Multiple platform build/check report for BioC 3.17 - CHECK results for TRONCO on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.2 LTS)	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4626
palomino3	Windows Server 2022 Datacenter	x64	4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"	4379
merida1	macOS 12.6.4 Monterey	x86_64	4.3.1 (2023-06-16) -- "Beagle Scouts"	4395
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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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TRONCO_2.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/TRONCO.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.32.0’
* 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.prim          4.824  0.072   6.262
tronco.capri         4.024  0.124   5.508
tronco.kfold.posterr 0.287  0.195   9.314
tronco.kfold.prederr 0.216  0.187   8.895
tronco.bootstrap     0.216  0.025  27.005
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TRONCO
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 51 (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:04s 
*** 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 57 (11%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:05s 
*** 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:04s 
*** 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 50 (16%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:04s 
[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 81.994   1.954 236.438

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.031	0.007	0.059
TCGA.remove.multiple.samples	0.033	0.030	0.084
TCGA.shorten.barcodes	0.025	0.030	0.084
annotate.description	0.022	0.028	0.109
annotate.stages	0.015	0.005	0.042
as.adj.matrix	0.021	0.036	0.099
as.alterations	0.008	0.004	0.023
as.bootstrap.scores	0.218	0.008	0.304
as.colors	0.003	0.003	0.012
as.confidence	0.023	0.044	0.086
as.description	0.002	0.003	0.005
as.events	0.004	0.004	0.012
as.events.in.patterns	0.009	0.003	0.013
as.events.in.sample	0.008	0.002	0.015
as.gene	0.008	0.007	0.016
as.genes	0.004	0.003	0.010
as.genes.in.patterns	0.007	0.003	0.012
as.genotypes	0.019	0.022	0.049
as.hypotheses	0.007	0.010	0.020
as.joint.probs	0.018	0.034	0.071
as.kfold.eloss	0.148	0.009	0.194
as.kfold.posterr	0.187	0.022	0.348
as.kfold.prederr	0.192	0.022	0.302
as.marginal.probs	0.008	0.005	0.017
as.models	0.037	0.090	0.161
as.parameters	0.005	0.003	0.011
as.pathway	0.011	0.005	0.020
as.patterns	0.004	0.003	0.009
as.samples	0.003	0.003	0.008
as.selective.advantage.relations	0.229	0.031	0.375
as.stages	0.015	0.006	0.022
as.types	0.003	0.002	0.005
as.types.in.patterns	0.008	0.003	0.011
change.color	0.004	0.002	0.007
consolidate.data	0.076	0.004	0.094
delete.event	0.010	0.003	0.016
delete.gene	0.010	0.002	0.015
delete.hypothesis	0.066	0.076	0.174
delete.model	0.007	0.002	0.013
delete.pattern	0.025	0.024	0.068
delete.samples	0.007	0.002	0.012
delete.type	0.009	0.003	0.020
duplicates	0.004	0.002	0.006
enforce.numeric	0.006	0.003	0.008
enforce.string	0.005	0.002	0.008
events.selection	0.009	0.003	0.014
export.graphml	0.157	0.017	0.218
export.mutex	0.030	0.007	0.059
has.duplicates	0.004	0.002	0.009
has.model	0.003	0.002	0.008
has.stages	0.012	0.004	0.019
import.GISTIC	0.011	0.003	0.015
import.MAF	0.136	0.011	0.227
intersect.datasets	0.003	0.003	0.005
is.compliant	0.004	0.002	0.013
join.events	0.008	0.002	0.021
join.types	0.098	0.054	0.231
keysToNames	0.009	0.007	0.020
nameToKey	0.005	0.003	0.007
nevents	0.002	0.003	0.005
ngenes	0.003	0.003	0.009
nhypotheses	0.003	0.002	0.005
npatterns	0.002	0.002	0.005
nsamples	0.002	0.002	0.009
ntypes	0.003	0.003	0.005
oncoprint.cbio	0.013	0.004	0.024
order.frequency	0.016	0.028	0.060
pheatmap	0.069	0.002	0.098
rank.recurrents	0.008	0.003	0.016
rename.gene	0.004	0.003	0.007
rename.type	0.004	0.002	0.007
samples.selection	0.007	0.002	0.016
trim	0.007	0.002	0.015
tronco.bootstrap	0.216	0.025	27.005
tronco.caprese	0.243	0.009	0.258
tronco.capri	4.024	0.124	5.508
tronco.chowliu	3.299	0.050	4.414
tronco.edmonds	2.460	0.023	3.273
tronco.gabow	2.850	0.041	3.888
tronco.kfold.eloss	0.212	0.146	0.519
tronco.kfold.posterr	0.287	0.195	9.314
tronco.kfold.prederr	0.216	0.187	8.895
tronco.plot	0.279	0.008	0.360
tronco.prim	4.824	0.072	6.262
view	0.009	0.003	0.017
which.samples	0.006	0.003	0.011

CHECK results for TRONCO on merida1

Summary

Command output

Installation output

Tests output

Example timings