Multiple platform build/check report for BioC 3.16 - CHECK results for TRONCO on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4502
palomino4	Windows Server 2022 Datacenter	x64	4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"	4282
lconway	macOS 12.5.1 Monterey	x86_64	4.2.3 (2023-03-15) -- "Shortstop Beagle"	4310
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*

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### Running command:
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###   /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_2.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/TRONCO.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.30.0’
* 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 R 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
tronco.bootstrap 0.099  0.018   7.465
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TRONCO
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 58 (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:01s 
*** 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 5 edges out of 51 (10%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / 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: 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 44 (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:01s 
*** 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:01s 
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 30.435   1.148  71.671

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.012	0.003	0.015
TCGA.remove.multiple.samples	0.010	0.008	0.018
TCGA.shorten.barcodes	0.050	0.008	0.058
annotate.description	0.007	0.008	0.015
annotate.stages	0.005	0.002	0.006
as.adj.matrix	0.006	0.010	0.016
as.alterations	0.003	0.001	0.004
as.bootstrap.scores	0.117	0.002	0.120
as.colors	0.001	0.001	0.002
as.confidence	0.006	0.012	0.018
as.description	0.001	0.001	0.001
as.events	0.001	0.001	0.003
as.events.in.patterns	0.002	0.000	0.004
as.events.in.sample	0.002	0.000	0.003
as.gene	0.002	0.001	0.004
as.genes	0.001	0.001	0.002
as.genes.in.patterns	0.003	0.001	0.004
as.genotypes	0.005	0.006	0.012
as.hypotheses	0.002	0.003	0.006
as.joint.probs	0.005	0.008	0.014
as.kfold.eloss	0.059	0.003	0.062
as.kfold.posterr	0.068	0.006	0.074
as.kfold.prederr	0.071	0.005	0.077
as.marginal.probs	0.003	0.001	0.004
as.models	0.010	0.025	0.036
as.parameters	0.002	0.001	0.003
as.pathway	0.006	0.002	0.007
as.patterns	0.002	0.001	0.003
as.samples	0.002	0.001	0.002
as.selective.advantage.relations	0.067	0.010	0.076
as.stages	0.004	0.002	0.006
as.types	0.001	0.001	0.002
as.types.in.patterns	0.003	0.001	0.003
change.color	0.002	0.000	0.002
consolidate.data	0.019	0.001	0.020
delete.event	0.003	0.001	0.004
delete.gene	0.004	0.001	0.004
delete.hypothesis	0.019	0.019	0.038
delete.model	0.003	0.001	0.003
delete.pattern	0.008	0.007	0.015
delete.samples	0.003	0.001	0.002
delete.type	0.003	0.001	0.004
duplicates	0.002	0.001	0.003
enforce.numeric	0.002	0.001	0.003
enforce.string	0.002	0.002	0.003
events.selection	0.003	0.001	0.004
export.graphml	0.052	0.004	0.057
export.mutex	0.006	0.002	0.008
has.duplicates	0.002	0.001	0.002
has.model	0.002	0.001	0.003
has.stages	0.004	0.002	0.005
import.GISTIC	0.003	0.001	0.004
import.MAF	0.059	0.005	0.064
intersect.datasets	0.001	0.001	0.003
is.compliant	0.001	0.001	0.003
join.events	0.003	0.001	0.005
join.types	0.031	0.011	0.043
keysToNames	0.004	0.002	0.006
nameToKey	0.002	0.000	0.002
nevents	0.001	0.001	0.003
ngenes	0.001	0.001	0.003
nhypotheses	0.001	0.001	0.001
npatterns	0.001	0.001	0.002
nsamples	0.001	0.001	0.001
ntypes	0.001	0.001	0.002
oncoprint.cbio	0.003	0.001	0.005
order.frequency	0.005	0.008	0.013
pheatmap	0.027	0.001	0.028
rank.recurrents	0.003	0.001	0.004
rename.gene	0.002	0.001	0.002
rename.type	0.002	0.001	0.003
samples.selection	0.003	0.001	0.005
trim	0.003	0.001	0.004
tronco.bootstrap	0.099	0.018	7.465
tronco.caprese	0.072	0.005	0.076
tronco.capri	1.393	0.062	1.458
tronco.chowliu	0.934	0.025	0.960
tronco.edmonds	0.988	0.025	1.014
tronco.gabow	0.985	0.023	1.010
tronco.kfold.eloss	0.058	0.036	0.094
tronco.kfold.posterr	0.107	0.066	2.851
tronco.kfold.prederr	0.082	0.057	2.385
tronco.plot	0.107	0.005	0.112
tronco.prim	1.810	0.052	1.868
view	0.003	0.001	0.004
which.samples	0.003	0.001	0.003

CHECK results for TRONCO on lconway

Summary

Command output

Installation output

Tests output

Example timings