Multiple platform build/check report for BioC 3.12 - 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_2.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/TRONCO.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.22.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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 0.223  0.107   5.556
tronco.kfold.prederr 0.179  0.087   6.024
tronco.bootstrap     0.162  0.017  12.305
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/TRONCO.Rcheck/00check.log’
for details.

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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 49 (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 11 edges out of 56 (20%)
*** 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 5 edges out of 43 (12%)
*** 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 46 (13%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s 
[ FAIL 0 | WARN 28 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 63.275   1.007 128.421

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.019	0.004	0.023
TCGA.remove.multiple.samples	0.027	0.017	0.045
TCGA.shorten.barcodes	0.018	0.018	0.036
annotate.description	0.016	0.014	0.031
annotate.stages	0.012	0.003	0.016
as.adj.matrix	0.015	0.020	0.035
as.alterations	0.005	0.002	0.006
as.bootstrap.scores	0.108	0.004	0.113
as.colors	0.002	0.002	0.003
as.confidence	0.015	0.022	0.037
as.description	0.002	0.002	0.003
as.events	0.004	0.003	0.006
as.events.in.patterns	0.005	0.002	0.006
as.events.in.sample	0.005	0.001	0.007
as.gene	0.004	0.003	0.007
as.genes	0.003	0.002	0.004
as.genes.in.patterns	0.107	0.002	0.109
as.genotypes	0.011	0.011	0.023
as.hypotheses	0.007	0.005	0.012
as.joint.probs	0.014	0.020	0.034
as.kfold.eloss	0.052	0.005	0.058
as.kfold.posterr	0.063	0.006	0.069
as.kfold.prederr	0.071	0.009	0.080
as.marginal.probs	0.004	0.002	0.007
as.models	0.020	0.034	0.054
as.parameters	0.003	0.001	0.004
as.pathway	0.006	0.002	0.008
as.patterns	0.002	0.001	0.002
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.122	0.020	0.143
as.stages	0.007	0.002	0.009
as.types	0.001	0.001	0.003
as.types.in.patterns	0.004	0.001	0.004
change.color	0.002	0.001	0.003
consolidate.data	0.036	0.001	0.038
delete.event	0.008	0.001	0.010
delete.gene	0.004	0.000	0.005
delete.hypothesis	0.038	0.029	0.067
delete.model	0.003	0.001	0.004
delete.pattern	0.015	0.010	0.023
delete.samples	0.003	0.001	0.003
delete.type	0.004	0.001	0.006
duplicates	0.002	0.001	0.002
enforce.numeric	0.003	0.001	0.004
enforce.string	0.003	0.001	0.003
events.selection	0.005	0.002	0.006
export.graphml	0.090	0.006	0.096
export.mutex	0.010	0.003	0.013
has.duplicates	0.002	0.001	0.002
has.model	0.001	0.001	0.003
has.stages	0.007	0.002	0.009
import.GISTIC	0.007	0.002	0.008
import.MAF	0.078	0.007	0.085
intersect.datasets	0.001	0.002	0.003
is.compliant	0.002	0.002	0.003
join.events	0.005	0.001	0.005
join.types	0.073	0.018	0.091
keysToNames	0.009	0.003	0.012
nameToKey	0.003	0.001	0.003
nevents	0.001	0.001	0.003
ngenes	0.002	0.001	0.003
nhypotheses	0.001	0.001	0.002
npatterns	0.002	0.001	0.003
nsamples	0.002	0.001	0.003
ntypes	0.002	0.001	0.002
oncoprint.cbio	0.009	0.001	0.010
order.frequency	0.013	0.014	0.027
pheatmap	0.047	0.002	0.049
rank.recurrents	0.004	0.001	0.005
rename.gene	0.002	0.001	0.003
rename.type	0.004	0.002	0.005
samples.selection	0.004	0.002	0.006
trim	0.005	0.002	0.006
tronco.bootstrap	0.162	0.017	12.305
tronco.caprese	0.164	0.004	0.168
tronco.capri	2.650	0.062	2.715
tronco.chowliu	2.402	0.038	2.449
tronco.edmonds	2.303	0.020	2.327
tronco.gabow	2.084	0.026	2.112
tronco.kfold.eloss	0.206	0.065	0.272
tronco.kfold.posterr	0.223	0.107	5.556
tronco.kfold.prederr	0.179	0.087	6.024
tronco.plot	0.209	0.005	0.216
tronco.prim	3.387	0.037	3.428
view	0.004	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