Multiple platform build/check report for BioC 3.11 - CHECK report for TRONCO on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings TRONCO_2.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/TRONCO.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.20.1’
* 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 (user + system) or elapsed time > 5s
                  user system elapsed
tronco.bootstrap 0.234  0.044  13.472
* 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

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL TRONCO
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* installing to library ‘/home/biocbuild/bbs-3.11-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)

Tests output


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 6 edges out of 48 (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: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 5 edges out of 47 (11%)
*** 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 7 edges out of 48 (15%)
*** 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 7 edges out of 47 (15%)
*** 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 
 52.896   1.129 114.168

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.024	0.000	0.023
TCGA.remove.multiple.samples	0.024	0.004	0.028
TCGA.shorten.barcodes	0.02	0.00	0.02
annotate.description	0.014	0.004	0.018
annotate.stages	0.009	0.004	0.013
as.adj.matrix	0.014	0.004	0.019
as.alterations	0.007	0.000	0.006
as.bootstrap.scores	0.107	0.000	0.107
as.colors	0.001	0.002	0.001
as.confidence	0.011	0.009	0.021
as.description	0.001	0.000	0.002
as.events	0.003	0.000	0.003
as.events.in.patterns	0.006	0.000	0.006
as.events.in.sample	0.006	0.000	0.006
as.gene	0.006	0.000	0.006
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.115	0.000	0.115
as.genotypes	0.01	0.00	0.01
as.hypotheses	0.003	0.000	0.003
as.joint.probs	0.002	0.008	0.010
as.kfold.eloss	0.036	0.000	0.036
as.kfold.posterr	0.053	0.000	0.052
as.kfold.prederr	0.051	0.008	0.059
as.marginal.probs	0.000	0.004	0.004
as.models	0.001	0.020	0.021
as.parameters	0.002	0.000	0.002
as.pathway	0.006	0.000	0.006
as.patterns	0.002	0.000	0.002
as.samples	0.001	0.000	0.002
as.selective.advantage.relations	0.080	0.016	0.096
as.stages	0.006	0.000	0.006
as.types	0.001	0.000	0.002
as.types.in.patterns	0.003	0.000	0.003
change.color	0.000	0.002	0.002
consolidate.data	0.026	0.001	0.028
delete.event	0.004	0.000	0.004
delete.gene	0.004	0.000	0.004
delete.hypothesis	0.018	0.016	0.034
delete.model	0.002	0.000	0.002
delete.pattern	0.009	0.004	0.013
delete.samples	0.002	0.000	0.002
delete.type	0.004	0.000	0.004
duplicates	0.002	0.000	0.001
enforce.numeric	0.002	0.000	0.002
enforce.string	0.002	0.000	0.003
events.selection	0.003	0.000	0.003
export.graphml	0.090	0.000	0.101
export.mutex	0.009	0.000	0.008
has.duplicates	0.002	0.000	0.001
has.model	0.009	0.000	0.009
has.stages	0.005	0.000	0.005
import.GISTIC	0.005	0.000	0.006
import.MAF	0.057	0.000	0.057
intersect.datasets	0.000	0.001	0.001
is.compliant	0.000	0.001	0.001
join.events	0.003	0.000	0.004
join.types	0.042	0.004	0.046
keysToNames	0.005	0.000	0.004
nameToKey	0.002	0.000	0.002
nevents	0.001	0.000	0.001
ngenes	0.001	0.000	0.001
nhypotheses	0.001	0.000	0.001
npatterns	0.001	0.000	0.001
nsamples	0.000	0.001	0.001
ntypes	0.000	0.001	0.001
oncoprint.cbio	0.006	0.000	0.006
order.frequency	0.009	0.000	0.008
pheatmap	0.030	0.000	0.029
rank.recurrents	0.004	0.000	0.003
rename.gene	0.002	0.000	0.002
rename.type	0.001	0.000	0.002
samples.selection	0.002	0.000	0.003
trim	0.003	0.000	0.002
tronco.bootstrap	0.234	0.044	13.472
tronco.caprese	0.200	0.000	0.212
tronco.capri	3.449	0.017	3.466
tronco.chowliu	2.14	0.00	2.14
tronco.edmonds	1.935	0.000	1.935
tronco.gabow	1.428	0.000	1.428
tronco.kfold.eloss	0.123	0.008	0.130
tronco.kfold.posterr	0.267	0.087	4.601
tronco.kfold.prederr	0.209	0.062	4.600
tronco.plot	0.267	0.020	0.289
tronco.prim	3.679	0.056	3.735
view	0.004	0.000	0.004
which.samples	0.003	0.000	0.003

CHECK report for TRONCO on malbec2

Summary

Command output

Installation output

Tests output

Example timings