Multiple platform build/check report for BioC 3.13 - CHECK results for TRONCO on nebbiolo1

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings TRONCO_2.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/TRONCO.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.24.0’
* 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 LazyData ... 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.bootstrap 0.117  0.016  14.912
* 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-3.13-bioc/meat/TRONCO.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL TRONCO
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* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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 53 (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 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: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 10 edges out of 47 (21%)
*** 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 56 (14%)
*** 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 ]
> 
> proc.time()
   user  system elapsed 
 38.033   1.218  93.424

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.014	0.000	0.013
TCGA.remove.multiple.samples	0.012	0.012	0.023
TCGA.shorten.barcodes	0.011	0.012	0.022
annotate.description	0.010	0.012	0.021
annotate.stages	0.015	0.000	0.015
as.adj.matrix	0.006	0.018	0.024
as.alterations	0.003	0.001	0.005
as.bootstrap.scores	0.038	0.000	0.038
as.colors	0.003	0.000	0.002
as.confidence	0.013	0.016	0.029
as.description	0.002	0.000	0.001
as.events	0.001	0.001	0.002
as.events.in.patterns	0.003	0.006	0.009
as.events.in.sample	0.004	0.000	0.004
as.gene	0.001	0.004	0.005
as.genes	0.001	0.000	0.001
as.genes.in.patterns	0.004	0.000	0.004
as.genotypes	0.004	0.012	0.016
as.hypotheses	0.006	0.000	0.007
as.joint.probs	0.011	0.012	0.023
as.kfold.eloss	0.234	0.007	0.242
as.kfold.posterr	0.051	0.004	0.054
as.kfold.prederr	0.052	0.004	0.055
as.marginal.probs	0.005	0.000	0.005
as.models	0.014	0.044	0.058
as.parameters	0.001	0.005	0.007
as.pathway	0.003	0.007	0.011
as.patterns	0.002	0.000	0.002
as.samples	0.002	0.000	0.002
as.selective.advantage.relations	0.074	0.016	0.090
as.stages	0.007	0.000	0.007
as.types	0.001	0.000	0.001
as.types.in.patterns	0.004	0.000	0.004
change.color	0.002	0.000	0.002
consolidate.data	0.022	0.008	0.030
delete.event	0.001	0.003	0.004
delete.gene	0.001	0.004	0.005
delete.hypothesis	0.038	0.064	0.102
delete.model	0.003	0.000	0.003
delete.pattern	0.008	0.016	0.023
delete.samples	0.004	0.000	0.004
delete.type	0.002	0.004	0.006
duplicates	0.002	0.000	0.003
enforce.numeric	0.003	0.000	0.003
enforce.string	0.003	0.000	0.003
events.selection	0.002	0.003	0.005
export.graphml	0.072	0.020	0.093
export.mutex	0.008	0.000	0.009
has.duplicates	0.002	0.000	0.002
has.model	0.002	0.000	0.001
has.stages	0.004	0.000	0.004
import.GISTIC	0.004	0.000	0.004
import.MAF	0.055	0.003	0.059
intersect.datasets	0.001	0.000	0.001
is.compliant	0.001	0.000	0.001
join.events	0.003	0.000	0.003
join.types	0.030	0.024	0.053
keysToNames	0.001	0.004	0.006
nameToKey	0.002	0.000	0.003
nevents	0.001	0.000	0.002
ngenes	0.001	0.000	0.001
nhypotheses	0.001	0.000	0.001
npatterns	0.001	0.000	0.001
nsamples	0.001	0.000	0.002
ntypes	0.001	0.000	0.001
oncoprint.cbio	0.006	0.000	0.005
order.frequency	0.009	0.008	0.017
pheatmap	0.028	0.000	0.028
rank.recurrents	0.003	0.000	0.003
rename.gene	0.001	0.000	0.002
rename.type	0.013	0.000	0.014
samples.selection	0.002	0.000	0.003
trim	0.000	0.002	0.003
tronco.bootstrap	0.117	0.016	14.912
tronco.caprese	0.156	0.008	0.320
tronco.capri	2.716	0.036	4.033
tronco.chowliu	1.437	0.008	1.446
tronco.edmonds	1.051	0.004	1.165
tronco.gabow	0.990	0.003	0.994
tronco.kfold.eloss	0.100	0.068	0.168
tronco.kfold.posterr	0.086	0.132	3.178
tronco.kfold.prederr	0.146	0.090	3.643
tronco.plot	0.142	0.035	0.177
tronco.prim	2.134	0.093	2.226
view	0.004	0.000	0.003
which.samples	0.003	0.000	0.002

CHECK results for TRONCO on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings