Multiple platform build/check report for BioC 3.22 - CHECK results for TRONCO on kjohnson1

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 kjohnson1

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: 2025-12-11 04:38:55 -0500 (Thu, 11 Dec 2025)

EndedAt: 2025-12-11 04:43:35 -0500 (Thu, 11 Dec 2025)

EllapsedTime: 280.4 seconds

RetCode: 0

Status: OK

CheckDir: TRONCO.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* 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.kfold.posterr 0.137  0.092   5.886
tronco.kfold.prederr 0.110  0.088   5.201
tronco.bootstrap     0.093  0.022  15.229
* 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-arm64/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 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 48 (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: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 4 edges out of 47 (9%)
*** Performing likelihood-fit with regularization: no_reg .
*** 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: 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 7 edges out of 56 (12%)
*** 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:02s 
*** 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 7 edges out of 48 (15%)
*** 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 
 39.411   1.569 134.244

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.020	0.005	0.047
TCGA.remove.multiple.samples	0.014	0.013	0.028
TCGA.shorten.barcodes	0.010	0.010	0.026
annotate.description	0.008	0.010	0.019
annotate.stages	0.008	0.004	0.013
as.adj.matrix	0.009	0.014	0.035
as.alterations	0.004	0.003	0.012
as.bootstrap.scores	0.194	0.006	0.274
as.colors	0.002	0.003	0.013
as.confidence	0.009	0.021	0.033
as.description	0.001	0.001	0.004
as.events	0.002	0.002	0.005
as.events.in.patterns	0.004	0.002	0.007
as.events.in.sample	0.004	0.002	0.006
as.gene	0.003	0.003	0.006
as.genes	0.002	0.002	0.003
as.genes.in.patterns	0.004	0.002	0.008
as.genotypes	0.007	0.008	0.021
as.hypotheses	0.004	0.007	0.010
as.joint.probs	0.008	0.014	0.024
as.kfold.eloss	0.083	0.004	0.118
as.kfold.posterr	0.097	0.009	0.160
as.kfold.prederr	0.098	0.007	0.263
as.marginal.probs	0.004	0.002	0.006
as.models	0.013	0.043	0.055
as.parameters	0.003	0.003	0.010
as.pathway	0.005	0.002	0.007
as.patterns	0.001	0.002	0.003
as.samples	0.001	0.002	0.003
as.selective.advantage.relations	0.062	0.013	0.121
as.stages	0.006	0.004	0.010
as.types	0.002	0.002	0.004
as.types.in.patterns	0.003	0.002	0.005
change.color	0.002	0.001	0.004
consolidate.data	0.037	0.005	0.075
delete.event	0.004	0.002	0.008
delete.gene	0.004	0.002	0.010
delete.hypothesis	0.025	0.031	0.069
delete.model	0.003	0.002	0.017
delete.pattern	0.011	0.011	0.039
delete.samples	0.003	0.002	0.007
delete.type	0.003	0.002	0.005
duplicates	0.002	0.002	0.004
enforce.numeric	0.003	0.002	0.005
enforce.string	0.003	0.002	0.005
events.selection	0.004	0.002	0.007
export.graphml	0.107	0.006	0.131
export.mutex	0.008	0.003	0.020
has.duplicates	0.001	0.001	0.003
has.model	0.001	0.002	0.003
has.stages	0.006	0.003	0.018
import.GISTIC	0.003	0.002	0.006
import.MAF	0.065	0.008	0.102
intersect.datasets	0.001	0.002	0.003
is.compliant	0.001	0.001	0.003
join.events	0.002	0.001	0.004
join.types	0.047	0.016	0.092
keysToNames	0.005	0.003	0.008
nameToKey	0.003	0.001	0.004
nevents	0.001	0.001	0.003
ngenes	0.001	0.001	0.003
nhypotheses	0.003	0.003	0.026
npatterns	0.002	0.002	0.002
nsamples	0.002	0.002	0.009
ntypes	0.001	0.002	0.004
oncoprint.cbio	0.004	0.003	0.007
order.frequency	0.006	0.011	0.022
pheatmap	0.035	0.001	0.045
rank.recurrents	0.004	0.002	0.005
rename.gene	0.002	0.002	0.004
rename.type	0.001	0.002	0.003
samples.selection	0.003	0.002	0.007
trim	0.003	0.001	0.005
tronco.bootstrap	0.093	0.022	15.229
tronco.caprese	0.141	0.005	0.153
tronco.capri	1.740	0.063	2.355
tronco.chowliu	1.379	0.034	1.897
tronco.edmonds	1.221	0.030	1.713
tronco.gabow	1.256	0.036	1.754
tronco.kfold.eloss	0.088	0.065	0.178
tronco.kfold.posterr	0.137	0.092	5.886
tronco.kfold.prederr	0.110	0.088	5.201
tronco.plot	0.142	0.007	0.155
tronco.prim	2.622	0.057	3.720
view	0.004	0.002	0.006
which.samples	0.003	0.003	0.007