Multiple platform build/check report for BioC 3.19 - CHECK results for TRONCO on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4529
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4479
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: 2.36.0

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_2.36.0.tar.gz

StartedAt: 2024-10-14 14:40:05 -0400 (Mon, 14 Oct 2024)

EndedAt: 2024-10-14 14:48:33 -0400 (Mon, 14 Oct 2024)

EllapsedTime: 507.4 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_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TRONCO.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘2.36.0’
* 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          4.976  0.077   5.887
tronco.capri         4.345  0.130   5.279
tronco.kfold.posterr 0.297  0.218   8.737
tronco.kfold.prederr 0.232  0.165   8.063
tronco.bootstrap     0.227  0.024  26.577
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 3 edges out of 49 (6%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:05s 
*** 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:05s 
*** 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 4 edges out of 45 (9%)
*** 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:05s 
*** 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 9 edges out of 54 (17%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:05s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 97.842   2.568 260.265

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.032	0.009	0.049
TCGA.remove.multiple.samples	0.033	0.031	0.065
TCGA.shorten.barcodes	0.025	0.027	0.061
annotate.description	0.022	0.028	0.061
annotate.stages	0.016	0.005	0.024
as.adj.matrix	0.021	0.036	0.065
as.alterations	0.008	0.004	0.015
as.bootstrap.scores	0.157	0.008	0.195
as.colors	0.003	0.003	0.004
as.confidence	0.022	0.046	0.079
as.description	0.003	0.003	0.005
as.events	0.003	0.004	0.008
as.events.in.patterns	0.009	0.003	0.015
as.events.in.sample	0.009	0.002	0.013
as.gene	0.008	0.006	0.016
as.genes	0.003	0.002	0.006
as.genes.in.patterns	0.138	0.003	0.159
as.genotypes	0.019	0.021	0.048
as.hypotheses	0.007	0.010	0.021
as.joint.probs	0.018	0.034	0.060
as.kfold.eloss	0.141	0.005	0.161
as.kfold.posterr	0.179	0.014	0.217
as.kfold.prederr	0.188	0.019	0.243
as.marginal.probs	0.008	0.005	0.016
as.models	0.037	0.093	0.149
as.parameters	0.005	0.004	0.010
as.pathway	0.012	0.004	0.018
as.patterns	0.004	0.002	0.008
as.samples	0.002	0.003	0.007
as.selective.advantage.relations	0.259	0.050	0.366
as.stages	0.015	0.006	0.027
as.types	0.003	0.003	0.007
as.types.in.patterns	0.009	0.002	0.012
change.color	0.004	0.002	0.007
consolidate.data	0.081	0.003	0.097
delete.event	0.009	0.002	0.012
delete.gene	0.010	0.003	0.013
delete.hypothesis	0.069	0.078	0.171
delete.model	0.007	0.003	0.011
delete.pattern	0.027	0.027	0.066
delete.samples	0.007	0.003	0.011
delete.type	0.010	0.002	0.017
duplicates	0.004	0.002	0.007
enforce.numeric	0.005	0.002	0.008
enforce.string	0.006	0.002	0.009
events.selection	0.009	0.003	0.014
export.graphml	0.236	0.011	0.280
export.mutex	0.018	0.008	0.036
has.duplicates	0.003	0.002	0.007
has.model	0.004	0.003	0.007
has.stages	0.014	0.006	0.025
import.GISTIC	0.013	0.004	0.021
import.MAF	0.156	0.016	0.203
intersect.datasets	0.002	0.002	0.006
is.compliant	0.004	0.003	0.007
join.events	0.007	0.002	0.011
join.types	0.103	0.039	0.173
keysToNames	0.010	0.006	0.021
nameToKey	0.005	0.003	0.009
nevents	0.002	0.002	0.005
ngenes	0.003	0.003	0.006
nhypotheses	0.003	0.002	0.005
npatterns	0.002	0.002	0.005
nsamples	0.003	0.002	0.007
ntypes	0.002	0.002	0.007
oncoprint.cbio	0.014	0.003	0.018
order.frequency	0.017	0.031	0.054
pheatmap	0.076	0.003	0.095
rank.recurrents	0.007	0.002	0.011
rename.gene	0.005	0.002	0.008
rename.type	0.004	0.002	0.008
samples.selection	0.007	0.002	0.011
trim	0.007	0.002	0.011
tronco.bootstrap	0.227	0.024	26.577
tronco.caprese	0.355	0.008	0.382
tronco.capri	4.345	0.130	5.279
tronco.chowliu	3.285	0.048	3.901
tronco.edmonds	3.154	0.041	3.841
tronco.gabow	2.995	0.051	3.799
tronco.kfold.eloss	0.231	0.161	0.472
tronco.kfold.posterr	0.297	0.218	8.737
tronco.kfold.prederr	0.232	0.165	8.063
tronco.plot	0.294	0.009	0.353
tronco.prim	4.976	0.077	5.887
view	0.008	0.002	0.012
which.samples	0.006	0.005	0.012