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	R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"	4676
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences"	4414
merida1	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"	4441
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences"	4417
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_2.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.35.0’
* 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 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          4.862  0.080   5.649
tronco.capri         4.466  0.140   5.185
tronco.kfold.posterr 0.284  0.211   7.561
tronco.kfold.prederr 0.218  0.196   7.419
tronco.bootstrap     0.211  0.023  24.228
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TRONCO
###
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* 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


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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 8 edges out of 55 (15%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:04s 
*** 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 47 (15%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:04s 
*** 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 55 (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: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 8 edges out of 53 (15%)
*** 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 
 91.900   2.434 247.715

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.030	0.008	0.043
TCGA.remove.multiple.samples	0.032	0.031	0.068
TCGA.shorten.barcodes	0.024	0.030	0.060
annotate.description	0.022	0.027	0.054
annotate.stages	0.014	0.006	0.021
as.adj.matrix	0.022	0.039	0.074
as.alterations	0.008	0.004	0.015
as.bootstrap.scores	0.153	0.008	0.179
as.colors	0.003	0.002	0.008
as.confidence	0.022	0.047	0.080
as.description	0.003	0.002	0.007
as.events	0.004	0.004	0.009
as.events.in.patterns	0.008	0.002	0.012
as.events.in.sample	0.009	0.003	0.011
as.gene	0.007	0.005	0.014
as.genes	0.003	0.003	0.006
as.genes.in.patterns	0.136	0.003	0.151
as.genotypes	0.019	0.020	0.043
as.hypotheses	0.006	0.010	0.025
as.joint.probs	0.019	0.036	0.063
as.kfold.eloss	0.139	0.004	0.162
as.kfold.posterr	0.177	0.014	0.212
as.kfold.prederr	0.182	0.019	0.219
as.marginal.probs	0.008	0.005	0.013
as.models	0.036	0.090	0.137
as.parameters	0.004	0.004	0.010
as.pathway	0.011	0.004	0.017
as.patterns	0.003	0.003	0.007
as.samples	0.003	0.004	0.007
as.selective.advantage.relations	0.254	0.051	0.351
as.stages	0.014	0.006	0.021
as.types	0.003	0.002	0.005
as.types.in.patterns	0.008	0.003	0.011
change.color	0.004	0.002	0.006
consolidate.data	0.076	0.004	0.089
delete.event	0.010	0.002	0.016
delete.gene	0.010	0.002	0.014
delete.hypothesis	0.068	0.079	0.173
delete.model	0.006	0.002	0.008
delete.pattern	0.027	0.026	0.059
delete.samples	0.006	0.003	0.011
delete.type	0.011	0.003	0.017
duplicates	0.004	0.003	0.007
enforce.numeric	0.005	0.002	0.008
enforce.string	0.005	0.002	0.008
events.selection	0.009	0.003	0.012
export.graphml	0.228	0.011	0.271
export.mutex	0.017	0.007	0.029
has.duplicates	0.003	0.003	0.007
has.model	0.004	0.002	0.006
has.stages	0.014	0.006	0.024
import.GISTIC	0.012	0.004	0.018
import.MAF	0.152	0.015	0.191
intersect.datasets	0.003	0.002	0.004
is.compliant	0.003	0.002	0.006
join.events	0.008	0.002	0.011
join.types	0.097	0.035	0.150
keysToNames	0.009	0.006	0.019
nameToKey	0.005	0.002	0.010
nevents	0.002	0.002	0.007
ngenes	0.003	0.002	0.005
nhypotheses	0.002	0.002	0.006
npatterns	0.003	0.002	0.005
nsamples	0.002	0.002	0.005
ntypes	0.002	0.002	0.005
oncoprint.cbio	0.013	0.003	0.019
order.frequency	0.017	0.029	0.050
pheatmap	0.070	0.002	0.078
rank.recurrents	0.007	0.003	0.011
rename.gene	0.004	0.003	0.007
rename.type	0.004	0.003	0.007
samples.selection	0.007	0.003	0.011
trim	0.007	0.003	0.011
tronco.bootstrap	0.211	0.023	24.228
tronco.caprese	0.330	0.010	0.344
tronco.capri	4.466	0.140	5.185
tronco.chowliu	3.383	0.059	3.872
tronco.edmonds	2.636	0.032	2.981
tronco.gabow	2.827	0.037	3.199
tronco.kfold.eloss	0.215	0.155	0.421
tronco.kfold.posterr	0.284	0.211	7.561
tronco.kfold.prederr	0.218	0.196	7.419
tronco.plot	0.281	0.010	0.310
tronco.prim	4.862	0.080	5.649
view	0.008	0.002	0.011
which.samples	0.006	0.003	0.010

CHECK results for TRONCO on merida1

Summary

Command output

Installation output

Tests output

Example timings