Multiple platform build/check report for BioC 3.15 - CHECK results for TRONCO on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 20.04.5 LTS)	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4386
palomino3	Windows Server 2022 Datacenter	x64	4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"	4138
merida1	macOS 10.14.6 Mojave	x86_64	4.2.1 (2022-06-23) -- "Funny-Looking Kid"	4205
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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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TRONCO_2.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TRONCO.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.28.0’
* 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 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’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/1_introduction.Rmd’
   ‘vignettes/2_loading_data.Rmd’
   ‘vignettes/3_data_visualization.Rmd’
   ‘vignettes/4_data_manipulation.Rmd’
   ‘vignettes/5_model_inference.Rmd’
   ‘vignettes/6_post_reconstruction.Rmd’
   ‘vignettes/7_import_export.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
tronco.kfold.prederr 0.160  0.099   6.045
tronco.bootstrap     0.103  0.013   7.526
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/TRONCO.Rcheck/00check.log’
for details.

Installation output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TRONCO
###
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* installing to library ‘/home/biocbuild/bbs-3.15-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 version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 49 (12%)
*** 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 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: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 44 (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: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 49 (14%)
*** 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 16 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 35.538   1.138  75.152

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.007	0.008	0.015
TCGA.remove.multiple.samples	0.012	0.012	0.024
TCGA.shorten.barcodes	0.013	0.008	0.020
annotate.description	0.007	0.012	0.019
annotate.stages	0.006	0.000	0.006
as.adj.matrix	0.008	0.018	0.026
as.alterations	0.003	0.000	0.004
as.bootstrap.scores	0.133	0.000	0.132
as.colors	0.001	0.000	0.002
as.confidence	0.014	0.016	0.030
as.description	0.001	0.000	0.002
as.events	0.001	0.001	0.003
as.events.in.patterns	0.002	0.001	0.004
as.events.in.sample	0.003	0.001	0.003
as.gene	0.005	0.000	0.005
as.genes	0.002	0.000	0.001
as.genes.in.patterns	0.003	0.000	0.003
as.genotypes	0.006	0.007	0.014
as.hypotheses	0.001	0.006	0.007
as.joint.probs	0.005	0.018	0.024
as.kfold.eloss	0.062	0.004	0.067
as.kfold.posterr	0.074	0.012	0.086
as.kfold.prederr	0.076	0.012	0.088
as.marginal.probs	0.005	0.000	0.005
as.models	0.014	0.044	0.057
as.parameters	0.003	0.000	0.003
as.pathway	0.006	0.000	0.006
as.patterns	0.002	0.000	0.002
as.samples	0.000	0.002	0.002
as.selective.advantage.relations	0.069	0.016	0.086
as.stages	0.005	0.000	0.006
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	0.023	0.000	0.023
delete.event	0.004	0.000	0.004
delete.gene	0.004	0.000	0.004
delete.hypothesis	0.017	0.040	0.058
delete.model	0.000	0.003	0.003
delete.pattern	0.007	0.012	0.020
delete.samples	0.003	0.000	0.003
delete.type	0.004	0.000	0.004
duplicates	0.001	0.000	0.002
enforce.numeric	0.002	0.000	0.002
enforce.string	0.002	0.000	0.003
events.selection	0.000	0.004	0.004
export.graphml	0.055	0.008	0.062
export.mutex	0.009	0.000	0.008
has.duplicates	0.002	0.000	0.002
has.model	0.002	0.000	0.002
has.stages	0.005	0.000	0.005
import.GISTIC	0.002	0.004	0.005
import.MAF	0.066	0.000	0.067
intersect.datasets	0.001	0.000	0.002
is.compliant	0.002	0.000	0.001
join.events	0.000	0.003	0.003
join.types	0.042	0.008	0.049
keysToNames	0.005	0.000	0.005
nameToKey	0.003	0.000	0.002
nevents	0.002	0.000	0.002
ngenes	0.001	0.000	0.002
nhypotheses	0.000	0.002	0.002
npatterns	0.000	0.001	0.002
nsamples	0.001	0.000	0.002
ntypes	0.001	0.000	0.001
oncoprint.cbio	0.005	0.000	0.005
order.frequency	0.001	0.016	0.017
pheatmap	0.028	0.000	0.028
rank.recurrents	0.000	0.004	0.004
rename.gene	0.003	0.000	0.002
rename.type	0.002	0.000	0.002
samples.selection	0.002	0.000	0.003
trim	0.000	0.003	0.002
tronco.bootstrap	0.103	0.013	7.526
tronco.caprese	0.085	0.001	0.086
tronco.capri	1.787	0.067	1.855
tronco.chowliu	1.192	0.032	1.224
tronco.edmonds	1.056	0.012	1.068
tronco.gabow	1.238	0.020	1.258
tronco.kfold.eloss	0.086	0.060	0.147
tronco.kfold.posterr	0.164	0.136	4.081
tronco.kfold.prederr	0.160	0.099	6.045
tronco.plot	0.225	0.003	0.230
tronco.prim	4.198	0.091	4.457
view	0.003	0.004	0.007
which.samples	0.005	0.000	0.005

CHECK results for TRONCO on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings