.003	0.004	0.007
delete.hypothesis	0.044	0.008	0.051
delete.model	0.004	0.000	0.004
delete.pattern	0.015	0.004	0.018
delete.samples	0.002	0.000	0.003
delete.type	0.004	0.000	0.004
duplicates	0.002	0.000	0.001
enforce.numeric	0.003	0.000	0.003
enforce.string	0.006	0.004	0.009
events.selection	0.003	0.000	0.003
export.graphml	0.129	0.000	0.147
export.mutex	0.013	0.000	0.014
has.duplicates	0.002	0.000	0.002
has.model	0.002	0.000	0.002
has.stages	0.01	0.00	0.01
import.GISTIC	0.007	0.000	0.007
import.MAF	0.103	0.000	0.103
intersect.datasets	0.001	0.000	0.001
is.compliant	0.002	0.000	0.002
join.events	0.005	0.000	0.005
join.types	0.070	0.008	0.077
keysToNames	0.006	0.000	0.007
nameToKey	0.003	0.000	0.003
nevents	0.002	0.000	0.002
ngenes	0.001	0.000	0.002
nhypotheses	0.002	0.000	0.001
npatterns	0.002	0.000	0.002
nsamples	0.001	0.000	0.002
ntypes	0.001	0.000	0.001
oncoprint.cbio	0.008	0.000	0.008
order.frequency	0.002	0.012	0.013
pheatmap	0.056	0.004	0.061
rank.recurrents	0.001	0.004	0.004
rename.gene	0.002	0.000	0.003
rename.type	0.002	0.000	0.002
samples.selection	0.000	0.004	0.004
trim	0.004	0.000	0.004
tronco.bootstrap	0.218	0.256	18.325
tronco.caprese	0.191	0.012	0.206
tronco.capri	2.730	0.012	2.741
tronco.chowliu	1.474	0.000	1.473
tronco.edmonds	1.39	0.00	1.39
tronco.gabow	1.555	0.000	1.556
tronco.kfold.eloss	0.118	0.012	0.129
tronco.kfold.posterr	0.259	0.349	9.609
tronco.kfold.prederr	0.177	0.358	9.300
tronco.plot	0.159	0.008	0.176
tronco.prim	2.141	0.044	2.185
view	0.006	0.000	0.005
which.samples	0.004	0.000	0.004