Multiple platform build/check report for BioC 3.15 - CHECK results for TRONCO on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4386
palomino3	Windows Server 2022 Datacenter	x64	4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"	4138
merida1	macOS 10.14.6 Mojave	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4205
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_2.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/TRONCO.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘2.28.0’
* 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 0.235  0.063   5.822
tronco.kfold.prederr 0.182  0.055   5.367
tronco.bootstrap     0.198  0.019  17.676
* 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-3.15-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/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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 7 edges out of 50 (14%)
*** 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 46 (9%)
*** 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 54 (15%)
*** 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 7 edges out of 49 (14%)
*** 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 14 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 75.126   1.260 160.250

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.026	0.004	0.029
TCGA.remove.multiple.samples	0.025	0.011	0.036
TCGA.shorten.barcodes	0.065	0.007	0.072
annotate.description	0.016	0.009	0.026
annotate.stages	0.013	0.003	0.016
as.adj.matrix	0.016	0.011	0.027
as.alterations	0.007	0.002	0.009
as.bootstrap.scores	0.189	0.003	0.193
as.colors	0.003	0.002	0.004
as.confidence	0.016	0.015	0.031
as.description	0.003	0.002	0.004
as.events	0.003	0.002	0.006
as.events.in.patterns	0.008	0.002	0.009
as.events.in.sample	0.008	0.001	0.009
as.gene	0.005	0.002	0.007
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.007	0.002	0.008
as.genotypes	0.015	0.007	0.023
as.hypotheses	0.005	0.004	0.009
as.joint.probs	0.014	0.011	0.025
as.kfold.eloss	0.136	0.004	0.141
as.kfold.posterr	0.168	0.012	0.179
as.kfold.prederr	0.173	0.012	0.185
as.marginal.probs	0.006	0.003	0.009
as.models	0.022	0.023	0.045
as.parameters	0.005	0.001	0.006
as.pathway	0.009	0.002	0.012
as.patterns	0.004	0.002	0.005
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.189	0.019	0.208
as.stages	0.014	0.003	0.016
as.types	0.003	0.001	0.004
as.types.in.patterns	0.006	0.002	0.007
change.color	0.004	0.002	0.005
consolidate.data	0.068	0.003	0.071
delete.event	0.009	0.002	0.010
delete.gene	0.009	0.002	0.010
delete.hypothesis	0.052	0.021	0.073
delete.model	0.006	0.001	0.007
delete.pattern	0.019	0.009	0.027
delete.samples	0.005	0.002	0.007
delete.type	0.009	0.002	0.011
duplicates	0.003	0.002	0.005
enforce.numeric	0.004	0.001	0.005
enforce.string	0.005	0.001	0.006
events.selection	0.007	0.002	0.009
export.graphml	0.129	0.008	0.137
export.mutex	0.015	0.004	0.019
has.duplicates	0.003	0.002	0.004
has.model	0.003	0.002	0.005
has.stages	0.012	0.004	0.015
import.GISTIC	0.010	0.003	0.012
import.MAF	0.139	0.007	0.145
intersect.datasets	0.002	0.001	0.004
is.compliant	0.002	0.001	0.004
join.events	0.007	0.001	0.008
join.types	0.075	0.009	0.084
keysToNames	0.008	0.003	0.011
nameToKey	0.005	0.002	0.007
nevents	0.002	0.001	0.004
ngenes	0.002	0.002	0.003
nhypotheses	0.003	0.001	0.003
npatterns	0.003	0.002	0.004
nsamples	0.003	0.001	0.003
ntypes	0.003	0.002	0.004
oncoprint.cbio	0.011	0.002	0.013
order.frequency	0.012	0.010	0.023
pheatmap	0.060	0.001	0.061
rank.recurrents	0.007	0.002	0.008
rename.gene	0.004	0.002	0.005
rename.type	0.004	0.001	0.006
samples.selection	0.006	0.001	0.008
trim	0.006	0.001	0.007
tronco.bootstrap	0.198	0.019	17.676
tronco.caprese	0.211	0.004	0.217
tronco.capri	3.664	0.093	3.761
tronco.chowliu	2.682	0.024	2.709
tronco.edmonds	2.455	0.015	2.473
tronco.gabow	2.356	0.021	2.381
tronco.kfold.eloss	0.189	0.042	0.231
tronco.kfold.posterr	0.235	0.063	5.822
tronco.kfold.prederr	0.182	0.055	5.367
tronco.plot	0.267	0.011	0.279
tronco.prim	4.598	0.054	4.664
view	0.008	0.002	0.009
which.samples	0.005	0.002	0.007

CHECK results for TRONCO on merida1

Summary

Command output

Installation output

Tests output

Example timings