Multiple platform build/check report for BioC 3.21 - CHECK results for TRONCO on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4823
palomino7	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4565
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4603
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4544
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 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: 2.40.0

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: 2025-08-09 14:15:28 -0400 (Sat, 09 Aug 2025)

EndedAt: 2025-08-09 14:18:41 -0400 (Sat, 09 Aug 2025)

EllapsedTime: 193.3 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 4.5.1 Patched (2025-06-14 r88325)
* 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 13.7.5
* 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.bootstrap 0.09   0.02  10.399
* 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
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 6 edges out of 50 (12%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** 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: 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 55 (16%)
*** 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 5 edges out of 48 (10%)
*** 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 5 edges out of 44 (11%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:01s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 33.853   1.498  87.458

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.018	0.005	0.024
TCGA.remove.multiple.samples	0.013	0.011	0.023
TCGA.shorten.barcodes	0.009	0.010	0.019
annotate.description	0.008	0.010	0.018
annotate.stages	0.006	0.003	0.010
as.adj.matrix	0.007	0.012	0.020
as.alterations	0.003	0.002	0.005
as.bootstrap.scores	0.173	0.003	0.176
as.colors	0.001	0.002	0.003
as.confidence	0.008	0.014	0.022
as.description	0.001	0.001	0.003
as.events	0.002	0.002	0.004
as.events.in.patterns	0.003	0.001	0.005
as.events.in.sample	0.004	0.002	0.005
as.gene	0.004	0.003	0.006
as.genes	0.002	0.002	0.003
as.genes.in.patterns	0.003	0.001	0.004
as.genotypes	0.007	0.007	0.013
as.hypotheses	0.003	0.004	0.007
as.joint.probs	0.007	0.012	0.019
as.kfold.eloss	0.082	0.004	0.086
as.kfold.posterr	0.097	0.008	0.105
as.kfold.prederr	0.097	0.008	0.105
as.marginal.probs	0.004	0.003	0.006
as.models	0.012	0.028	0.040
as.parameters	0.003	0.002	0.005
as.pathway	0.005	0.002	0.007
as.patterns	0.002	0.001	0.003
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.057	0.012	0.070
as.stages	0.006	0.004	0.009
as.types	0.002	0.001	0.003
as.types.in.patterns	0.003	0.001	0.004
change.color	0.001	0.001	0.003
consolidate.data	0.032	0.006	0.039
delete.event	0.003	0.002	0.005
delete.gene	0.003	0.001	0.005
delete.hypothesis	0.023	0.024	0.047
delete.model	0.003	0.002	0.005
delete.pattern	0.009	0.009	0.018
delete.samples	0.002	0.002	0.004
delete.type	0.003	0.001	0.004
duplicates	0.001	0.001	0.003
enforce.numeric	0.003	0.002	0.003
enforce.string	0.002	0.002	0.004
events.selection	0.003	0.002	0.005
export.graphml	0.099	0.016	0.115
export.mutex	0.008	0.004	0.011
has.duplicates	0.002	0.002	0.003
has.model	0.002	0.001	0.003
has.stages	0.006	0.003	0.009
import.GISTIC	0.004	0.002	0.006
import.MAF	0.062	0.011	0.073
intersect.datasets	0.002	0.002	0.003
is.compliant	0.002	0.002	0.003
join.events	0.003	0.002	0.005
join.types	0.045	0.014	0.060
keysToNames	0.005	0.003	0.007
nameToKey	0.003	0.001	0.004
nevents	0.001	0.001	0.002
ngenes	0.001	0.002	0.003
nhypotheses	0.002	0.001	0.003
npatterns	0.001	0.001	0.002
nsamples	0.001	0.001	0.003
ntypes	0.002	0.002	0.002
oncoprint.cbio	0.005	0.002	0.007
order.frequency	0.006	0.009	0.016
pheatmap	0.034	0.002	0.035
rank.recurrents	0.004	0.002	0.005
rename.gene	0.002	0.001	0.003
rename.type	0.003	0.001	0.004
samples.selection	0.003	0.001	0.004
trim	0.003	0.001	0.004
tronco.bootstrap	0.090	0.020	10.399
tronco.caprese	0.133	0.005	0.138
tronco.capri	1.708	0.077	1.789
tronco.chowliu	1.117	0.031	1.149
tronco.edmonds	0.962	0.022	0.985
tronco.gabow	1.107	0.046	1.157
tronco.kfold.eloss	0.076	0.047	0.124
tronco.kfold.posterr	0.128	0.084	4.380
tronco.kfold.prederr	0.108	0.064	3.407
tronco.plot	0.119	0.006	0.124
tronco.prim	2.219	0.048	2.270
view	0.003	0.002	0.006
which.samples	0.003	0.002	0.005