Multiple platform build/check report for BioC 3.21 - CHECK results for TRONCO on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4566
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
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: 2.40.0

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_2.40.0.tar.gz

StartedAt: 2025-08-12 12:12:51 -0400 (Tue, 12 Aug 2025)

EndedAt: 2025-08-12 12:20:08 -0400 (Tue, 12 Aug 2025)

EllapsedTime: 437.2 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_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TRONCO.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘2.40.0’
* 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          5.196  0.074   5.849
tronco.kfold.posterr 0.282  0.201   7.513
tronco.kfold.prederr 0.213  0.159   7.445
tronco.bootstrap     0.201  0.022  21.027
* 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 ‘2.40.0’
** 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 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"
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: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:05s 
*** 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 53 (17%)
*** Performing likelihood-fit with regularization: no_reg .
*** 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: 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 5 edges out of 53 (9%)
*** 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 11 edges out of 55 (20%)
*** 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 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 96.909   2.104 223.566

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.031	0.008	0.039
TCGA.remove.multiple.samples	0.031	0.034	0.065
TCGA.shorten.barcodes	0.023	0.027	0.050
annotate.description	0.022	0.030	0.053
annotate.stages	0.015	0.005	0.020
as.adj.matrix	0.019	0.040	0.059
as.alterations	0.006	0.004	0.010
as.bootstrap.scores	0.189	0.007	0.196
as.colors	0.002	0.003	0.005
as.confidence	0.023	0.050	0.073
as.description	0.002	0.002	0.005
as.events	0.004	0.004	0.008
as.events.in.patterns	0.006	0.003	0.009
as.events.in.sample	0.008	0.003	0.010
as.gene	0.007	0.006	0.013
as.genes	0.003	0.003	0.006
as.genes.in.patterns	0.006	0.003	0.008
as.genotypes	0.018	0.021	0.040
as.hypotheses	0.007	0.011	0.018
as.joint.probs	0.018	0.039	0.058
as.kfold.eloss	0.141	0.005	0.146
as.kfold.posterr	0.171	0.015	0.187
as.kfold.prederr	0.183	0.020	0.203
as.marginal.probs	0.006	0.005	0.011
as.models	0.034	0.089	0.123
as.parameters	0.005	0.004	0.008
as.pathway	0.009	0.004	0.014
as.patterns	0.004	0.002	0.006
as.samples	0.003	0.003	0.006
as.selective.advantage.relations	0.158	0.037	0.196
as.stages	0.015	0.006	0.022
as.types	0.003	0.003	0.005
as.types.in.patterns	0.006	0.003	0.009
change.color	0.003	0.002	0.005
consolidate.data	0.087	0.007	0.094
delete.event	0.007	0.002	0.009
delete.gene	0.007	0.002	0.009
delete.hypothesis	0.064	0.077	0.140
delete.model	0.005	0.002	0.008
delete.pattern	0.025	0.028	0.053
delete.samples	0.005	0.002	0.008
delete.type	0.007	0.002	0.009
duplicates	0.003	0.003	0.006
enforce.numeric	0.005	0.002	0.008
enforce.string	0.005	0.003	0.006
events.selection	0.008	0.003	0.012
export.graphml	0.212	0.009	0.220
export.mutex	0.012	0.006	0.018
has.duplicates	0.003	0.002	0.005
has.model	0.003	0.002	0.005
has.stages	0.013	0.005	0.017
import.GISTIC	0.009	0.003	0.012
import.MAF	0.121	0.014	0.135
intersect.datasets	0.002	0.002	0.005
is.compliant	0.003	0.002	0.005
join.events	0.007	0.003	0.009
join.types	0.104	0.040	0.145
keysToNames	0.008	0.006	0.013
nameToKey	0.004	0.002	0.007
nevents	0.003	0.002	0.004
ngenes	0.003	0.002	0.005
nhypotheses	0.002	0.002	0.004
npatterns	0.003	0.002	0.005
nsamples	0.002	0.002	0.005
ntypes	0.002	0.002	0.005
oncoprint.cbio	0.010	0.003	0.013
order.frequency	0.015	0.027	0.042
pheatmap	0.073	0.003	0.076
rank.recurrents	0.006	0.002	0.010
rename.gene	0.004	0.002	0.006
rename.type	0.005	0.002	0.006
samples.selection	0.006	0.003	0.009
trim	0.006	0.002	0.008
tronco.bootstrap	0.201	0.022	21.027
tronco.caprese	0.335	0.008	0.343
tronco.capri	4.207	0.128	4.353
tronco.chowliu	2.792	0.034	2.832
tronco.edmonds	2.988	0.034	3.030
tronco.gabow	2.998	0.045	3.051
tronco.kfold.eloss	0.206	0.145	0.352
tronco.kfold.posterr	0.282	0.201	7.513
tronco.kfold.prederr	0.213	0.159	7.445
tronco.plot	0.290	0.008	0.301
tronco.prim	5.196	0.074	5.849
view	0.007	0.003	0.011
which.samples	0.006	0.004	0.010