Multiple platform build/check report for BioC 3.8 - CHECK report for TRONCO on merida1

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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_2.14.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/TRONCO.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.14.2’
* 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 0.312  0.143  11.400
tronco.kfold.prederr 0.275  0.126  11.292
tronco.bootstrap     0.255  0.089  20.707
* 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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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TRONCO
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘TRONCO’ ...
** 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
* DONE (TRONCO)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 6 edges out of 51 (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: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 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 
*** 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 3 edges out of 44 (7%)
*** 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 55 (9%)
*** 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 
 62.938   1.609 150.461

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.022	0.004	0.026
TCGA.remove.multiple.samples	0.031	0.010	0.042
TCGA.shorten.barcodes	0.020	0.007	0.027
annotate.description	0.032	0.009	0.042
annotate.stages	0.014	0.002	0.016
as.adj.matrix	0.019	0.013	0.032
as.alterations	0.006	0.001	0.008
as.bootstrap.scores	0.067	0.004	0.072
as.colors	0.002	0.001	0.003
as.confidence	0.020	0.014	0.034
as.description	0.001	0.001	0.003
as.events	0.004	0.001	0.005
as.events.in.patterns	0.005	0.001	0.006
as.events.in.sample	0.006	0.001	0.008
as.gene	0.005	0.002	0.008
as.genes	0.002	0.001	0.004
as.genes.in.patterns	0.006	0.001	0.007
as.genotypes	0.015	0.006	0.025
as.hypotheses	0.009	0.004	0.013
as.joint.probs	0.015	0.010	0.025
as.kfold.eloss	0.054	0.006	0.061
as.kfold.posterr	0.106	0.008	0.114
as.kfold.prederr	0.159	0.004	0.163
as.marginal.probs	0.006	0.002	0.008
as.models	0.036	0.026	0.062
as.parameters	0.003	0.001	0.005
as.pathway	0.116	0.002	0.120
as.patterns	0.002	0.001	0.002
as.samples	0.003	0.002	0.004
as.selective.advantage.relations	0.119	0.010	0.133
as.stages	0.013	0.003	0.017
as.types	0.002	0.001	0.005
as.types.in.patterns	0.004	0.001	0.004
change.color	0.003	0.002	0.005
consolidate.data	0.057	0.008	0.073
delete.event	0.007	0.002	0.014
delete.gene	0.006	0.002	0.012
delete.hypothesis	0.064	0.024	0.118
delete.model	0.004	0.002	0.007
delete.pattern	0.025	0.009	0.034
delete.samples	0.004	0.001	0.005
delete.type	0.007	0.002	0.009
duplicates	0.002	0.001	0.005
enforce.numeric	0.005	0.002	0.006
enforce.string	0.004	0.002	0.006
events.selection	0.007	0.002	0.009
export.graphml	0.165	0.005	0.172
export.mutex	0.014	0.002	0.018
has.duplicates	0.002	0.001	0.003
has.model	0.003	0.001	0.004
has.stages	0.010	0.002	0.014
import.GISTIC	0.006	0.000	0.012
import.MAF	0.112	0.006	0.121
intersect.datasets	0.002	0.001	0.002
is.compliant	0.002	0.001	0.003
join.events	0.005	0.001	0.005
join.types	0.065	0.010	0.078
keysToNames	0.010	0.002	0.013
nameToKey	0.004	0.001	0.005
nevents	0.002	0.001	0.003
ngenes	0.001	0.002	0.002
nhypotheses	0.002	0.001	0.003
npatterns	0.002	0.001	0.003
nsamples	0.002	0.002	0.003
ntypes	0.001	0.001	0.003
oncoprint.cbio	0.010	0.001	0.011
order.frequency	0.017	0.009	0.027
pheatmap	0.074	0.001	0.075
rank.recurrents	0.005	0.001	0.007
rename.gene	0.003	0.001	0.004
rename.type	0.003	0.002	0.004
samples.selection	0.004	0.001	0.006
trim	0.005	0.001	0.006
tronco.bootstrap	0.255	0.089	20.707
tronco.caprese	0.180	0.006	0.197
tronco.capri	3.243	0.111	3.392
tronco.chowliu	2.248	0.023	2.293
tronco.edmonds	2.099	0.027	2.173
tronco.gabow	2.130	0.023	2.174
tronco.kfold.eloss	0.222	0.041	0.264
tronco.kfold.posterr	0.312	0.143	11.400
tronco.kfold.prederr	0.275	0.126	11.292
tronco.plot	0.267	0.003	0.302
tronco.prim	3.063	0.063	3.152
view	0.006	0.001	0.006
which.samples	0.003	0.001	0.004

CHECK report for TRONCO on merida1

Summary

Command output

Installation output

Tests output

Example timings