Multiple platform build/check report for BioC 3.19 - CHECK results for TRONCO on palomino3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4708
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"	4446
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"	4471
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"	4426
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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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TRONCO.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings TRONCO_2.35.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/TRONCO.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TRONCO/DESCRIPTION' ... OK
* this is package 'TRONCO' version '2.35.1'
* 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 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 0.08   0.06    10.8
* 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:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL TRONCO
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 5 edges out of 45 (11%)
*** 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 51 (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 9 edges out of 55 (16%)
*** 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 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:02s 
[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
  49.82    2.39  109.39

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.01	0.00	0.02
TCGA.remove.multiple.samples	0.02	0.00	0.01
TCGA.shorten.barcodes	0.02	0.00	0.01
annotate.description	0.00	0.04	0.03
annotate.stages	0.01	0.00	0.02
as.adj.matrix	0.00	0.01	0.01
as.alterations	0.02	0.00	0.02
as.bootstrap.scores	0.16	0.00	0.16
as.colors	0	0	0
as.confidence	0.01	0.02	0.03
as.description	0	0	0
as.events	0.02	0.00	0.01
as.events.in.patterns	0.01	0.00	0.02
as.events.in.sample	0	0	0
as.gene	0.02	0.00	0.01
as.genes	0.01	0.00	0.02
as.genes.in.patterns	0	0	0
as.genotypes	0.00	0.01	0.02
as.hypotheses	0.02	0.00	0.01
as.joint.probs	0.00	0.03	0.03
as.kfold.eloss	0.06	0.00	0.06
as.kfold.posterr	0.06	0.02	0.08
as.kfold.prederr	0.07	0.01	0.08
as.marginal.probs	0	0	0
as.models	0.03	0.02	0.04
as.parameters	0	0	0
as.pathway	0.01	0.00	0.02
as.patterns	0	0	0
as.samples	0.02	0.00	0.01
as.selective.advantage.relations	0.11	0.00	0.11
as.stages	0.00	0.01	0.02
as.types	0.00	0.02	0.02
as.types.in.patterns	0	0	0
change.color	0	0	0
consolidate.data	0.04	0.00	0.03
delete.event	0	0	0
delete.gene	0.01	0.00	0.01
delete.hypothesis	0.03	0.02	0.05
delete.model	0	0	0
delete.pattern	0.02	0.00	0.02
delete.samples	0.00	0.01	0.01
delete.type	0	0	0
duplicates	0.00	0.02	0.02
enforce.numeric	0	0	0
enforce.string	0.01	0.00	0.01
events.selection	0	0	0
export.graphml	0.13	0.00	0.13
export.mutex	0.01	0.00	0.01
has.duplicates	0.00	0.02	0.02
has.model	0	0	0
has.stages	0.02	0.00	0.01
import.GISTIC	0	0	0
import.MAF	0.08	0.00	0.08
intersect.datasets	0	0	0
is.compliant	0	0	0
join.events	0	0	0
join.types	0.05	0.00	0.05
keysToNames	0.02	0.00	0.01
nameToKey	0	0	0
nevents	0	0	0
ngenes	0.01	0.00	0.02
nhypotheses	0	0	0
npatterns	0	0	0
nsamples	0.00	0.01	0.01
ntypes	0	0	0
oncoprint.cbio	0.02	0.00	0.02
order.frequency	0.00	0.02	0.01
pheatmap	0.04	0.00	0.05
rank.recurrents	0	0	0
rename.gene	0	0	0
rename.type	0	0	0
samples.selection	0	0	0
trim	0.00	0.01	0.01
tronco.bootstrap	0.08	0.06	10.80
tronco.caprese	0.11	0.05	0.15
tronco.capri	2.19	0.11	2.30
tronco.chowliu	1.39	0.06	1.45
tronco.edmonds	1.31	0.05	1.36
tronco.gabow	1.58	0.05	1.62
tronco.kfold.eloss	0.08	0.04	0.13
tronco.kfold.posterr	0.19	0.02	3.53
tronco.kfold.prederr	0.15	0.03	3.14
tronco.plot	0.16	0.00	0.16
tronco.prim	2.64	0.05	2.69
view	0.00	0.01	0.01
which.samples	0	0	0

CHECK results for TRONCO on palomino3

Summary

Command output

Installation output

Tests output

Example timings