Multiple platform build/check report for BioC 3.14 - CHECK results for TRONCO on machv2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TRONCO_2.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/TRONCO.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.26.0’
* 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 0.242  0.130   6.025
tronco.kfold.prederr 0.179  0.124   6.205
tronco.bootstrap     0.201  0.019  14.854
* 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-3.14-bioc/meat/TRONCO.Rcheck/00check.log’
for details.

Installation output

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TRONCO
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘TRONCO’ ...
** using staged installation
** R
** data
** 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 54 (11%)
*** 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 4 edges out of 49 (8%)
*** 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 8 edges out of 49 (16%)
*** 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 52 (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 ]

[ FAIL 0 | WARN 28 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 66.445   1.354 145.447

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.016	0.003	0.020
TCGA.remove.multiple.samples	0.034	0.017	0.052
TCGA.shorten.barcodes	0.017	0.012	0.029
annotate.description	0.017	0.019	0.037
annotate.stages	0.013	0.003	0.017
as.adj.matrix	0.018	0.023	0.041
as.alterations	0.006	0.002	0.007
as.bootstrap.scores	0.129	0.005	0.135
as.colors	0.002	0.001	0.002
as.confidence	0.016	0.027	0.042
as.description	0.002	0.002	0.004
as.events	0.003	0.003	0.006
as.events.in.patterns	0.137	0.003	0.139
as.events.in.sample	0.007	0.002	0.009
as.gene	0.007	0.004	0.011
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.006	0.001	0.008
as.genotypes	0.014	0.012	0.026
as.hypotheses	0.005	0.005	0.010
as.joint.probs	0.013	0.017	0.030
as.kfold.eloss	0.127	0.003	0.130
as.kfold.posterr	0.128	0.008	0.136
as.kfold.prederr	0.163	0.010	0.174
as.marginal.probs	0.007	0.003	0.011
as.models	0.025	0.049	0.074
as.parameters	0.005	0.002	0.007
as.pathway	0.010	0.003	0.013
as.patterns	0.003	0.002	0.005
as.samples	0.002	0.002	0.004
as.selective.advantage.relations	0.156	0.024	0.179
as.stages	0.009	0.003	0.012
as.types	0.003	0.002	0.004
as.types.in.patterns	0.005	0.002	0.006
change.color	0.004	0.001	0.005
consolidate.data	0.063	0.002	0.066
delete.event	0.009	0.001	0.010
delete.gene	0.007	0.001	0.009
delete.hypothesis	0.059	0.051	0.110
delete.model	0.006	0.001	0.007
delete.pattern	0.021	0.014	0.034
delete.samples	0.003	0.002	0.005
delete.type	0.007	0.002	0.009
duplicates	0.004	0.002	0.005
enforce.numeric	0.004	0.002	0.006
enforce.string	0.005	0.002	0.007
events.selection	0.008	0.003	0.011
export.graphml	0.145	0.007	0.152
export.mutex	0.015	0.005	0.020
has.duplicates	0.003	0.002	0.005
has.model	0.003	0.002	0.005
has.stages	0.010	0.004	0.015
import.GISTIC	0.011	0.003	0.014
import.MAF	0.123	0.009	0.132
intersect.datasets	0.002	0.002	0.004
is.compliant	0.002	0.001	0.003
join.events	0.007	0.002	0.009
join.types	0.082	0.025	0.107
keysToNames	0.008	0.004	0.012
nameToKey	0.003	0.001	0.004
nevents	0.001	0.000	0.002
ngenes	0.002	0.001	0.003
nhypotheses	0.003	0.002	0.003
npatterns	0.003	0.002	0.003
nsamples	0.002	0.001	0.004
ntypes	0.002	0.001	0.004
oncoprint.cbio	0.010	0.002	0.013
order.frequency	0.007	0.010	0.018
pheatmap	0.049	0.001	0.051
rank.recurrents	0.004	0.001	0.006
rename.gene	0.004	0.002	0.005
rename.type	0.002	0.001	0.004
samples.selection	0.006	0.001	0.008
trim	0.006	0.001	0.007
tronco.bootstrap	0.201	0.019	14.854
tronco.caprese	0.212	0.005	0.219
tronco.capri	3.162	0.094	3.262
tronco.chowliu	1.858	0.017	1.877
tronco.edmonds	2.297	0.031	2.334
tronco.gabow	3.363	0.045	3.411
tronco.kfold.eloss	0.240	0.092	0.333
tronco.kfold.posterr	0.242	0.130	6.025
tronco.kfold.prederr	0.179	0.124	6.205
tronco.plot	0.266	0.006	0.272
tronco.prim	3.576	0.047	3.626
view	0.005	0.002	0.006
which.samples	0.003	0.002	0.004

CHECK results for TRONCO on machv2

Summary

Command output

Installation output

Tests output

Example timings