Mac ARM64 build report for BioC 3.19 - CHECK results for TRONCO on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	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*

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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_2.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/TRONCO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* 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
* 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

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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/4.4-arm64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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 7 edges out of 55 (13%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / 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: 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 55 (15%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / 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: 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 48 (8%)
*** 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:00s 
*** 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 4 edges out of 44 (9%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:00s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 10.916   0.471  27.047

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.006	0.002	0.008
TCGA.remove.multiple.samples	0.005	0.004	0.008
TCGA.shorten.barcodes	0.003	0.003	0.006
annotate.description	0.003	0.003	0.006
annotate.stages	0.002	0.001	0.003
as.adj.matrix	0.003	0.004	0.007
as.alterations	0.001	0.001	0.002
as.bootstrap.scores	0.036	0.001	0.037
as.colors	0.000	0.001	0.001
as.confidence	0.003	0.004	0.007
as.description	0.000	0.001	0.001
as.events	0.000	0.000	0.002
as.events.in.patterns	0.001	0.001	0.001
as.events.in.sample	0.001	0.000	0.001
as.gene	0.001	0.001	0.002
as.genes	0.001	0.001	0.001
as.genes.in.patterns	0.052	0.000	0.054
as.genotypes	0.002	0.003	0.005
as.hypotheses	0.001	0.001	0.002
as.joint.probs	0.002	0.004	0.006
as.kfold.eloss	0.028	0.001	0.028
as.kfold.posterr	0.032	0.002	0.035
as.kfold.prederr	0.032	0.002	0.035
as.marginal.probs	0.002	0.000	0.002
as.models	0.004	0.009	0.013
as.parameters	0.001	0.001	0.002
as.pathway	0.002	0.000	0.002
as.patterns	0.000	0.000	0.001
as.samples	0.000	0.001	0.001
as.selective.advantage.relations	0.030	0.005	0.034
as.stages	0.002	0.001	0.003
as.types	0.000	0.000	0.001
as.types.in.patterns	0.001	0.000	0.002
change.color	0.001	0.000	0.001
consolidate.data	0.008	0.000	0.009
delete.event	0.002	0.001	0.002
delete.gene	0.001	0.000	0.001
delete.hypothesis	0.008	0.008	0.015
delete.model	0.001	0.000	0.002
delete.pattern	0.003	0.003	0.006
delete.samples	0.001	0.001	0.002
delete.type	0.001	0.000	0.002
duplicates	0.001	0.001	0.001
enforce.numeric	0.001	0.000	0.001
enforce.string	0.001	0.001	0.001
events.selection	0.001	0.000	0.001
export.graphml	0.031	0.002	0.033
export.mutex	0.003	0.001	0.003
has.duplicates	0.001	0.001	0.001
has.model	0.000	0.000	0.001
has.stages	0.001	0.001	0.003
import.GISTIC	0.002	0.000	0.002
import.MAF	0.027	0.003	0.030
intersect.datasets	0.001	0.001	0.001
is.compliant	0.000	0.000	0.001
join.events	0.001	0.001	0.001
join.types	0.010	0.004	0.014
keysToNames	0.001	0.001	0.002
nameToKey	0.001	0.000	0.002
nevents	0.001	0.000	0.001
ngenes	0.000	0.000	0.001
nhypotheses	0.001	0.000	0.001
npatterns	0.000	0.000	0.001
nsamples	0.001	0.000	0.001
ntypes	0.000	0.000	0.001
oncoprint.cbio	0.002	0.001	0.002
order.frequency	0.002	0.003	0.005
pheatmap	0.010	0.001	0.011
rank.recurrents	0.002	0.000	0.001
rename.gene	0.000	0.001	0.002
rename.type	0.001	0.000	0.001
samples.selection	0.001	0.001	0.001
trim	0.001	0.000	0.001
tronco.bootstrap	0.034	0.007	3.289
tronco.caprese	0.037	0.002	0.039
tronco.capri	0.484	0.019	0.504
tronco.chowliu	0.366	0.010	0.376
tronco.edmonds	0.381	0.009	0.391
tronco.gabow	0.321	0.010	0.336
tronco.kfold.eloss	0.025	0.014	0.040
tronco.kfold.posterr	0.039	0.025	1.161
tronco.kfold.prederr	0.034	0.022	0.958
tronco.plot	0.037	0.001	0.038
tronco.prim	0.701	0.024	0.723
view	0.001	0.001	0.001
which.samples	0.001	0.000	0.001

CHECK results for TRONCO on kjohnson3

Summary

Command output

Installation output

Tests output

Example timings