Build/check report for BioC 3.18 - CHECK results for TRONCO on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.3.0 (2023-04-21) -- "Already Tomorrow"	4366
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/R/R-4.3.0/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings TRONCO_2.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/TRONCO.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.33.0’
* 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 0.135   0.02  11.327
* 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/R/R-4.3.0/bin/R CMD INSTALL TRONCO
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/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 (2023-04-21) -- "Already Tomorrow"
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 7 edges out of 49 (14%)
*** 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 10 edges out of 53 (19%)
*** 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 47 (17%)
*** 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 7 edges out of 53 (13%)
*** 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 
 47.925   1.613 102.230

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.016	0.004	0.020
TCGA.remove.multiple.samples	0.069	0.004	0.073
TCGA.shorten.barcodes	0.014	0.000	0.015
annotate.description	0.009	0.004	0.013
annotate.stages	0.008	0.000	0.008
as.adj.matrix	0.006	0.008	0.014
as.alterations	0.125	0.000	0.126
as.bootstrap.scores	0.052	0.000	0.051
as.colors	0.002	0.000	0.002
as.confidence	0.008	0.008	0.016
as.description	0.001	0.000	0.002
as.events	0.002	0.000	0.002
as.events.in.patterns	0.005	0.000	0.005
as.events.in.sample	0.004	0.000	0.005
as.gene	0.004	0.000	0.004
as.genes	0.001	0.000	0.001
as.genes.in.patterns	0.004	0.000	0.004
as.genotypes	0.002	0.008	0.010
as.hypotheses	0.004	0.000	0.004
as.joint.probs	0.000	0.012	0.012
as.kfold.eloss	0.073	0.008	0.081
as.kfold.posterr	0.090	0.012	0.103
as.kfold.prederr	0.096	0.008	0.104
as.marginal.probs	0.004	0.000	0.004
as.models	0.008	0.016	0.024
as.parameters	0.003	0.000	0.003
as.pathway	0.000	0.007	0.007
as.patterns	0.002	0.001	0.002
as.samples	0.002	0.000	0.002
as.selective.advantage.relations	0.118	0.012	0.130
as.stages	0.008	0.000	0.008
as.types	0.000	0.002	0.002
as.types.in.patterns	0.004	0.002	0.005
change.color	0.003	0.000	0.002
consolidate.data	0.040	0.000	0.039
delete.event	0.006	0.000	0.006
delete.gene	0.006	0.000	0.005
delete.hypothesis	0.031	0.008	0.040
delete.model	0.003	0.000	0.004
delete.pattern	0.015	0.000	0.015
delete.samples	0.003	0.000	0.003
delete.type	0.006	0.000	0.005
duplicates	0.003	0.000	0.002
enforce.numeric	0.003	0.000	0.003
enforce.string	0.003	0.000	0.003
events.selection	0.005	0.000	0.005
export.graphml	0.097	0.004	0.103
export.mutex	0.008	0.002	0.010
has.duplicates	0.000	0.001	0.002
has.model	0.002	0.000	0.002
has.stages	0.007	0.000	0.007
import.GISTIC	0.006	0.000	0.007
import.MAF	0.083	0.000	0.083
intersect.datasets	0.001	0.000	0.001
is.compliant	0.002	0.000	0.002
join.events	0.005	0.000	0.005
join.types	0.045	0.012	0.057
keysToNames	0.001	0.004	0.005
nameToKey	0.003	0.000	0.003
nevents	0.002	0.000	0.002
ngenes	0.002	0.000	0.002
nhypotheses	0.002	0.000	0.002
npatterns	0.002	0.000	0.002
nsamples	0.002	0.000	0.002
ntypes	0.000	0.001	0.002
oncoprint.cbio	0.006	0.002	0.008
order.frequency	0.006	0.004	0.010
pheatmap	0.035	0.016	0.051
rank.recurrents	0.005	0.000	0.006
rename.gene	0.003	0.000	0.003
rename.type	0.002	0.000	0.003
samples.selection	0.004	0.000	0.004
trim	0.004	0.000	0.005
tronco.bootstrap	0.135	0.020	11.327
tronco.caprese	0.131	0.008	0.140
tronco.capri	2.298	0.032	2.335
tronco.chowliu	1.725	0.004	1.733
tronco.edmonds	1.664	0.020	1.688
tronco.gabow	1.768	0.000	1.771
tronco.kfold.eloss	0.10	0.02	0.12
tronco.kfold.posterr	0.137	0.062	3.715
tronco.kfold.prederr	0.107	0.032	3.379
tronco.plot	0.162	0.008	0.170
tronco.prim	3.154	0.072	3.232
view	0.006	0.000	0.005
which.samples	0.004	0.000	0.004

CHECK results for TRONCO on kunpeng2

Summary

Command output

Installation output

Tests output

Example timings