Package: TRONCO

Version: 2.15.2

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_2.15.2.tar.gz

StartedAt: 2019-04-09 04:10:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:14:56 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 245.5 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_2.15.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.15.2’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.187  0.347   9.236
tronco.kfold.prederr 0.186  0.347   9.452
tronco.bootstrap     0.170  0.273  16.820
* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 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: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 56 (11%)
*** 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 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:02s 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 253 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 47.325   2.222 121.600 

name	user	system	elapsed
TCGA.multiple.samples	0.013	0.000	0.012
TCGA.remove.multiple.samples	0.011	0.004	0.014
TCGA.shorten.barcodes	0.006	0.004	0.011
annotate.description	0.009	0.004	0.013
annotate.stages	0.015	0.000	0.015
as.adj.matrix	0.003	0.008	0.011
as.alterations	0.004	0.000	0.004
as.bootstrap.scores	0.035	0.000	0.034
as.colors	0.001	0.000	0.001
as.confidence	0.012	0.000	0.012
as.description	0.001	0.000	0.001
as.events	0.001	0.000	0.002
as.events.in.patterns	0.008	0.000	0.008
as.events.in.sample	0.003	0.000	0.004
as.gene	0.003	0.000	0.003
as.genes	0.001	0.000	0.001
as.genes.in.patterns	0.004	0.000	0.003
as.genotypes	0.004	0.004	0.008
as.hypotheses	0.003	0.000	0.003
as.joint.probs	0.009	0.000	0.009
as.kfold.eloss	0.035	0.004	0.038
as.kfold.posterr	0.048	0.008	0.055
as.kfold.prederr	0.092	0.000	0.092
as.marginal.probs	0.002	0.001	0.004
as.models	0.011	0.010	0.021
as.parameters	0.002	0.000	0.002
as.pathway	0.005	0.000	0.005
as.patterns	0.002	0.000	0.002
as.samples	0.001	0.000	0.002
as.selective.advantage.relations	0.184	0.000	0.185
as.stages	0.006	0.000	0.006
as.types	0.001	0.000	0.001
as.types.in.patterns	0.003	0.000	0.003
change.color	0.000	0.002	0.002
consolidate.data	0.026	0.002	0.028
delete.event	0.004	0.000	0.004
delete.gene	0.004	0.000	0.004
delete.hypothesis	0.019	0.012	0.030
delete.model	0.003	0.000	0.003
delete.pattern	0.008	0.004	0.012
delete.samples	0.003	0.000	0.002
delete.type	0.004	0.000	0.003
duplicates	0.001	0.000	0.001
enforce.numeric	0.000	0.002	0.002
enforce.string	0.001	0.001	0.002
events.selection	0.004	0.000	0.004
export.graphml	0.077	0.004	0.085
export.mutex	0.007	0.000	0.008
has.duplicates	0.001	0.000	0.001
has.model	0.000	0.001	0.001
has.stages	0.003	0.002	0.005
import.GISTIC	0.004	0.000	0.004
import.MAF	0.092	0.000	0.091
intersect.datasets	0.001	0.000	0.001
is.compliant	0.002	0.000	0.002
join.events	0.006	0.000	0.006
join.types	0.067	0.008	0.075
keysToNames	0.006	0.000	0.007
nameToKey	0.003	0.000	0.004
nevents	0.000	0.002	0.002
ngenes	0.000	0.001	0.001
nhypotheses	0.001	0.000	0.002
npatterns	0.002	0.000	0.002
nsamples	0.002	0.000	0.001
ntypes	0.001	0.000	0.001
oncoprint.cbio	0.004	0.004	0.009
order.frequency	0.006	0.008	0.014
pheatmap	0.061	0.000	0.061
rank.recurrents	0.005	0.000	0.005
rename.gene	0.003	0.000	0.002
rename.type	0.002	0.000	0.002
samples.selection	0.004	0.000	0.004
trim	0.004	0.000	0.004
tronco.bootstrap	0.170	0.273	16.820
tronco.caprese	0.108	0.008	0.117
tronco.capri	1.872	0.028	1.900
tronco.chowliu	1.429	0.005	1.433
tronco.edmonds	1.258	0.000	1.258
tronco.gabow	1.819	0.004	1.824
tronco.kfold.eloss	0.129	0.008	0.137
tronco.kfold.posterr	0.187	0.347	9.236
tronco.kfold.prederr	0.186	0.347	9.452
tronco.plot	0.258	0.013	0.270
tronco.prim	3.332	0.055	3.388
view	0.005	0.000	0.005
which.samples	0.000	0.004	0.004