Multiple platform build/check report for BioC 3.22 - CHECK results for TRONCO on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4879
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4670
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4604
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4669
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 merida1

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: 2.42.0

Command: /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_2.42.0.tar.gz

StartedAt: 2025-12-09 13:44:35 -0500 (Tue, 09 Dec 2025)

EndedAt: 2025-12-09 13:56:15 -0500 (Tue, 09 Dec 2025)

EllapsedTime: 700.4 seconds

RetCode: 0

Status: OK

CheckDir: TRONCO.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /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_2.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/TRONCO.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.42.0’
* 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 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.prim          4.790  0.137   8.495
tronco.capri         4.095  0.126   6.867
tronco.chowliu       3.281  0.043   5.235
tronco.edmonds       3.193  0.044   5.149
tronco.kfold.posterr 0.281  0.247  12.037
tronco.kfold.prederr 0.219  0.198  12.473
tronco.bootstrap     0.205  0.025  33.803
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

TRONCO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘TRONCO’ ...
** this is package ‘TRONCO’ version ‘2.42.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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:01s 
*** 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 5 edges out of 44 (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:07s 
*** 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 41 (10%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:05s 
*** 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 48 (17%)
*** 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:05s 
*** 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 9 edges out of 50 (18%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:06s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 93.665   2.955 340.947

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.030	0.007	0.060
TCGA.remove.multiple.samples	0.030	0.030	0.098
TCGA.shorten.barcodes	0.025	0.030	0.086
annotate.description	0.022	0.029	0.087
annotate.stages	0.015	0.006	0.038
as.adj.matrix	0.019	0.038	0.092
as.alterations	0.006	0.004	0.017
as.bootstrap.scores	0.193	0.008	0.316
as.colors	0.003	0.003	0.011
as.confidence	0.022	0.047	0.103
as.description	0.002	0.003	0.005
as.events	0.004	0.004	0.013
as.events.in.patterns	0.006	0.002	0.015
as.events.in.sample	0.008	0.003	0.024
as.gene	0.007	0.006	0.018
as.genes	0.003	0.002	0.012
as.genes.in.patterns	0.006	0.002	0.013
as.genotypes	0.018	0.021	0.065
as.hypotheses	0.007	0.011	0.033
as.joint.probs	0.017	0.035	0.084
as.kfold.eloss	0.143	0.006	0.233
as.kfold.posterr	0.180	0.018	0.330
as.kfold.prederr	0.187	0.021	0.335
as.marginal.probs	0.007	0.005	0.019
as.models	0.038	0.118	0.260
as.parameters	0.004	0.003	0.017
as.pathway	0.010	0.004	0.027
as.patterns	0.003	0.002	0.005
as.samples	0.003	0.003	0.006
as.selective.advantage.relations	0.163	0.040	0.333
as.stages	0.016	0.008	0.036
as.types	0.003	0.002	0.011
as.types.in.patterns	0.007	0.003	0.018
change.color	0.003	0.003	0.017
consolidate.data	0.091	0.008	0.155
delete.event	0.007	0.003	0.017
delete.gene	0.007	0.002	0.009
delete.hypothesis	0.064	0.077	0.220
delete.model	0.005	0.003	0.012
delete.pattern	0.024	0.027	0.082
delete.samples	0.005	0.002	0.007
delete.type	0.008	0.002	0.015
duplicates	0.003	0.003	0.006
enforce.numeric	0.004	0.003	0.012
enforce.string	0.006	0.002	0.014
events.selection	0.007	0.004	0.017
export.graphml	0.227	0.008	0.383
export.mutex	0.014	0.005	0.048
has.duplicates	0.002	0.002	0.011
has.model	0.003	0.003	0.005
has.stages	0.013	0.005	0.022
import.GISTIC	0.009	0.002	0.016
import.MAF	0.125	0.014	0.221
intersect.datasets	0.003	0.003	0.006
is.compliant	0.003	0.002	0.005
join.events	0.006	0.003	0.016
join.types	0.106	0.040	0.241
keysToNames	0.008	0.006	0.021
nameToKey	0.005	0.002	0.006
nevents	0.002	0.002	0.004
ngenes	0.002	0.002	0.013
nhypotheses	0.003	0.002	0.005
npatterns	0.003	0.003	0.011
nsamples	0.003	0.002	0.005
ntypes	0.003	0.002	0.005
oncoprint.cbio	0.011	0.004	0.030
order.frequency	0.015	0.029	0.064
pheatmap	0.076	0.002	0.133
rank.recurrents	0.007	0.003	0.013
rename.gene	0.004	0.003	0.007
rename.type	0.004	0.002	0.013
samples.selection	0.006	0.004	0.016
trim	0.006	0.003	0.015
tronco.bootstrap	0.205	0.025	33.803
tronco.caprese	0.375	0.010	0.489
tronco.capri	4.095	0.126	6.867
tronco.chowliu	3.281	0.043	5.235
tronco.edmonds	3.193	0.044	5.149
tronco.gabow	2.767	0.056	4.666
tronco.kfold.eloss	0.217	0.190	0.673
tronco.kfold.posterr	0.281	0.247	12.037
tronco.kfold.prederr	0.219	0.198	12.473
tronco.plot	0.285	0.014	0.533
tronco.prim	4.790	0.137	8.495
view	0.006	0.002	0.009
which.samples	0.006	0.004	0.026