Multiple platform build/check report for BioC 3.17 - CHECK results for TRONCO on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)	x86_64	4.3.0 alpha (2023-04-03 r84154)	4547
nebbiolo2	Linux (Ubuntu 20.04.5 LTS)	x86_64	R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"	4333
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-3.17-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TRONCO_2.31.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TRONCO.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.31.5’
* 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 0.141  0.008   8.016
* 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
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TRONCO
###
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* installing to library ‘/home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 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 10 edges out of 55 (18%)
*** 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 8 edges out of 56 (14%)
*** 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 8 edges out of 53 (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 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 14 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 33.968   1.194  76.116

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.016	0.000	0.016
TCGA.remove.multiple.samples	0.063	0.007	0.071
TCGA.shorten.barcodes	0.012	0.004	0.016
annotate.description	0.011	0.004	0.015
annotate.stages	0.006	0.000	0.006
as.adj.matrix	0.005	0.014	0.019
as.alterations	0.113	0.001	0.114
as.bootstrap.scores	0.029	0.004	0.033
as.colors	0.001	0.000	0.001
as.confidence	0.018	0.004	0.022
as.description	0.000	0.002	0.002
as.events	0.001	0.002	0.002
as.events.in.patterns	0.004	0.000	0.004
as.events.in.sample	0.004	0.000	0.004
as.gene	0.004	0.000	0.004
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.004	0.000	0.004
as.genotypes	0.006	0.008	0.013
as.hypotheses	0.002	0.004	0.006
as.joint.probs	0.012	0.008	0.019
as.kfold.eloss	0.052	0.016	0.068
as.kfold.posterr	0.062	0.024	0.085
as.kfold.prederr	0.085	0.000	0.085
as.marginal.probs	0.005	0.000	0.005
as.models	0.005	0.040	0.045
as.parameters	0.003	0.000	0.003
as.pathway	0.007	0.000	0.006
as.patterns	0.002	0.000	0.002
as.samples	0.001	0.000	0.002
as.selective.advantage.relations	0.079	0.008	0.087
as.stages	0.006	0.000	0.006
as.types	0.002	0.000	0.001
as.types.in.patterns	0.004	0.000	0.003
change.color	0.002	0.000	0.002
consolidate.data	0.024	0.000	0.024
delete.event	0.005	0.000	0.004
delete.gene	0.004	0.000	0.005
delete.hypothesis	0.022	0.027	0.050
delete.model	0.002	0.000	0.003
delete.pattern	0.014	0.004	0.018
delete.samples	0.003	0.000	0.003
delete.type	0.004	0.000	0.004
duplicates	0.002	0.000	0.002
enforce.numeric	0.002	0.000	0.002
enforce.string	0.000	0.002	0.003
events.selection	0.003	0.001	0.004
export.graphml	0.073	0.004	0.077
export.mutex	0.008	0.000	0.008
has.duplicates	0.001	0.000	0.002
has.model	0.002	0.000	0.002
has.stages	0.005	0.000	0.005
import.GISTIC	0.005	0.000	0.004
import.MAF	0.063	0.000	0.062
intersect.datasets	0.002	0.000	0.001
is.compliant	0.002	0.000	0.001
join.events	0.004	0.000	0.003
join.types	0.032	0.016	0.048
keysToNames	0.005	0.000	0.005
nameToKey	0.003	0.000	0.002
nevents	0.001	0.000	0.001
ngenes	0.001	0.000	0.001
nhypotheses	0.002	0.000	0.001
npatterns	0.001	0.000	0.001
nsamples	0.001	0.000	0.001
ntypes	0.001	0.000	0.001
oncoprint.cbio	0.002	0.004	0.005
order.frequency	0.012	0.004	0.016
pheatmap	0.030	0.000	0.031
rank.recurrents	0.003	0.000	0.004
rename.gene	0.002	0.000	0.002
rename.type	0.001	0.000	0.002
samples.selection	0.000	0.003	0.003
trim	0.000	0.003	0.003
tronco.bootstrap	0.141	0.008	8.016
tronco.caprese	0.143	0.000	0.143
tronco.capri	1.649	0.072	1.721
tronco.chowliu	1.198	0.000	1.198
tronco.edmonds	1.015	0.000	1.016
tronco.gabow	1.057	0.000	1.057
tronco.kfold.eloss	0.082	0.044	0.126
tronco.kfold.posterr	0.170	0.113	3.017
tronco.kfold.prederr	0.123	0.059	2.685
tronco.plot	0.130	0.000	0.131
tronco.prim	2.276	0.040	2.316
view	0.004	0.000	0.004
which.samples	0.003	0.000	0.003

CHECK results for TRONCO on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings