Multiple platform build/check report for BioC 3.19 - CHECK results for TRONCO on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4751
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4485
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	3444
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-3.19-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings TRONCO_2.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/TRONCO.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* 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 ‘2.36.0’
* 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 loading without being on the library search path ... 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 0.121      0   9.829
* 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 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-3.19-bioc/R/bin/R CMD INSTALL TRONCO
###
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* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 8 edges out of 48 (17%)
*** 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 51 (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 54 (13%)
*** 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 56 (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 
 37.828   1.550  85.427

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.015	0.009	0.023
TCGA.remove.multiple.samples	0.019	0.008	0.027
TCGA.shorten.barcodes	0.009	0.009	0.017
annotate.description	0.005	0.011	0.016
annotate.stages	0.006	0.000	0.007
as.adj.matrix	0.012	0.008	0.020
as.alterations	0.001	0.003	0.004
as.bootstrap.scores	0.082	0.005	0.087
as.colors	0.002	0.000	0.002
as.confidence	0.007	0.015	0.022
as.description	0.117	0.000	0.118
as.events	0.003	0.000	0.003
as.events.in.patterns	0.004	0.001	0.004
as.events.in.sample	0.004	0.000	0.004
as.gene	0.005	0.000	0.004
as.genes	0.000	0.001	0.001
as.genes.in.patterns	0.003	0.001	0.004
as.genotypes	0.004	0.008	0.013
as.hypotheses	0.000	0.006	0.006
as.joint.probs	0.006	0.013	0.019
as.kfold.eloss	0.064	0.002	0.066
as.kfold.posterr	0.082	0.002	0.084
as.kfold.prederr	0.087	0.003	0.091
as.marginal.probs	0.002	0.003	0.005
as.models	0.017	0.028	0.045
as.parameters	0.002	0.001	0.003
as.pathway	0.004	0.003	0.007
as.patterns	0.001	0.000	0.002
as.samples	0.002	0.000	0.002
as.selective.advantage.relations	0.092	0.007	0.099
as.stages	0.006	0.001	0.006
as.types	0.000	0.001	0.002
as.types.in.patterns	0.002	0.001	0.004
change.color	0.002	0.001	0.002
consolidate.data	0.022	0.003	0.024
delete.event	0.005	0.001	0.005
delete.gene	0.005	0.000	0.004
delete.hypothesis	0.019	0.031	0.050
delete.model	0.004	0.000	0.004
delete.pattern	0.007	0.011	0.019
delete.samples	0.003	0.000	0.003
delete.type	0.004	0.001	0.004
duplicates	0.001	0.002	0.002
enforce.numeric	0.001	0.002	0.002
enforce.string	0.003	0.000	0.002
events.selection	0.000	0.003	0.003
export.graphml	0.101	0.004	0.105
export.mutex	0.009	0.001	0.009
has.duplicates	0.002	0.000	0.002
has.model	0.002	0.000	0.002
has.stages	0.002	0.003	0.006
import.GISTIC	0.005	0.000	0.005
import.MAF	0.070	0.008	0.078
intersect.datasets	0.002	0.000	0.002
is.compliant	0.002	0.000	0.002
join.events	0.004	0.000	0.003
join.types	0.034	0.015	0.050
keysToNames	0.005	0.001	0.005
nameToKey	0.002	0.000	0.003
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	0.002
nsamples	0.001	0.000	0.002
ntypes	0.001	0.000	0.002
oncoprint.cbio	0.005	0.000	0.005
order.frequency	0.011	0.004	0.015
pheatmap	0.032	0.000	0.032
rank.recurrents	0.005	0.000	0.004
rename.gene	0.003	0.000	0.003
rename.type	0.002	0.000	0.002
samples.selection	0.003	0.000	0.003
trim	0.000	0.003	0.004
tronco.bootstrap	0.121	0.000	9.829
tronco.caprese	0.130	0.000	0.131
tronco.capri	1.885	0.184	2.069
tronco.chowliu	1.390	0.004	1.394
tronco.edmonds	1.183	0.052	1.236
tronco.gabow	1.129	0.019	1.147
tronco.kfold.eloss	0.076	0.052	0.128
tronco.kfold.posterr	0.176	0.084	2.894
tronco.kfold.prederr	0.144	0.104	2.701
tronco.plot	0.141	0.023	0.164
tronco.prim	2.088	0.108	2.196
view	0.000	0.006	0.006
which.samples	0.001	0.002	0.004

CHECK results for TRONCO on nebbiolo1

Summary

Command output

Installation output

Tests output

Example timings