Multiple platform build/check report for BioC 3.11 - CHECK report for TRONCO on machv2

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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_2.20.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TRONCO.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.264  0.155   5.166
tronco.bootstrap     0.194  0.046  19.523
* 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/4.0/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)

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-apple-darwin17.0 (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 45 (13%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:04s 
*** 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 12 edges out of 58 (21%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:04s 
*** 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 9 edges out of 54 (17%)
*** 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:04s 
*** 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:04s 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 225 | SKIPPED: 0 | WARNINGS: 28 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 84.515   1.279 158.771

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.016	0.004	0.019
TCGA.remove.multiple.samples	0.028	0.020	0.047
TCGA.shorten.barcodes	0.022	0.021	0.043
annotate.description	0.022	0.018	0.039
annotate.stages	0.009	0.002	0.011
as.adj.matrix	0.019	0.023	0.043
as.alterations	0.007	0.003	0.011
as.bootstrap.scores	0.113	0.004	0.117
as.colors	0.001	0.001	0.003
as.confidence	0.017	0.025	0.041
as.description	0.002	0.002	0.003
as.events	0.003	0.002	0.005
as.events.in.patterns	0.007	0.002	0.010
as.events.in.sample	0.007	0.001	0.009
as.gene	0.007	0.004	0.011
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.005	0.002	0.007
as.genotypes	0.116	0.013	0.130
as.hypotheses	0.008	0.007	0.015
as.joint.probs	0.018	0.023	0.041
as.kfold.eloss	0.067	0.006	0.074
as.kfold.posterr	0.097	0.008	0.106
as.kfold.prederr	0.108	0.013	0.122
as.marginal.probs	0.006	0.004	0.011
as.models	0.031	0.051	0.083
as.parameters	0.004	0.002	0.005
as.pathway	0.008	0.003	0.011
as.patterns	0.002	0.001	0.004
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.189	0.030	0.219
as.stages	0.013	0.004	0.016
as.types	0.002	0.001	0.004
as.types.in.patterns	0.006	0.002	0.008
change.color	0.004	0.002	0.004
consolidate.data	0.048	0.002	0.051
delete.event	0.008	0.001	0.009
delete.gene	0.008	0.002	0.009
delete.hypothesis	0.052	0.038	0.090
delete.model	0.002	0.001	0.004
delete.pattern	0.020	0.011	0.031
delete.samples	0.004	0.001	0.004
delete.type	0.008	0.002	0.010
duplicates	0.003	0.002	0.004
enforce.numeric	0.004	0.001	0.006
enforce.string	0.005	0.002	0.007
events.selection	0.006	0.003	0.008
export.graphml	0.139	0.010	0.149
export.mutex	0.011	0.004	0.014
has.duplicates	0.001	0.001	0.002
has.model	0.002	0.001	0.003
has.stages	0.022	0.003	0.025
import.GISTIC	0.009	0.001	0.010
import.MAF	0.091	0.006	0.098
intersect.datasets	0.001	0.001	0.003
is.compliant	0.003	0.001	0.004
join.events	0.007	0.002	0.009
join.types	0.057	0.015	0.072
keysToNames	0.009	0.004	0.013
nameToKey	0.003	0.002	0.006
nevents	0.001	0.000	0.002
ngenes	0.001	0.001	0.002
nhypotheses	0.001	0.002	0.003
npatterns	0.002	0.002	0.003
nsamples	0.002	0.002	0.003
ntypes	0.002	0.001	0.003
oncoprint.cbio	0.009	0.002	0.012
order.frequency	0.014	0.017	0.031
pheatmap	0.047	0.002	0.050
rank.recurrents	0.006	0.001	0.008
rename.gene	0.003	0.001	0.004
rename.type	0.003	0.001	0.004
samples.selection	0.005	0.001	0.006
trim	0.006	0.002	0.007
tronco.bootstrap	0.194	0.046	19.523
tronco.caprese	0.209	0.006	0.227
tronco.capri	3.370	0.090	3.465
tronco.chowliu	2.425	0.020	2.446
tronco.edmonds	2.324	0.019	2.346
tronco.gabow	2.620	0.027	2.649
tronco.kfold.eloss	0.225	0.084	0.309
tronco.kfold.posterr	0.264	0.155	5.166
tronco.kfold.prederr	0.191	0.156	4.837
tronco.plot	0.180	0.005	0.185
tronco.prim	4.179	0.052	4.238
view	0.007	0.002	0.008
which.samples	0.003	0.001	0.005

CHECK report for TRONCO on machv2

Summary

Command output

Installation output

Tests output

Example timings