Multiple platform build/check report for BioC 3.14 - CHECK results for TRONCO on nebbiolo2

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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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings TRONCO_2.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/TRONCO.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.26.0’
* 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 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.prederr 0.182  0.075   6.964
tronco.kfold.posterr 0.200  0.039   8.409
tronco.bootstrap     0.135  0.005   7.391
* 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-3.14-bioc/meat/TRONCO.Rcheck/00check.log’
for details.

Installation output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL TRONCO
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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-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 54 (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:01s 
*** 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 5 edges out of 42 (12%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:01s 
*** 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 53 (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:01s 
*** 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 8 edges out of 51 (16%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:01s 
[ FAIL 0 | WARN 28 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 28 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 33.287   1.206  74.444

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.016	0.000	0.017
TCGA.remove.multiple.samples	0.019	0.003	0.023
TCGA.shorten.barcodes	0.006	0.004	0.010
annotate.description	0.009	0.000	0.009
annotate.stages	0.007	0.000	0.006
as.adj.matrix	0.006	0.004	0.009
as.alterations	0.003	0.000	0.004
as.bootstrap.scores	0.087	0.004	0.091
as.colors	0.001	0.000	0.002
as.confidence	0.007	0.004	0.011
as.description	0.001	0.000	0.001
as.events	0.001	0.000	0.002
as.events.in.patterns	0.004	0.000	0.003
as.events.in.sample	0.003	0.000	0.003
as.gene	0.003	0.000	0.003
as.genes	0.002	0.000	0.001
as.genes.in.patterns	0.003	0.000	0.004
as.genotypes	0.007	0.000	0.007
as.hypotheses	0.003	0.000	0.003
as.joint.probs	0.004	0.004	0.008
as.kfold.eloss	0.062	0.004	0.066
as.kfold.posterr	0.073	0.008	0.081
as.kfold.prederr	0.063	0.020	0.083
as.marginal.probs	0.004	0.000	0.003
as.models	0.016	0.000	0.017
as.parameters	0.002	0.000	0.003
as.pathway	0.005	0.000	0.005
as.patterns	0.002	0.000	0.001
as.samples	0.002	0.000	0.001
as.selective.advantage.relations	0.072	0.012	0.084
as.stages	0.006	0.000	0.006
as.types	0.002	0.000	0.001
as.types.in.patterns	0.004	0.000	0.003
change.color	0.002	0.000	0.001
consolidate.data	0.022	0.000	0.023
delete.event	0.004	0.000	0.004
delete.gene	0.004	0.000	0.004
delete.hypothesis	0.022	0.004	0.026
delete.model	0.003	0.000	0.003
delete.pattern	0.01	0.00	0.01
delete.samples	0.003	0.000	0.002
delete.type	0.004	0.000	0.004
duplicates	0.002	0.000	0.001
enforce.numeric	0.002	0.000	0.002
enforce.string	0.002	0.000	0.003
events.selection	0.003	0.000	0.003
export.graphml	0.066	0.004	0.070
export.mutex	0.008	0.000	0.008
has.duplicates	0.002	0.000	0.001
has.model	0.002	0.000	0.001
has.stages	0.005	0.000	0.005
import.GISTIC	0.004	0.000	0.004
import.MAF	0.066	0.000	0.066
intersect.datasets	0.001	0.000	0.002
is.compliant	0.001	0.000	0.002
join.events	0.002	0.000	0.003
join.types	0.036	0.000	0.037
keysToNames	0.002	0.001	0.004
nameToKey	0.001	0.002	0.002
nevents	0.001	0.000	0.002
ngenes	0.001	0.000	0.001
nhypotheses	0.002	0.000	0.001
npatterns	0.001	0.000	0.001
nsamples	0.001	0.000	0.001
ntypes	0.001	0.000	0.001
oncoprint.cbio	0.005	0.000	0.004
order.frequency	0.007	0.000	0.006
pheatmap	0.026	0.000	0.026
rank.recurrents	0.003	0.000	0.003
rename.gene	0.002	0.000	0.002
rename.type	0.002	0.000	0.002
samples.selection	0.003	0.000	0.003
trim	0.003	0.000	0.003
tronco.bootstrap	0.135	0.005	7.391
tronco.caprese	0.082	0.000	0.082
tronco.capri	1.587	0.047	1.634
tronco.chowliu	1.254	0.019	1.274
tronco.edmonds	1.081	0.004	1.085
tronco.gabow	1.616	0.000	1.838
tronco.kfold.eloss	0.230	0.012	0.453
tronco.kfold.posterr	0.200	0.039	8.409
tronco.kfold.prederr	0.182	0.075	6.964
tronco.plot	0.244	0.040	0.283
tronco.prim	1.995	0.060	2.054
view	0.004	0.000	0.004
which.samples	0.002	0.000	0.003

CHECK results for TRONCO on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings