Mac ARM64 build report for BioC 3.18 - CHECK results for TRONCO on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.1 Ventura	arm64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4376
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_2.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/TRONCO.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.34.0’
* 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 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.bootstrap 0.108  0.025   9.872
* 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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 6 edges out of 50 (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: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 10 edges out of 58 (17%)
*** 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 2 edges out of 45 (4%)
*** 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:02s 
*** 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 10 edges out of 57 (18%)
*** 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 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 37.541   1.525  94.395

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.020	0.005	0.025
TCGA.remove.multiple.samples	0.079	0.012	0.091
TCGA.shorten.barcodes	0.010	0.009	0.019
annotate.description	0.009	0.009	0.019
annotate.stages	0.006	0.003	0.010
as.adj.matrix	0.009	0.012	0.021
as.alterations	0.145	0.003	0.149
as.bootstrap.scores	0.037	0.003	0.041
as.colors	0.001	0.001	0.003
as.confidence	0.009	0.015	0.023
as.description	0.002	0.001	0.003
as.events	0.002	0.002	0.004
as.events.in.patterns	0.004	0.001	0.006
as.events.in.sample	0.005	0.001	0.006
as.gene	0.004	0.002	0.006
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.004	0.002	0.006
as.genotypes	0.007	0.007	0.014
as.hypotheses	0.004	0.003	0.008
as.joint.probs	0.008	0.013	0.021
as.kfold.eloss	0.108	0.004	0.113
as.kfold.posterr	0.122	0.009	0.136
as.kfold.prederr	0.126	0.008	0.135
as.marginal.probs	0.005	0.003	0.007
as.models	0.013	0.031	0.044
as.parameters	0.003	0.002	0.005
as.pathway	0.005	0.002	0.008
as.patterns	0.002	0.001	0.004
as.samples	0.002	0.002	0.004
as.selective.advantage.relations	0.087	0.011	0.099
as.stages	0.007	0.003	0.010
as.types	0.002	0.001	0.004
as.types.in.patterns	0.004	0.002	0.006
change.color	0.002	0.001	0.004
consolidate.data	0.026	0.003	0.029
delete.event	0.005	0.002	0.008
delete.gene	0.005	0.002	0.008
delete.hypothesis	0.026	0.026	0.053
delete.model	0.003	0.001	0.005
delete.pattern	0.010	0.009	0.018
delete.samples	0.003	0.002	0.005
delete.type	0.005	0.002	0.007
duplicates	0.003	0.002	0.005
enforce.numeric	0.003	0.002	0.005
enforce.string	0.003	0.001	0.005
events.selection	0.003	0.001	0.005
export.graphml	0.120	0.008	0.129
export.mutex	0.008	0.004	0.012
has.duplicates	0.002	0.001	0.004
has.model	0.002	0.001	0.004
has.stages	0.005	0.002	0.008
import.GISTIC	0.005	0.001	0.005
import.MAF	0.077	0.006	0.085
intersect.datasets	0.001	0.001	0.003
is.compliant	0.002	0.001	0.004
join.events	0.004	0.001	0.005
join.types	0.037	0.012	0.048
keysToNames	0.005	0.003	0.008
nameToKey	0.003	0.002	0.005
nevents	0.002	0.002	0.003
ngenes	0.002	0.002	0.003
nhypotheses	0.001	0.002	0.003
npatterns	0.001	0.001	0.002
nsamples	0.002	0.002	0.003
ntypes	0.001	0.001	0.003
oncoprint.cbio	0.005	0.002	0.006
order.frequency	0.007	0.010	0.017
pheatmap	0.033	0.002	0.035
rank.recurrents	0.003	0.001	0.006
rename.gene	0.002	0.001	0.004
rename.type	0.002	0.002	0.003
samples.selection	0.002	0.001	0.004
trim	0.003	0.001	0.004
tronco.bootstrap	0.108	0.025	9.872
tronco.caprese	0.133	0.005	0.138
tronco.capri	1.813	0.085	1.907
tronco.chowliu	1.125	0.024	1.155
tronco.edmonds	1.255	0.029	1.299
tronco.gabow	1.236	0.038	1.281
tronco.kfold.eloss	0.079	0.048	0.132
tronco.kfold.posterr	0.144	0.082	4.097
tronco.kfold.prederr	0.113	0.082	3.677
tronco.plot	0.140	0.007	0.155
tronco.prim	2.423	0.052	2.509
view	0.005	0.002	0.007
which.samples	0.004	0.002	0.005

CHECK results for TRONCO on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings