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"	4494
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"	4395
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: 2025-01-24 13:20:31 -0500 (Fri, 24 Jan 2025)

EndedAt: 2025-01-24 13:31:07 -0500 (Fri, 24 Jan 2025)

EllapsedTime: 636.2 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          4.963  0.071   7.091
tronco.capri         4.502  0.130   6.600
tronco.edmonds       3.555  0.055   5.339
tronco.kfold.posterr 0.286  0.240   9.928
tronco.kfold.prederr 0.220  0.180   8.945
tronco.bootstrap     0.228  0.032  31.747
* 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:01s 
*** 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 48 (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:06s 
*** 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 50 (8%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:07s 
*** 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 9 edges out of 56 (16%)
*** 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:06s 
*** 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 6 edges out of 54 (11%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:07s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 97.056   2.721 330.683

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.030	0.008	0.051
TCGA.remove.multiple.samples	0.032	0.029	0.093
TCGA.shorten.barcodes	0.025	0.027	0.072
annotate.description	0.022	0.030	0.065
annotate.stages	0.014	0.005	0.025
as.adj.matrix	0.022	0.037	0.081
as.alterations	0.008	0.004	0.025
as.bootstrap.scores	0.159	0.008	0.231
as.colors	0.003	0.002	0.006
as.confidence	0.023	0.048	0.097
as.description	0.002	0.002	0.009
as.events	0.004	0.003	0.011
as.events.in.patterns	0.009	0.003	0.013
as.events.in.sample	0.009	0.002	0.022
as.gene	0.008	0.006	0.027
as.genes	0.003	0.002	0.007
as.genes.in.patterns	0.137	0.003	0.182
as.genotypes	0.018	0.020	0.057
as.hypotheses	0.007	0.011	0.031
as.joint.probs	0.018	0.034	0.066
as.kfold.eloss	0.149	0.005	0.202
as.kfold.posterr	0.188	0.017	0.298
as.kfold.prederr	0.193	0.022	0.288
as.marginal.probs	0.008	0.006	0.016
as.models	0.037	0.094	0.195
as.parameters	0.004	0.002	0.010
as.pathway	0.012	0.004	0.032
as.patterns	0.003	0.002	0.011
as.samples	0.003	0.004	0.009
as.selective.advantage.relations	0.253	0.052	0.422
as.stages	0.015	0.006	0.025
as.types	0.003	0.002	0.005
as.types.in.patterns	0.008	0.003	0.012
change.color	0.004	0.003	0.007
consolidate.data	0.082	0.004	0.123
delete.event	0.010	0.003	0.015
delete.gene	0.011	0.002	0.018
delete.hypothesis	0.069	0.104	0.303
delete.model	0.006	0.002	0.010
delete.pattern	0.027	0.023	0.056
delete.samples	0.007	0.002	0.016
delete.type	0.010	0.003	0.019
duplicates	0.004	0.003	0.007
enforce.numeric	0.006	0.002	0.010
enforce.string	0.005	0.003	0.008
events.selection	0.009	0.004	0.013
export.graphml	0.233	0.012	0.318
export.mutex	0.018	0.006	0.035
has.duplicates	0.003	0.002	0.006
has.model	0.004	0.002	0.010
has.stages	0.014	0.006	0.027
import.GISTIC	0.012	0.004	0.024
import.MAF	0.154	0.016	0.228
intersect.datasets	0.003	0.003	0.010
is.compliant	0.003	0.003	0.010
join.events	0.008	0.003	0.015
join.types	0.101	0.039	0.177
keysToNames	0.009	0.006	0.021
nameToKey	0.006	0.002	0.012
nevents	0.003	0.002	0.007
ngenes	0.002	0.002	0.006
nhypotheses	0.003	0.002	0.010
npatterns	0.002	0.002	0.006
nsamples	0.003	0.002	0.005
ntypes	0.002	0.002	0.007
oncoprint.cbio	0.014	0.004	0.024
order.frequency	0.016	0.028	0.059
pheatmap	0.076	0.002	0.100
rank.recurrents	0.008	0.003	0.013
rename.gene	0.005	0.003	0.007
rename.type	0.005	0.002	0.010
samples.selection	0.007	0.002	0.014
trim	0.008	0.003	0.011
tronco.bootstrap	0.228	0.032	31.747
tronco.caprese	0.368	0.008	0.445
tronco.capri	4.502	0.130	6.600
tronco.chowliu	3.158	0.041	4.712
tronco.edmonds	3.555	0.055	5.339
tronco.gabow	3.103	0.038	4.421
tronco.kfold.eloss	0.228	0.140	0.536
tronco.kfold.posterr	0.286	0.240	9.928
tronco.kfold.prederr	0.220	0.180	8.945
tronco.plot	0.298	0.009	0.408
tronco.prim	4.963	0.071	7.091
view	0.008	0.002	0.014
which.samples	0.006	0.003	0.009