Build/check report for BioC 3.18 - 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) (2023-03-12 r83975) -- "Unsuffered Consequences"	6211
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_2.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 22.04.2 LTS
* 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 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 0.137  0.013  11.955
* 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-devel_2023-03-12_r83975-bin/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 Under development (unstable) (2023-03-12 r83975) -- "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 7 edges out of 54 (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 58 (16%)
*** 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 4 edges out of 39 (10%)
*** 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 8 edges out of 49 (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 14 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 47.812   1.450 100.566

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.012	0.008	0.019
TCGA.remove.multiple.samples	0.012	0.007	0.020
TCGA.shorten.barcodes	0.006	0.008	0.015
annotate.description	0.009	0.004	0.014
annotate.stages	0.008	0.000	0.008
as.adj.matrix	0.005	0.010	0.015
as.alterations	0.000	0.005	0.005
as.bootstrap.scores	0.176	0.000	0.177
as.colors	0.002	0.000	0.002
as.confidence	0.010	0.008	0.017
as.description	0.002	0.000	0.002
as.events	0.001	0.001	0.002
as.events.in.patterns	0.003	0.002	0.005
as.events.in.sample	0.005	0.000	0.005
as.gene	0.001	0.003	0.005
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.004	0.001	0.005
as.genotypes	0.010	0.002	0.011
as.hypotheses	0.005	0.000	0.004
as.joint.probs	0.007	0.006	0.014
as.kfold.eloss	0.086	0.005	0.091
as.kfold.posterr	0.109	0.004	0.113
as.kfold.prederr	0.102	0.012	0.113
as.marginal.probs	0.006	0.000	0.005
as.models	0.007	0.020	0.026
as.parameters	0.004	0.000	0.004
as.pathway	0.007	0.000	0.007
as.patterns	0.002	0.000	0.003
as.samples	0.002	0.000	0.002
as.selective.advantage.relations	0.120	0.008	0.128
as.stages	0.008	0.000	0.008
as.types	0.002	0.000	0.002
as.types.in.patterns	0.005	0.000	0.005
change.color	0.002	0.000	0.003
consolidate.data	0.037	0.000	0.037
delete.event	0.006	0.000	0.006
delete.gene	0.005	0.000	0.006
delete.hypothesis	0.027	0.012	0.039
delete.model	0.004	0.000	0.005
delete.pattern	0.011	0.004	0.016
delete.samples	0.000	0.004	0.004
delete.type	0.002	0.004	0.006
duplicates	0.002	0.000	0.002
enforce.numeric	0.003	0.000	0.003
enforce.string	0.002	0.002	0.003
events.selection	0.003	0.002	0.005
export.graphml	0.087	0.004	0.092
export.mutex	0.022	0.000	0.023
has.duplicates	0.002	0.000	0.002
has.model	0.002	0.000	0.002
has.stages	0.007	0.000	0.006
import.GISTIC	0.006	0.000	0.006
import.MAF	0.084	0.000	0.084
intersect.datasets	0.002	0.000	0.002
is.compliant	0.002	0.000	0.002
join.events	0.005	0.000	0.005
join.types	0.053	0.012	0.065
keysToNames	0.004	0.002	0.007
nameToKey	0.003	0.001	0.003
nevents	0.002	0.000	0.002
ngenes	0.002	0.000	0.002
nhypotheses	0.000	0.002	0.002
npatterns	0.000	0.001	0.002
nsamples	0.000	0.001	0.002
ntypes	0.001	0.001	0.002
oncoprint.cbio	0.008	0.000	0.009
order.frequency	0.000	0.011	0.012
pheatmap	0.035	0.012	0.047
rank.recurrents	0.005	0.000	0.005
rename.gene	0.003	0.000	0.003
rename.type	0.000	0.003	0.003
samples.selection	0.004	0.000	0.004
trim	0.001	0.003	0.005
tronco.bootstrap	0.137	0.013	11.955
tronco.caprese	0.121	0.008	0.129
tronco.capri	2.782	0.076	2.859
tronco.chowliu	1.586	0.040	1.627
tronco.edmonds	1.734	0.020	1.754
tronco.gabow	1.567	0.024	1.591
tronco.kfold.eloss	0.106	0.020	0.126
tronco.kfold.posterr	0.138	0.040	3.583
tronco.kfold.prederr	0.095	0.049	3.361
tronco.plot	0.166	0.016	0.182
tronco.prim	3.019	0.040	3.059
view	0.005	0.000	0.005
which.samples	0.004	0.000	0.004

CHECK results for TRONCO on kunpeng1

Summary

Command output

Installation output

Tests output

Example timings