Multiple platform build/check report for BioC 3.23 - CHECK results for TRONCO on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4988
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 Patched (2026-04-24 r89963) -- "Because it was There"	4718
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*

CHECK results for TRONCO on nebbiolo1

To the developers/maintainers of the TRONCO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TRONCO.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: TRONCO

Version: 2.44.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings TRONCO_2.44.0.tar.gz

StartedAt: 2026-04-30 05:58:45 -0400 (Thu, 30 Apr 2026)

EndedAt: 2026-04-30 06:02:52 -0400 (Thu, 30 Apr 2026)

EllapsedTime: 246.4 seconds

RetCode: 0

Status: OK

CheckDir: TRONCO.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings TRONCO_2.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/TRONCO.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-30 09:58:46 UTC
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.44.0’
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
tronco.bootstrap 0.092  0.007   8.575
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

TRONCO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘TRONCO’ ...
** this is package ‘TRONCO’ version ‘2.44.0’
** 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

TRONCO.Rcheck/tests/testthat.Rout


R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 54 (13%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s 
*** 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 9 edges out of 52 (17%)
*** 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 12 edges out of 59 (20%)
*** 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 6 edges out of 57 (11%)
*** 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 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 39.143   1.211  89.926

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.014	0.002	0.016
TCGA.remove.multiple.samples	0.01	0.01	0.02
TCGA.shorten.barcodes	0.009	0.007	0.016
annotate.description	0.007	0.009	0.016
annotate.stages	0.005	0.001	0.007
as.adj.matrix	0.007	0.012	0.019
as.alterations	0.002	0.002	0.003
as.bootstrap.scores	0.137	0.001	0.137
as.colors	0.001	0.000	0.001
as.confidence	0.011	0.011	0.023
as.description	0.001	0.000	0.002
as.events	0.001	0.001	0.003
as.events.in.patterns	0.003	0.000	0.003
as.events.in.sample	0.004	0.000	0.003
as.gene	0.002	0.003	0.004
as.genes	0.001	0.000	0.001
as.genes.in.patterns	0.002	0.000	0.003
as.genotypes	0.005	0.009	0.014
as.hypotheses	0.002	0.004	0.006
as.joint.probs	0.006	0.013	0.020
as.kfold.eloss	0.066	0.001	0.067
as.kfold.posterr	0.083	0.006	0.090
as.kfold.prederr	0.08	0.01	0.09
as.marginal.probs	0.003	0.002	0.005
as.models	0.006	0.041	0.047
as.parameters	0.002	0.000	0.003
as.pathway	0.005	0.001	0.006
as.patterns	0.002	0.000	0.002
as.samples	0.000	0.001	0.001
as.selective.advantage.relations	0.054	0.015	0.070
as.stages	0.006	0.001	0.007
as.types	0.001	0.000	0.002
as.types.in.patterns	0.001	0.002	0.004
change.color	0.000	0.002	0.002
consolidate.data	0.031	0.001	0.032
delete.event	0.003	0.000	0.003
delete.gene	0.003	0.000	0.003
delete.hypothesis	0.017	0.035	0.052
delete.model	0.002	0.000	0.002
delete.pattern	0.006	0.011	0.017
delete.samples	0.001	0.001	0.002
delete.type	0.002	0.001	0.003
duplicates	0.000	0.001	0.001
enforce.numeric	0.001	0.001	0.002
enforce.string	0.000	0.002	0.002
events.selection	0.002	0.002	0.004
export.graphml	0.067	0.002	0.069
export.mutex	0.005	0.001	0.007
has.duplicates	0.001	0.000	0.001
has.model	0.002	0.000	0.002
has.stages	0.003	0.002	0.005
import.GISTIC	0.002	0.001	0.004
import.MAF	0.051	0.002	0.053
intersect.datasets	0.001	0.000	0.001
is.compliant	0.000	0.001	0.001
join.events	0.003	0.000	0.003
join.types	0.033	0.020	0.053
keysToNames	0.001	0.003	0.005
nameToKey	0.000	0.002	0.002
nevents	0.001	0.000	0.001
ngenes	0.011	0.000	0.012
nhypotheses	0.002	0.000	0.002
npatterns	0.001	0.000	0.002
nsamples	0.001	0.000	0.001
ntypes	0.000	0.001	0.001
oncoprint.cbio	0.004	0.000	0.004
order.frequency	0.003	0.013	0.016
pheatmap	0.029	0.000	0.029
rank.recurrents	0.003	0.000	0.003
rename.gene	0.002	0.000	0.002
rename.type	0.001	0.001	0.001
samples.selection	0.002	0.001	0.003
trim	0.003	0.000	0.003
tronco.bootstrap	0.092	0.007	8.575
tronco.caprese	0.124	0.001	0.125
tronco.capri	1.612	0.065	1.677
tronco.chowliu	1.034	0.003	1.037
tronco.edmonds	0.952	0.002	0.955
tronco.gabow	1.047	0.056	1.103
tronco.kfold.eloss	0.064	0.060	0.124
tronco.kfold.posterr	0.124	0.115	3.490
tronco.kfold.prederr	0.080	0.106	3.164
tronco.plot	0.119	0.012	0.130
tronco.prim	2.280	0.083	2.363
view	0.003	0.001	0.004
which.samples	0.003	0.000	0.003