Build/check report for BioC 3.17 - CHECK results for TRONCO on kunpeng1

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng1	Linux (Ubuntu 22.04.1 LTS)	aarch64	R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"	4164
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-3.17-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings TRONCO_2.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.31.0’
* 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’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.148  0.027   9.135
tronco.bootstrap     0.134  0.004  11.908
* 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 ...
  ‘vignette.Rnw’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 46 (13%)
*** 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 9 edges out of 50 (18%)
*** 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 8 edges out of 51 (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 5 edges out of 41 (12%)
*** 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 14 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 48.445   0.357 101.257

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.020	0.000	0.021
TCGA.remove.multiple.samples	0.071	0.004	0.075
TCGA.shorten.barcodes	0.010	0.004	0.014
annotate.description	0.009	0.004	0.013
annotate.stages	0.009	0.000	0.009
as.adj.matrix	0.134	0.004	0.138
as.alterations	0.001	0.004	0.004
as.bootstrap.scores	0.052	0.000	0.052
as.colors	0.002	0.000	0.002
as.confidence	0.015	0.000	0.015
as.description	0.000	0.002	0.002
as.events	0.001	0.002	0.002
as.events.in.patterns	0.002	0.003	0.005
as.events.in.sample	0.001	0.004	0.005
as.gene	0.004	0.000	0.004
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.002	0.003	0.005
as.genotypes	0.007	0.004	0.011
as.hypotheses	0.001	0.003	0.003
as.joint.probs	0.007	0.005	0.012
as.kfold.eloss	0.091	0.000	0.091
as.kfold.posterr	0.101	0.012	0.113
as.kfold.prederr	0.104	0.008	0.112
as.marginal.probs	0.003	0.003	0.005
as.models	0.008	0.012	0.021
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	0.002	0.000	0.002
as.selective.advantage.relations	0.121	0.007	0.129
as.stages	0.007	0.000	0.008
as.types	0.002	0.000	0.001
as.types.in.patterns	0.005	0.000	0.005
change.color	0.003	0.000	0.003
consolidate.data	0.039	0.000	0.039
delete.event	0.006	0.000	0.006
delete.gene	0.006	0.000	0.006
delete.hypothesis	0.028	0.008	0.036
delete.model	0.004	0.000	0.004
delete.pattern	0.015	0.000	0.015
delete.samples	0.004	0.000	0.004
delete.type	0.006	0.000	0.006
duplicates	0.002	0.000	0.002
enforce.numeric	0.003	0.000	0.003
enforce.string	0.003	0.000	0.003
events.selection	0.004	0.000	0.004
export.graphml	0.099	0.000	0.110
export.mutex	0.010	0.001	0.010
has.duplicates	0.002	0.000	0.002
has.model	0.002	0.000	0.002
has.stages	0.007	0.000	0.007
import.GISTIC	0.007	0.000	0.006
import.MAF	0.085	0.000	0.092
intersect.datasets	0.001	0.000	0.002
is.compliant	0.002	0.000	0.002
join.events	0.005	0.000	0.005
join.types	0.051	0.004	0.054
keysToNames	0.005	0.000	0.005
nameToKey	0.003	0.000	0.003
nevents	0.001	0.000	0.001
ngenes	0.001	0.000	0.001
nhypotheses	0.000	0.001	0.001
npatterns	0.000	0.002	0.001
nsamples	0.002	0.000	0.001
ntypes	0.002	0.000	0.001
oncoprint.cbio	0.008	0.000	0.007
order.frequency	0.002	0.008	0.009
pheatmap	0.038	0.004	0.043
rank.recurrents	0.005	0.000	0.004
rename.gene	0.003	0.000	0.002
rename.type	0.003	0.000	0.002
samples.selection	0.004	0.000	0.004
trim	0.004	0.000	0.004
tronco.bootstrap	0.134	0.004	11.908
tronco.caprese	0.133	0.000	0.133
tronco.capri	2.421	0.008	2.428
tronco.chowliu	1.83	0.00	1.83
tronco.edmonds	1.578	0.000	1.579
tronco.gabow	1.662	0.000	1.663
tronco.kfold.eloss	0.097	0.020	0.117
tronco.kfold.posterr	0.148	0.027	9.135
tronco.kfold.prederr	0.120	0.014	3.369
tronco.plot	0.171	0.008	0.195
tronco.prim	3.322	0.008	3.442
view	0.000	0.005	0.006
which.samples	0.003	0.001	0.004

CHECK results for TRONCO on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings