Multiple platform build/check report for BioC 3.21 - CHECK results for TRONCO on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4831
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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 kjohnson3

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: 2025-04-21 22:13:01 -0400 (Mon, 21 Apr 2025)

EndedAt: 2025-04-21 22:14:11 -0400 (Mon, 21 Apr 2025)

EllapsedTime: 69.9 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_2.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TRONCO.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-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 Ventura 13.7.1
* 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
* 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 ‘2.40.0’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
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 47 (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:00s 
*** 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 44 (9%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / 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: 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 6 edges out of 48 (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:00s 
*** 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 5 edges out of 50 (10%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:00s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 11.719   0.578  30.697

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.008	0.002	0.010
TCGA.remove.multiple.samples	0.007	0.003	0.011
TCGA.shorten.barcodes	0.003	0.004	0.007
annotate.description	0.003	0.004	0.006
annotate.stages	0.002	0.001	0.003
as.adj.matrix	0.002	0.005	0.007
as.alterations	0.001	0.000	0.002
as.bootstrap.scores	0.032	0.001	0.032
as.colors	0.001	0.001	0.001
as.confidence	0.002	0.005	0.008
as.description	0.001	0.001	0.001
as.events	0.000	0.001	0.001
as.events.in.patterns	0.001	0.001	0.002
as.events.in.sample	0.001	0.000	0.002
as.gene	0.001	0.001	0.002
as.genes	0.000	0.001	0.001
as.genes.in.patterns	0.000	0.001	0.001
as.genotypes	0.002	0.002	0.005
as.hypotheses	0.001	0.001	0.003
as.joint.probs	0.002	0.004	0.006
as.kfold.eloss	0.076	0.001	0.078
as.kfold.posterr	0.031	0.002	0.034
as.kfold.prederr	0.033	0.002	0.035
as.marginal.probs	0.001	0.001	0.002
as.models	0.004	0.011	0.014
as.parameters	0.001	0.001	0.001
as.pathway	0.002	0.001	0.002
as.patterns	0.000	0.000	0.002
as.samples	0.000	0.001	0.001
as.selective.advantage.relations	0.019	0.005	0.023
as.stages	0.002	0.002	0.004
as.types	0.000	0.001	0.001
as.types.in.patterns	0.001	0.001	0.001
change.color	0.001	0.001	0.001
consolidate.data	0.008	0.002	0.010
delete.event	0.001	0.000	0.002
delete.gene	0.001	0.000	0.002
delete.hypothesis	0.012	0.010	0.022
delete.model	0.001	0.001	0.002
delete.pattern	0.003	0.003	0.006
delete.samples	0.000	0.001	0.001
delete.type	0.001	0.001	0.002
duplicates	0.001	0.000	0.001
enforce.numeric	0.001	0.001	0.001
enforce.string	0.000	0.000	0.002
events.selection	0.001	0.000	0.001
export.graphml	0.030	0.002	0.032
export.mutex	0.002	0.001	0.003
has.duplicates	0.001	0.001	0.002
has.model	0.001	0.001	0.001
has.stages	0.001	0.001	0.003
import.GISTIC	0.002	0.001	0.002
import.MAF	0.021	0.003	0.023
intersect.datasets	0.000	0.000	0.001
is.compliant	0.001	0.001	0.000
join.events	0.001	0.000	0.001
join.types	0.010	0.005	0.016
keysToNames	0.002	0.001	0.003
nameToKey	0.001	0.001	0.002
nevents	0.000	0.000	0.001
ngenes	0.000	0.000	0.001
nhypotheses	0.000	0.001	0.001
npatterns	0.000	0.001	0.000
nsamples	0.000	0.001	0.001
ntypes	0.000	0.000	0.001
oncoprint.cbio	0.007	0.001	0.008
order.frequency	0.002	0.004	0.006
pheatmap	0.010	0.000	0.011
rank.recurrents	0.001	0.001	0.001
rename.gene	0.000	0.001	0.001
rename.type	0.000	0.001	0.002
samples.selection	0.001	0.001	0.001
trim	0.001	0.000	0.001
tronco.bootstrap	0.029	0.007	4.207
tronco.caprese	0.043	0.001	0.046
tronco.capri	0.532	0.031	0.569
tronco.chowliu	0.366	0.012	0.383
tronco.edmonds	0.356	0.015	0.371
tronco.gabow	0.339	0.010	0.355
tronco.kfold.eloss	0.026	0.015	0.041
tronco.kfold.posterr	0.042	0.030	1.336
tronco.kfold.prederr	0.035	0.024	1.047
tronco.plot	0.042	0.002	0.043
tronco.prim	0.784	0.022	0.809
view	0.002	0.000	0.002
which.samples	0.001	0.000	0.001