Multiple platform build/check report for BioC 3.18 - CHECK results for TRONCO on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4676
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4414
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4437
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*

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings TRONCO_2.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/TRONCO.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 0.111  0.005   9.401
* 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 ...
  ‘f1_introduction.rmd’ using ‘UTF-8’... OK
  ‘f2_loading_data.Rmd’ using ‘UTF-8’... OK
  ‘f3_data_visualization.Rmd’ using ‘UTF-8’... OK
  ‘f4_data_manipulation.Rmd’ using ‘UTF-8’... OK
  ‘f5_model_inference.Rmd’ using ‘UTF-8’... OK
  ‘f6_post_reconstruction.Rmd’ using ‘UTF-8’... OK
  ‘f7_import_export.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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: x86_64-pc-linux-gnu (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 55 (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: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 6 edges out of 49 (12%)
*** 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 7 edges out of 46 (15%)
*** 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:01s 
*** 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 58 (12%)
*** 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 
 36.822   1.306  82.201

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.017	0.000	0.018
TCGA.remove.multiple.samples	0.066	0.000	0.067
TCGA.shorten.barcodes	0.006	0.003	0.010
annotate.description	0.005	0.005	0.008
annotate.stages	0.006	0.000	0.005
as.adj.matrix	0.004	0.006	0.010
as.alterations	0.125	0.001	0.127
as.bootstrap.scores	0.034	0.000	0.035
as.colors	0.001	0.000	0.002
as.confidence	0.011	0.000	0.012
as.description	0.001	0.000	0.002
as.events	0.001	0.000	0.002
as.events.in.patterns	0.004	0.000	0.004
as.events.in.sample	0.004	0.000	0.003
as.gene	0.004	0.000	0.003
as.genes	0.001	0.000	0.001
as.genes.in.patterns	0.003	0.000	0.004
as.genotypes	0.007	0.000	0.008
as.hypotheses	0.003	0.000	0.003
as.joint.probs	0.000	0.009	0.009
as.kfold.eloss	0.068	0.003	0.070
as.kfold.posterr	0.075	0.012	0.086
as.kfold.prederr	0.071	0.016	0.087
as.marginal.probs	0.004	0.000	0.004
as.models	0.013	0.004	0.017
as.parameters	0.002	0.000	0.003
as.pathway	0.005	0.000	0.006
as.patterns	0.002	0.000	0.002
as.samples	0.001	0.000	0.001
as.selective.advantage.relations	0.063	0.019	0.083
as.stages	0.006	0.001	0.005
as.types	0.001	0.000	0.002
as.types.in.patterns	0.003	0.000	0.004
change.color	0.002	0.000	0.002
consolidate.data	0.030	0.000	0.029
delete.event	0.001	0.003	0.006
delete.gene	0.004	0.000	0.005
delete.hypothesis	0.016	0.012	0.027
delete.model	0.000	0.003	0.003
delete.pattern	0.007	0.005	0.012
delete.samples	0.001	0.001	0.003
delete.type	0.003	0.002	0.005
duplicates	0.002	0.000	0.001
enforce.numeric	0.003	0.000	0.002
enforce.string	0.002	0.000	0.002
events.selection	0.003	0.000	0.004
export.graphml	0.094	0.027	0.123
export.mutex	0.007	0.000	0.008
has.duplicates	0.001	0.000	0.002
has.model	0.001	0.000	0.002
has.stages	0.002	0.003	0.005
import.GISTIC	0.004	0.001	0.005
import.MAF	0.066	0.000	0.067
intersect.datasets	0.001	0.000	0.001
is.compliant	0.002	0.000	0.002
join.events	0.003	0.000	0.003
join.types	0.037	0.000	0.038
keysToNames	0.004	0.000	0.004
nameToKey	0.003	0.000	0.002
nevents	0.001	0.000	0.001
ngenes	0.001	0.000	0.002
nhypotheses	0.001	0.000	0.001
npatterns	0.001	0.000	0.002
nsamples	0.001	0.000	0.001
ntypes	0.001	0.000	0.001
oncoprint.cbio	0.001	0.003	0.005
order.frequency	0.007	0.001	0.007
pheatmap	0.03	0.00	0.03
rank.recurrents	0.003	0.000	0.004
rename.gene	0.002	0.000	0.002
rename.type	0.002	0.000	0.001
samples.selection	0.003	0.000	0.002
trim	0.003	0.000	0.003
tronco.bootstrap	0.111	0.005	9.401
tronco.caprese	0.129	0.000	0.129
tronco.capri	1.877	0.072	1.949
tronco.chowliu	1.309	0.008	1.317
tronco.edmonds	1.169	0.060	1.229
tronco.gabow	1.122	0.004	1.126
tronco.kfold.eloss	0.084	0.008	0.092
tronco.kfold.posterr	0.094	0.043	2.976
tronco.kfold.prederr	0.102	0.033	2.674
tronco.plot	0.144	0.008	0.152
tronco.prim	2.190	0.020	2.211
view	0.003	0.000	0.004
which.samples	0.002	0.000	0.003

CHECK results for TRONCO on nebbiolo2

Summary

Command output

Installation output

Tests output

Example timings