Mac ARM64 build report for BioC 3.17 - CHECK results for TRONCO on kjohnson2

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson2	macOS 12.6.1 Monterey	arm64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4347
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_2.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TRONCO.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.32.0’
* 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.kfold.posterr 0.143  0.075   7.180
tronco.kfold.prederr 0.099  0.062   6.257
tronco.bootstrap     0.110  0.018  14.748
* 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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 12 edges out of 57 (21%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** 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: 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 57 (16%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s 
*** 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 10 edges out of 56 (18%)
*** 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:03s 
*** 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 52 (13%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s 
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 39.163   1.314 164.408

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.017	0.003	0.040
TCGA.remove.multiple.samples	0.014	0.010	0.044
TCGA.shorten.barcodes	0.010	0.010	0.031
annotate.description	0.008	0.009	0.031
annotate.stages	0.007	0.002	0.019
as.adj.matrix	0.008	0.012	0.037
as.alterations	0.004	0.001	0.009
as.bootstrap.scores	0.147	0.004	0.270
as.colors	0.002	0.001	0.007
as.confidence	0.009	0.015	0.046
as.description	0.001	0.000	0.002
as.events	0.002	0.002	0.006
as.events.in.patterns	0.005	0.002	0.010
as.events.in.sample	0.004	0.001	0.009
as.gene	0.003	0.002	0.014
as.genes	0.002	0.002	0.008
as.genes.in.patterns	0.004	0.001	0.004
as.genotypes	0.007	0.007	0.025
as.hypotheses	0.003	0.004	0.012
as.joint.probs	0.008	0.012	0.031
as.kfold.eloss	0.082	0.005	0.151
as.kfold.posterr	0.099	0.009	0.196
as.kfold.prederr	0.100	0.008	0.195
as.marginal.probs	0.005	0.003	0.009
as.models	0.013	0.029	0.074
as.parameters	0.003	0.002	0.011
as.pathway	0.006	0.002	0.015
as.patterns	0.002	0.001	0.008
as.samples	0.001	0.001	0.003
as.selective.advantage.relations	0.104	0.012	0.216
as.stages	0.007	0.003	0.017
as.types	0.001	0.001	0.003
as.types.in.patterns	0.004	0.002	0.010
change.color	0.002	0.002	0.008
consolidate.data	0.031	0.003	0.056
delete.event	0.005	0.002	0.014
delete.gene	0.005	0.002	0.012
delete.hypothesis	0.027	0.026	0.093
delete.model	0.003	0.002	0.009
delete.pattern	0.012	0.009	0.033
delete.samples	0.004	0.001	0.008
delete.type	0.006	0.002	0.012
duplicates	0.003	0.001	0.005
enforce.numeric	0.002	0.001	0.007
enforce.string	0.003	0.001	0.007
events.selection	0.004	0.002	0.012
export.graphml	0.089	0.013	0.206
export.mutex	0.022	0.004	0.045
has.duplicates	0.002	0.001	0.006
has.model	0.002	0.001	0.006
has.stages	0.006	0.003	0.012
import.GISTIC	0.006	0.002	0.010
import.MAF	0.078	0.008	0.137
intersect.datasets	0.001	0.001	0.006
is.compliant	0.002	0.001	0.007
join.events	0.004	0.001	0.006
join.types	0.048	0.014	0.108
keysToNames	0.005	0.002	0.011
nameToKey	0.003	0.001	0.007
nevents	0.001	0.001	0.005
ngenes	0.001	0.001	0.007
nhypotheses	0.002	0.001	0.007
npatterns	0.002	0.002	0.006
nsamples	0.001	0.001	0.005
ntypes	0.001	0.001	0.006
oncoprint.cbio	0.006	0.002	0.015
order.frequency	0.006	0.009	0.027
pheatmap	0.035	0.002	0.063
rank.recurrents	0.004	0.001	0.006
rename.gene	0.002	0.001	0.007
rename.type	0.002	0.001	0.006
samples.selection	0.003	0.001	0.007
trim	0.004	0.002	0.012
tronco.bootstrap	0.110	0.018	14.748
tronco.caprese	0.101	0.005	0.177
tronco.capri	1.953	0.066	3.508
tronco.chowliu	1.408	0.028	2.523
tronco.edmonds	1.312	0.023	2.345
tronco.gabow	1.299	0.026	2.391
tronco.kfold.eloss	0.087	0.048	0.235
tronco.kfold.posterr	0.143	0.075	7.180
tronco.kfold.prederr	0.099	0.062	6.257
tronco.plot	0.145	0.007	0.279
tronco.prim	2.598	0.054	4.725
view	0.004	0.001	0.008
which.samples	0.004	0.002	0.012

CHECK results for TRONCO on kjohnson2

Summary

Command output

Installation output

Tests output

Example timings