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"	4709
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4483
merida1	macOS 12.7.4 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4512
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4461
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: 2024-07-08 13:26:04 -0400 (Mon, 08 Jul 2024)

EndedAt: 2024-07-08 13:33:47 -0400 (Mon, 08 Jul 2024)

EllapsedTime: 463.2 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_2.36.0.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 12.7.4
* 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          4.988  0.075   5.727
tronco.capri         4.818  0.162   5.280
tronco.kfold.posterr 0.301  0.211   7.602
tronco.kfold.prederr 0.223  0.195   7.995
tronco.bootstrap     0.234  0.024  22.098
* 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: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 51 (12%)
*** 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 7 edges out of 48 (15%)
*** 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 11 edges out of 59 (19%)
*** 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 6 edges out of 47 (13%)
*** 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 
 97.133   2.456 241.900

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.031	0.007	0.040
TCGA.remove.multiple.samples	0.035	0.033	0.071
TCGA.shorten.barcodes	0.026	0.029	0.056
annotate.description	0.023	0.030	0.055
annotate.stages	0.015	0.005	0.021
as.adj.matrix	0.023	0.040	0.064
as.alterations	0.008	0.004	0.012
as.bootstrap.scores	0.151	0.008	0.169
as.colors	0.003	0.003	0.006
as.confidence	0.022	0.047	0.072
as.description	0.003	0.002	0.004
as.events	0.003	0.004	0.007
as.events.in.patterns	0.008	0.003	0.011
as.events.in.sample	0.009	0.002	0.011
as.gene	0.008	0.006	0.014
as.genes	0.003	0.003	0.006
as.genes.in.patterns	0.133	0.004	0.140
as.genotypes	0.019	0.022	0.043
as.hypotheses	0.007	0.011	0.020
as.joint.probs	0.019	0.035	0.056
as.kfold.eloss	0.143	0.005	0.154
as.kfold.posterr	0.182	0.013	0.202
as.kfold.prederr	0.190	0.018	0.217
as.marginal.probs	0.008	0.006	0.014
as.models	0.038	0.098	0.148
as.parameters	0.005	0.004	0.008
as.pathway	0.011	0.005	0.015
as.patterns	0.003	0.003	0.006
as.samples	0.003	0.003	0.005
as.selective.advantage.relations	0.253	0.048	0.318
as.stages	0.015	0.005	0.021
as.types	0.003	0.002	0.006
as.types.in.patterns	0.008	0.003	0.011
change.color	0.004	0.002	0.007
consolidate.data	0.078	0.004	0.083
delete.event	0.010	0.003	0.012
delete.gene	0.010	0.003	0.013
delete.hypothesis	0.069	0.075	0.145
delete.model	0.006	0.002	0.009
delete.pattern	0.028	0.026	0.055
delete.samples	0.006	0.002	0.008
delete.type	0.010	0.002	0.011
duplicates	0.003	0.002	0.006
enforce.numeric	0.005	0.002	0.007
enforce.string	0.006	0.002	0.008
events.selection	0.009	0.004	0.013
export.graphml	0.229	0.012	0.250
export.mutex	0.018	0.008	0.026
has.duplicates	0.003	0.003	0.006
has.model	0.003	0.002	0.005
has.stages	0.013	0.005	0.019
import.GISTIC	0.013	0.004	0.017
import.MAF	0.152	0.014	0.170
intersect.datasets	0.003	0.003	0.005
is.compliant	0.003	0.003	0.006
join.events	0.008	0.002	0.011
join.types	0.103	0.037	0.177
keysToNames	0.010	0.006	0.017
nameToKey	0.005	0.003	0.008
nevents	0.003	0.002	0.006
ngenes	0.002	0.002	0.005
nhypotheses	0.003	0.002	0.005
npatterns	0.003	0.002	0.006
nsamples	0.002	0.003	0.005
ntypes	0.003	0.003	0.005
oncoprint.cbio	0.013	0.004	0.018
order.frequency	0.017	0.030	0.048
pheatmap	0.073	0.003	0.076
rank.recurrents	0.008	0.002	0.012
rename.gene	0.005	0.002	0.012
rename.type	0.004	0.003	0.007
samples.selection	0.007	0.002	0.010
trim	0.008	0.003	0.011
tronco.bootstrap	0.234	0.024	22.098
tronco.caprese	0.355	0.008	0.368
tronco.capri	4.818	0.162	5.280
tronco.chowliu	3.190	0.037	3.362
tronco.edmonds	2.828	0.031	2.979
tronco.gabow	3.239	0.040	3.441
tronco.kfold.eloss	0.23	0.16	0.41
tronco.kfold.posterr	0.301	0.211	7.602
tronco.kfold.prederr	0.223	0.195	7.995
tronco.plot	0.303	0.009	0.354
tronco.prim	4.988	0.075	5.727
view	0.009	0.004	0.018
which.samples	0.005	0.003	0.008