Multiple platform build/check report for BioC 3.21 - CHECK results for TRONCO on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4716
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4478
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4489
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4442
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 nebbiolo1

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: 2.39.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings TRONCO_2.39.0.tar.gz

StartedAt: 2025-02-04 03:40:50 -0500 (Tue, 04 Feb 2025)

EndedAt: 2025-02-04 03:44:38 -0500 (Tue, 04 Feb 2025)

EllapsedTime: 228.4 seconds

RetCode: 0

Status: OK

CheckDir: TRONCO.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings TRONCO_2.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.39.0’
* 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 loading without being on the library search path ... 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 0.095   0.01   8.556
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

TRONCO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘TRONCO’ ...
** this is package ‘TRONCO’ version ‘2.39.0’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 4 edges out of 43 (9%)
*** 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 8 edges out of 54 (15%)
*** 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 49 (14%)
*** 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 8 edges out of 52 (15%)
*** 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 
 37.878   1.350  83.504

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.020	0.003	0.022
TCGA.remove.multiple.samples	0.021	0.008	0.030
TCGA.shorten.barcodes	0.008	0.008	0.016
annotate.description	0.007	0.009	0.015
annotate.stages	0.006	0.000	0.006
as.adj.matrix	0.008	0.010	0.018
as.alterations	0.003	0.001	0.003
as.bootstrap.scores	0.078	0.001	0.078
as.colors	0.000	0.001	0.002
as.confidence	0.008	0.015	0.023
as.description	0.002	0.000	0.002
as.events	0.001	0.001	0.003
as.events.in.patterns	0.002	0.001	0.003
as.events.in.sample	0.002	0.001	0.003
as.gene	0.002	0.002	0.004
as.genes	0.001	0.000	0.001
as.genes.in.patterns	0.002	0.001	0.003
as.genotypes	0.006	0.007	0.013
as.hypotheses	0.001	0.004	0.006
as.joint.probs	0.007	0.011	0.018
as.kfold.eloss	0.190	0.000	0.191
as.kfold.posterr	0.081	0.003	0.084
as.kfold.prederr	0.083	0.005	0.087
as.marginal.probs	0.001	0.003	0.004
as.models	0.002	0.042	0.045
as.parameters	0.002	0.001	0.003
as.pathway	0.004	0.001	0.005
as.patterns	0.002	0.000	0.002
as.samples	0.001	0.001	0.002
as.selective.advantage.relations	0.053	0.015	0.069
as.stages	0.003	0.003	0.007
as.types	0.001	0.000	0.002
as.types.in.patterns	0.001	0.002	0.003
change.color	0.001	0.001	0.002
consolidate.data	0.023	0.007	0.031
delete.event	0.004	0.000	0.004
delete.gene	0.002	0.002	0.004
delete.hypothesis	0.032	0.031	0.063
delete.model	0.002	0.001	0.003
delete.pattern	0.004	0.013	0.017
delete.samples	0.000	0.002	0.003
delete.type	0.004	0.000	0.004
duplicates	0.001	0.001	0.001
enforce.numeric	0.001	0.001	0.002
enforce.string	0.002	0.000	0.003
events.selection	0.001	0.002	0.004
export.graphml	0.093	0.001	0.095
export.mutex	0.007	0.000	0.007
has.duplicates	0.001	0.000	0.002
has.model	0.001	0.000	0.002
has.stages	0.005	0.000	0.005
import.GISTIC	0.004	0.000	0.004
import.MAF	0.060	0.002	0.062
intersect.datasets	0.000	0.001	0.001
is.compliant	0.001	0.000	0.002
join.events	0.002	0.000	0.003
join.types	0.032	0.017	0.049
keysToNames	0.003	0.002	0.005
nameToKey	0.002	0.001	0.002
nevents	0.002	0.000	0.001
ngenes	0.002	0.000	0.001
nhypotheses	0.002	0.000	0.001
npatterns	0.001	0.001	0.001
nsamples	0.000	0.001	0.001
ntypes	0.002	0.000	0.001
oncoprint.cbio	0.016	0.001	0.017
order.frequency	0.006	0.009	0.016
pheatmap	0.032	0.000	0.032
rank.recurrents	0.003	0.001	0.004
rename.gene	0.002	0.000	0.002
rename.type	0.001	0.001	0.002
samples.selection	0.003	0.000	0.003
trim	0.000	0.003	0.003
tronco.bootstrap	0.095	0.010	8.556
tronco.caprese	0.183	0.000	0.183
tronco.capri	1.650	0.072	1.722
tronco.chowliu	1.192	0.003	1.195
tronco.edmonds	1.081	0.019	1.100
tronco.gabow	1.261	0.037	1.298
tronco.kfold.eloss	0.073	0.058	0.130
tronco.kfold.posterr	0.172	0.172	3.460
tronco.kfold.prederr	0.113	0.110	3.157
tronco.plot	0.133	0.003	0.135
tronco.prim	2.203	0.106	2.309
view	0.003	0.001	0.004
which.samples	0.002	0.001	0.003