Multiple platform build/check report for BioC 3.19 - CHECK results for TRONCO on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4753
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4518
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/meat/TRONCO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 ‘2.36.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
tronco.bootstrap 0.116  0.019  10.564
* 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-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
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 11 edges out of 53 (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 7 edges out of 49 (14%)
*** Performing likelihood-fit with regularization: no_reg .
*** 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: 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 8 edges out of 47 (17%)
*** 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 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:02s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 45.269   1.707 104.647

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.016	0.005	0.021
TCGA.remove.multiple.samples	0.016	0.013	0.028
TCGA.shorten.barcodes	0.012	0.014	0.027
annotate.description	0.010	0.013	0.023
annotate.stages	0.009	0.004	0.013
as.adj.matrix	0.011	0.017	0.028
as.alterations	0.003	0.002	0.006
as.bootstrap.scores	0.107	0.005	0.112
as.colors	0.002	0.002	0.003
as.confidence	0.01	0.02	0.03
as.description	0.002	0.001	0.002
as.events	0.002	0.002	0.003
as.events.in.patterns	0.004	0.002	0.006
as.events.in.sample	0.005	0.002	0.007
as.gene	0.004	0.003	0.008
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.128	0.004	0.133
as.genotypes	0.008	0.009	0.017
as.hypotheses	0.004	0.006	0.010
as.joint.probs	0.009	0.016	0.025
as.kfold.eloss	0.087	0.002	0.090
as.kfold.posterr	0.107	0.007	0.115
as.kfold.prederr	0.112	0.009	0.125
as.marginal.probs	0.004	0.003	0.007
as.models	0.014	0.033	0.047
as.parameters	0.003	0.002	0.005
as.pathway	0.005	0.002	0.006
as.patterns	0.002	0.002	0.004
as.samples	0.001	0.002	0.003
as.selective.advantage.relations	0.103	0.021	0.125
as.stages	0.007	0.003	0.010
as.types	0.002	0.001	0.003
as.types.in.patterns	0.005	0.002	0.006
change.color	0.003	0.001	0.004
consolidate.data	0.033	0.002	0.036
delete.event	0.007	0.002	0.008
delete.gene	0.007	0.002	0.008
delete.hypothesis	0.034	0.038	0.073
delete.model	0.004	0.002	0.007
delete.pattern	0.015	0.014	0.028
delete.samples	0.005	0.002	0.006
delete.type	0.007	0.002	0.008
duplicates	0.003	0.001	0.005
enforce.numeric	0.004	0.002	0.005
enforce.string	0.003	0.002	0.005
events.selection	0.005	0.002	0.007
export.graphml	0.121	0.008	0.129
export.mutex	0.009	0.003	0.012
has.duplicates	0.002	0.001	0.003
has.model	0.002	0.002	0.004
has.stages	0.006	0.003	0.009
import.GISTIC	0.005	0.002	0.007
import.MAF	0.089	0.010	0.101
intersect.datasets	0.001	0.002	0.003
is.compliant	0.001	0.001	0.002
join.events	0.004	0.001	0.005
join.types	0.048	0.014	0.062
keysToNames	0.006	0.003	0.009
nameToKey	0.003	0.001	0.003
nevents	0.001	0.002	0.002
ngenes	0.001	0.001	0.004
nhypotheses	0.002	0.001	0.002
npatterns	0.002	0.001	0.003
nsamples	0.001	0.000	0.002
ntypes	0.001	0.001	0.002
oncoprint.cbio	0.006	0.002	0.008
order.frequency	0.007	0.011	0.019
pheatmap	0.036	0.002	0.039
rank.recurrents	0.005	0.001	0.006
rename.gene	0.003	0.001	0.005
rename.type	0.003	0.001	0.004
samples.selection	0.004	0.001	0.004
trim	0.004	0.002	0.006
tronco.bootstrap	0.116	0.019	10.564
tronco.caprese	0.161	0.007	0.168
tronco.capri	1.975	0.074	2.065
tronco.chowliu	1.497	0.033	1.544
tronco.edmonds	1.538	0.039	1.586
tronco.gabow	1.453	0.034	1.498
tronco.kfold.eloss	0.100	0.049	0.150
tronco.kfold.posterr	0.146	0.103	3.978
tronco.kfold.prederr	0.106	0.069	3.562
tronco.plot	0.153	0.007	0.162
tronco.prim	2.504	0.059	2.586
view	0.004	0.002	0.005
which.samples	0.002	0.002	0.004

CHECK results for TRONCO on lconway

Summary

Command output

Installation output

Tests output

Example timings