Multiple platform build/check report for BioC 3.11 - CHECK report for TRONCO on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TRONCO_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.19.0’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.509  0.294  18.295
tronco.kfold.prederr 0.371  0.256  17.541
tronco.bootstrap     0.370  0.178  35.561
* 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/Versions/Current/Resources/bin/R CMD INSTALL TRONCO
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘TRONCO’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 58 (12%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s 
*** 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:03s 
*** 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 3 edges out of 50 (6%)
*** 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 7 edges out of 54 (13%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s 
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 225 | SKIPPED: 0 | WARNINGS: 31 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 86.523   3.234 219.224

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.027	0.007	0.034
TCGA.remove.multiple.samples	0.036	0.019	0.054
TCGA.shorten.barcodes	0.034	0.022	0.055
annotate.description	0.028	0.019	0.046
annotate.stages	0.019	0.005	0.025
as.adj.matrix	0.020	0.019	0.040
as.alterations	0.007	0.004	0.011
as.bootstrap.scores	0.109	0.006	0.115
as.colors	0.002	0.002	0.004
as.confidence	0.030	0.033	0.063
as.description	0.002	0.002	0.005
as.events	0.005	0.004	0.009
as.events.in.patterns	0.109	0.003	0.111
as.events.in.sample	0.005	0.001	0.006
as.gene	0.005	0.003	0.008
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.005	0.001	0.006
as.genotypes	0.014	0.009	0.021
as.hypotheses	0.008	0.006	0.013
as.joint.probs	0.015	0.014	0.029
as.kfold.eloss	0.044	0.011	0.055
as.kfold.posterr	0.091	0.022	0.112
as.kfold.prederr	0.103	0.032	0.135
as.marginal.probs	0.009	0.004	0.013
as.models	0.048	0.054	0.102
as.parameters	0.004	0.002	0.006
as.pathway	0.011	0.003	0.013
as.patterns	0.002	0.001	0.004
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.262	0.057	0.319
as.stages	0.013	0.003	0.016
as.types	0.001	0.001	0.003
as.types.in.patterns	0.008	0.003	0.010
change.color	0.004	0.002	0.005
consolidate.data	0.051	0.003	0.053
delete.event	0.007	0.002	0.009
delete.gene	0.009	0.002	0.011
delete.hypothesis	0.088	0.051	0.138
delete.model	0.005	0.002	0.007
delete.pattern	0.030	0.013	0.043
delete.samples	0.006	0.002	0.008
delete.type	0.009	0.002	0.011
duplicates	0.002	0.001	0.004
enforce.numeric	0.005	0.002	0.007
enforce.string	0.005	0.002	0.007
events.selection	0.009	0.003	0.012
export.graphml	0.225	0.027	0.253
export.mutex	0.017	0.004	0.022
has.duplicates	0.003	0.001	0.005
has.model	0.003	0.002	0.005
has.stages	0.010	0.003	0.013
import.GISTIC	0.010	0.001	0.010
import.MAF	0.143	0.006	0.150
intersect.datasets	0.001	0.001	0.003
is.compliant	0.003	0.001	0.004
join.events	0.008	0.002	0.011
join.types	0.097	0.023	0.121
keysToNames	0.010	0.003	0.014
nameToKey	0.004	0.002	0.006
nevents	0.002	0.002	0.004
ngenes	0.002	0.002	0.005
nhypotheses	0.002	0.001	0.004
npatterns	0.003	0.002	0.004
nsamples	0.002	0.002	0.004
ntypes	0.003	0.002	0.004
oncoprint.cbio	0.013	0.002	0.015
order.frequency	0.021	0.016	0.037
pheatmap	0.071	0.002	0.073
rank.recurrents	0.007	0.003	0.009
rename.gene	0.002	0.001	0.004
rename.type	0.003	0.001	0.005
samples.selection	0.006	0.002	0.008
trim	0.007	0.002	0.009
tronco.bootstrap	0.370	0.178	35.561
tronco.caprese	0.253	0.011	0.278
tronco.capri	3.979	0.198	4.177
tronco.chowliu	2.405	0.053	2.458
tronco.edmonds	2.346	0.062	2.408
tronco.gabow	2.696	0.071	2.767
tronco.kfold.eloss	0.301	0.077	0.378
tronco.kfold.posterr	0.509	0.294	18.295
tronco.kfold.prederr	0.371	0.256	17.541
tronco.plot	0.289	0.006	0.322
tronco.prim	4.232	0.137	4.370
view	0.007	0.002	0.010
which.samples	0.006	0.003	0.008

CHECK report for TRONCO on celaya2

Summary

Command output

Installation output

Tests output

Example timings