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"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4358
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: 2025-01-03 11:59:14 -0500 (Fri, 03 Jan 2025)

EndedAt: 2025-01-03 12:06:39 -0500 (Fri, 03 Jan 2025)

EllapsedTime: 445.1 seconds

RetCode: 0

Status: OK

CheckDir: TRONCO.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### 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.prim          5.181  0.081   6.193
tronco.kfold.posterr 0.297  0.211   7.535
tronco.kfold.prederr 0.224  0.167   7.521
tronco.bootstrap     0.233  0.027  20.957
* 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 9 edges out of 55 (16%)
*** 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 8 edges out of 50 (16%)
*** 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 55 (11%)
*** 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 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:04s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 95.691   2.221 222.123

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.031	0.007	0.039
TCGA.remove.multiple.samples	0.033	0.032	0.066
TCGA.shorten.barcodes	0.026	0.027	0.056
annotate.description	0.023	0.030	0.055
annotate.stages	0.016	0.006	0.021
as.adj.matrix	0.022	0.040	0.063
as.alterations	0.008	0.003	0.012
as.bootstrap.scores	0.153	0.008	0.179
as.colors	0.003	0.003	0.005
as.confidence	0.022	0.046	0.069
as.description	0.002	0.002	0.005
as.events	0.004	0.004	0.008
as.events.in.patterns	0.009	0.003	0.012
as.events.in.sample	0.008	0.003	0.012
as.gene	0.008	0.006	0.015
as.genes	0.003	0.003	0.007
as.genes.in.patterns	0.133	0.004	0.143
as.genotypes	0.019	0.022	0.042
as.hypotheses	0.007	0.011	0.020
as.joint.probs	0.017	0.034	0.053
as.kfold.eloss	0.140	0.005	0.148
as.kfold.posterr	0.179	0.014	0.198
as.kfold.prederr	0.185	0.018	0.210
as.marginal.probs	0.008	0.005	0.014
as.models	0.037	0.092	0.132
as.parameters	0.005	0.004	0.008
as.pathway	0.012	0.005	0.015
as.patterns	0.003	0.003	0.006
as.samples	0.003	0.003	0.007
as.selective.advantage.relations	0.248	0.050	0.305
as.stages	0.015	0.006	0.021
as.types	0.003	0.003	0.006
as.types.in.patterns	0.008	0.002	0.011
change.color	0.004	0.002	0.007
consolidate.data	0.079	0.004	0.084
delete.event	0.010	0.002	0.013
delete.gene	0.010	0.002	0.012
delete.hypothesis	0.069	0.079	0.153
delete.model	0.006	0.002	0.009
delete.pattern	0.029	0.027	0.058
delete.samples	0.006	0.003	0.009
delete.type	0.010	0.002	0.013
duplicates	0.004	0.002	0.006
enforce.numeric	0.005	0.003	0.009
enforce.string	0.006	0.002	0.009
events.selection	0.009	0.004	0.015
export.graphml	0.229	0.011	0.245
export.mutex	0.018	0.007	0.026
has.duplicates	0.003	0.002	0.006
has.model	0.004	0.003	0.006
has.stages	0.014	0.006	0.021
import.GISTIC	0.012	0.004	0.017
import.MAF	0.157	0.016	0.177
intersect.datasets	0.002	0.002	0.005
is.compliant	0.004	0.002	0.005
join.events	0.008	0.002	0.010
join.types	0.098	0.034	0.137
keysToNames	0.009	0.005	0.015
nameToKey	0.006	0.003	0.007
nevents	0.002	0.002	0.005
ngenes	0.003	0.002	0.005
nhypotheses	0.002	0.002	0.005
npatterns	0.003	0.002	0.005
nsamples	0.003	0.003	0.005
ntypes	0.002	0.002	0.005
oncoprint.cbio	0.014	0.004	0.018
order.frequency	0.015	0.025	0.042
pheatmap	0.073	0.003	0.076
rank.recurrents	0.007	0.002	0.010
rename.gene	0.004	0.002	0.006
rename.type	0.005	0.003	0.007
samples.selection	0.007	0.003	0.010
trim	0.007	0.003	0.010
tronco.bootstrap	0.233	0.027	20.957
tronco.caprese	0.347	0.008	0.357
tronco.capri	4.651	0.153	4.857
tronco.chowliu	3.081	0.042	3.150
tronco.edmonds	2.844	0.029	2.913
tronco.gabow	3.032	0.039	3.233
tronco.kfold.eloss	0.226	0.146	0.377
tronco.kfold.posterr	0.297	0.211	7.535
tronco.kfold.prederr	0.224	0.167	7.521
tronco.plot	0.301	0.009	0.321
tronco.prim	5.181	0.081	6.193
view	0.008	0.003	0.012
which.samples	0.006	0.003	0.010