Multiple platform build/check report for BioC 3.12 - CHECK report for TRONCO on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings TRONCO_2.22.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/TRONCO.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.22.0’
* 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’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/1_introduction.Rmd’
   ‘vignettes/2_loading_data.Rmd’
   ‘vignettes/3_data_visualization.Rmd’
   ‘vignettes/4_data_manipulation.Rmd’
   ‘vignettes/5_model_inference.Rmd’
   ‘vignettes/6_post_reconstruction.Rmd’
   ‘vignettes/7_import_export.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.212  0.048   5.122
tronco.kfold.prederr 0.140  0.092   5.414
tronco.bootstrap     0.188  0.032  12.031
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/TRONCO.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL TRONCO
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* installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 8 edges out of 52 (15%)
*** 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 54 (13%)
*** 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 3 edges out of 46 (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 6 edges out of 49 (12%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s 
[ FAIL 0 | WARN 28 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 57.688   1.164 122.614

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.024	0.000	0.023
TCGA.remove.multiple.samples	0.024	0.004	0.027
TCGA.shorten.barcodes	0.012	0.008	0.019
annotate.description	0.016	0.004	0.018
annotate.stages	0.012	0.000	0.013
as.adj.matrix	0.020	0.000	0.017
as.alterations	0.004	0.000	0.006
as.bootstrap.scores	0.108	0.000	0.110
as.colors	0.004	0.000	0.002
as.confidence	0.016	0.004	0.018
as.description	0.000	0.000	0.001
as.events	0.000	0.004	0.002
as.events.in.patterns	0.008	0.000	0.006
as.events.in.sample	0.004	0.000	0.006
as.gene	0.116	0.000	0.116
as.genes	0.004	0.000	0.002
as.genes.in.patterns	0.004	0.000	0.004
as.genotypes	0.004	0.004	0.008
as.hypotheses	0.000	0.000	0.004
as.joint.probs	0.000	0.012	0.010
as.kfold.eloss	0.036	0.000	0.036
as.kfold.posterr	0.052	0.004	0.054
as.kfold.prederr	0.040	0.016	0.057
as.marginal.probs	0.004	0.000	0.004
as.models	0.016	0.004	0.020
as.parameters	0.004	0.000	0.002
as.pathway	0.004	0.000	0.005
as.patterns	0.004	0.000	0.002
as.samples	0.000	0.000	0.002
as.selective.advantage.relations	0.072	0.020	0.093
as.stages	0.004	0.000	0.006
as.types	0.004	0.000	0.001
as.types.in.patterns	0.000	0.000	0.004
change.color	0.000	0.000	0.002
consolidate.data	0.024	0.000	0.026
delete.event	0.004	0.000	0.004
delete.gene	0.004	0.000	0.004
delete.hypothesis	0.020	0.012	0.031
delete.model	0.000	0.000	0.002
delete.pattern	0.012	0.000	0.012
delete.samples	0.004	0.000	0.002
delete.type	0.004	0.000	0.004
duplicates	0.000	0.004	0.001
enforce.numeric	0.000	0.000	0.001
enforce.string	0.004	0.000	0.002
events.selection	0.004	0.000	0.006
export.graphml	0.076	0.004	0.083
export.mutex	0.012	0.000	0.009
has.duplicates	0.000	0.000	0.001
has.model	0.000	0.004	0.001
has.stages	0.000	0.004	0.006
import.GISTIC	0.000	0.004	0.005
import.MAF	0.064	0.000	0.067
intersect.datasets	0.000	0.000	0.001
is.compliant	0.004	0.000	0.002
join.events	0.004	0.000	0.003
join.types	0.056	0.008	0.063
keysToNames	0.008	0.000	0.007
nameToKey	0.004	0.000	0.003
nevents	0.000	0.000	0.002
ngenes	0.004	0.000	0.001
nhypotheses	0.000	0.000	0.002
npatterns	0.000	0.000	0.002
nsamples	0.004	0.000	0.001
ntypes	0.000	0.000	0.002
oncoprint.cbio	0.012	0.000	0.009
order.frequency	0.016	0.000	0.014
pheatmap	0.048	0.000	0.050
rank.recurrents	0.008	0.000	0.005
rename.gene	0.004	0.000	0.003
rename.type	0.004	0.000	0.003
samples.selection	0.004	0.000	0.005
trim	0.004	0.000	0.005
tronco.bootstrap	0.188	0.032	12.031
tronco.caprese	0.180	0.016	0.195
tronco.capri	2.792	0.016	2.824
tronco.chowliu	1.864	0.000	1.867
tronco.edmonds	1.468	0.000	1.468
tronco.gabow	2.084	0.004	2.094
tronco.kfold.eloss	0.152	0.020	0.176
tronco.kfold.posterr	0.212	0.048	5.122
tronco.kfold.prederr	0.140	0.092	5.414
tronco.plot	0.260	0.016	0.276
tronco.prim	2.564	0.028	2.596
view	0.008	0.000	0.004
which.samples	0.004	0.000	0.004

CHECK report for TRONCO on malbec1

Summary

Command output

Installation output

Tests output

Example timings