Multiple platform build/check report for BioC 3.20 - CHECK results for TRONCO on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4489
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4387
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: 2.38.0

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_2.38.0.tar.gz

StartedAt: 2025-01-14 11:06:00 -0500 (Tue, 14 Jan 2025)

EndedAt: 2025-01-14 11:13:16 -0500 (Tue, 14 Jan 2025)

EllapsedTime: 435.9 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_2.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/TRONCO.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘2.38.0’
* 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.capri         4.680  0.153   5.152
tronco.prim          4.767  0.059   5.652
tronco.kfold.posterr 0.291  0.203   8.150
tronco.kfold.prederr 0.233  0.162   7.704
tronco.bootstrap     0.230  0.027  19.853
* 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/4.4-x86_64/Resources/library’
* installing *source* package ‘TRONCO’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 6 edges out of 56 (11%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** 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: 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 7 edges out of 53 (13%)
*** 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 6 edges out of 47 (13%)
*** 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 7 edges out of 47 (15%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:04s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 94.526   2.047 219.316

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.030	0.008	0.039
TCGA.remove.multiple.samples	0.030	0.026	0.057
TCGA.shorten.barcodes	0.025	0.030	0.059
annotate.description	0.023	0.028	0.051
annotate.stages	0.015	0.006	0.022
as.adj.matrix	0.022	0.039	0.061
as.alterations	0.008	0.005	0.012
as.bootstrap.scores	0.150	0.009	0.160
as.colors	0.002	0.003	0.005
as.confidence	0.021	0.041	0.062
as.description	0.002	0.002	0.004
as.events	0.003	0.003	0.006
as.events.in.patterns	0.008	0.003	0.011
as.events.in.sample	0.009	0.002	0.010
as.gene	0.007	0.006	0.013
as.genes	0.003	0.003	0.006
as.genes.in.patterns	0.141	0.003	0.153
as.genotypes	0.019	0.020	0.042
as.hypotheses	0.006	0.009	0.016
as.joint.probs	0.019	0.036	0.056
as.kfold.eloss	0.142	0.004	0.154
as.kfold.posterr	0.174	0.014	0.192
as.kfold.prederr	0.185	0.019	0.211
as.marginal.probs	0.008	0.006	0.014
as.models	0.037	0.094	0.132
as.parameters	0.005	0.003	0.009
as.pathway	0.011	0.005	0.016
as.patterns	0.004	0.002	0.007
as.samples	0.003	0.004	0.007
as.selective.advantage.relations	0.251	0.052	0.307
as.stages	0.014	0.005	0.020
as.types	0.003	0.003	0.005
as.types.in.patterns	0.008	0.003	0.012
change.color	0.004	0.002	0.006
consolidate.data	0.080	0.004	0.086
delete.event	0.010	0.002	0.012
delete.gene	0.010	0.002	0.015
delete.hypothesis	0.071	0.084	0.158
delete.model	0.006	0.002	0.009
delete.pattern	0.029	0.028	0.059
delete.samples	0.006	0.003	0.008
delete.type	0.010	0.002	0.012
duplicates	0.004	0.003	0.006
enforce.numeric	0.005	0.003	0.008
enforce.string	0.006	0.002	0.009
events.selection	0.009	0.004	0.014
export.graphml	0.235	0.011	0.253
export.mutex	0.017	0.008	0.026
has.duplicates	0.004	0.002	0.005
has.model	0.003	0.002	0.006
has.stages	0.014	0.006	0.022
import.GISTIC	0.012	0.004	0.016
import.MAF	0.149	0.016	0.168
intersect.datasets	0.002	0.002	0.005
is.compliant	0.003	0.002	0.005
join.events	0.008	0.002	0.010
join.types	0.096	0.037	0.135
keysToNames	0.009	0.007	0.015
nameToKey	0.005	0.002	0.007
nevents	0.002	0.002	0.005
ngenes	0.003	0.002	0.005
nhypotheses	0.003	0.002	0.005
npatterns	0.002	0.002	0.004
nsamples	0.002	0.002	0.005
ntypes	0.003	0.002	0.005
oncoprint.cbio	0.014	0.004	0.018
order.frequency	0.015	0.026	0.042
pheatmap	0.075	0.002	0.077
rank.recurrents	0.007	0.002	0.010
rename.gene	0.004	0.002	0.006
rename.type	0.003	0.002	0.005
samples.selection	0.007	0.001	0.009
trim	0.007	0.003	0.009
tronco.bootstrap	0.230	0.027	19.853
tronco.caprese	0.366	0.009	0.377
tronco.capri	4.680	0.153	5.152
tronco.chowliu	3.262	0.040	3.507
tronco.edmonds	3.077	0.034	3.271
tronco.gabow	2.918	0.028	3.113
tronco.kfold.eloss	0.220	0.149	0.399
tronco.kfold.posterr	0.291	0.203	8.150
tronco.kfold.prederr	0.233	0.162	7.704
tronco.plot	0.292	0.010	0.343
tronco.prim	4.767	0.059	5.652
view	0.008	0.002	0.015
which.samples	0.006	0.003	0.012