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 06:08:08 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 06:14:34 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 385.9 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) (2019-03-18 r76245)
* 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 0.424  0.265  16.799
tronco.kfold.prederr 0.381  0.249  16.779
tronco.bootstrap     0.340  0.176  30.354
* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 8 edges out of 50 (16%)
*** 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 7 edges out of 51 (14%)
*** 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 7 edges out of 50 (14%)
*** 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 9 edges out of 53 (17%)
*** 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 
 74.433   3.184 198.070 

name	user	system	elapsed
TCGA.multiple.samples	0.019	0.006	0.025
TCGA.remove.multiple.samples	0.035	0.022	0.058
TCGA.shorten.barcodes	0.027	0.014	0.041
annotate.description	0.018	0.011	0.030
annotate.stages	0.018	0.004	0.022
as.adj.matrix	0.016	0.014	0.030
as.alterations	0.008	0.002	0.011
as.bootstrap.scores	0.066	0.005	0.070
as.colors	0.002	0.002	0.005
as.confidence	0.023	0.024	0.047
as.description	0.001	0.001	0.003
as.events	0.003	0.001	0.005
as.events.in.patterns	0.005	0.002	0.007
as.events.in.sample	0.009	0.001	0.011
as.gene	0.005	0.002	0.007
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.004	0.001	0.005
as.genotypes	0.013	0.008	0.021
as.hypotheses	0.007	0.004	0.010
as.joint.probs	0.014	0.013	0.028
as.kfold.eloss	0.041	0.008	0.049
as.kfold.posterr	0.066	0.010	0.077
as.kfold.prederr	0.156	0.005	0.162
as.marginal.probs	0.009	0.004	0.012
as.models	0.047	0.050	0.096
as.parameters	0.003	0.001	0.004
as.pathway	0.006	0.002	0.009
as.patterns	0.002	0.001	0.003
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.277	0.018	0.295
as.stages	0.016	0.007	0.022
as.types	0.002	0.001	0.004
as.types.in.patterns	0.008	0.004	0.012
change.color	0.003	0.002	0.004
consolidate.data	0.073	0.018	0.091
delete.event	0.008	0.004	0.012
delete.gene	0.008	0.003	0.010
delete.hypothesis	0.066	0.040	0.105
delete.model	0.004	0.002	0.005
delete.pattern	0.021	0.012	0.034
delete.samples	0.004	0.002	0.006
delete.type	0.007	0.003	0.009
duplicates	0.002	0.001	0.004
enforce.numeric	0.006	0.003	0.010
enforce.string	0.005	0.002	0.007
events.selection	0.018	0.006	0.025
export.graphml	0.148	0.006	0.154
export.mutex	0.017	0.005	0.021
has.duplicates	0.003	0.002	0.005
has.model	0.003	0.002	0.005
has.stages	0.014	0.004	0.018
import.GISTIC	0.009	0.001	0.009
import.MAF	0.133	0.012	0.146
intersect.datasets	0.001	0.001	0.003
is.compliant	0.003	0.001	0.003
join.events	0.005	0.001	0.007
join.types	0.095	0.023	0.117
keysToNames	0.009	0.004	0.013
nameToKey	0.003	0.002	0.005
nevents	0.002	0.002	0.004
ngenes	0.002	0.002	0.003
nhypotheses	0.002	0.001	0.002
npatterns	0.002	0.001	0.002
nsamples	0.002	0.002	0.004
ntypes	0.002	0.002	0.005
oncoprint.cbio	0.010	0.003	0.013
order.frequency	0.018	0.017	0.035
pheatmap	0.070	0.002	0.073
rank.recurrents	0.006	0.002	0.008
rename.gene	0.003	0.001	0.004
rename.type	0.002	0.001	0.003
samples.selection	0.006	0.001	0.008
trim	0.005	0.002	0.006
tronco.bootstrap	0.340	0.176	30.354
tronco.caprese	0.227	0.012	0.250
tronco.capri	3.229	0.196	3.424
tronco.chowliu	2.677	0.061	2.739
tronco.edmonds	2.802	0.100	2.929
tronco.gabow	2.506	0.049	2.553
tronco.kfold.eloss	0.264	0.070	0.336
tronco.kfold.posterr	0.424	0.265	16.799
tronco.kfold.prederr	0.381	0.249	16.779
tronco.plot	0.303	0.006	0.313
tronco.prim	3.222	0.098	3.366
view	0.004	0.001	0.006
which.samples	0.004	0.002	0.005