Multiple platform build/check report for BioC 3.13 - CHECK results for TRONCO on machv2

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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_2.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TRONCO.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/1_introduction.Rmd’
   ‘vignettes/2_loading_data.Rmd’
   ‘vignettes/3_data_visualization.Rmd’
   ‘vignettes/4_data_manipulation.Rmd’
   ‘vignettes/5_model_inference.Rmd’
   ‘vignettes/6_post_reconstruction.Rmd’
   ‘vignettes/7_import_export.Rmd’
(Is a VignetteBuilder field missing?)
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.221  0.109   5.203
tronco.kfold.prederr 0.155  0.095   5.420
tronco.bootstrap     0.162  0.016  12.203
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/TRONCO.Rcheck/00check.log’
for details.

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/4.1/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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 10 edges out of 56 (18%)
*** 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 7 edges out of 52 (13%)
*** 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 7 edges out of 54 (13%)
*** 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 6 edges out of 43 (14%)
*** 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 28 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 54.816   1.209 119.049

Example timings

name	user	system	elapsed
TCGA.multiple.samples	0.025	0.005	0.029
TCGA.remove.multiple.samples	0.018	0.012	0.030
TCGA.shorten.barcodes	0.016	0.017	0.033
annotate.description	0.014	0.014	0.028
annotate.stages	0.009	0.003	0.011
as.adj.matrix	0.024	0.023	0.046
as.alterations	0.006	0.003	0.009
as.bootstrap.scores	0.068	0.004	0.074
as.colors	0.001	0.001	0.002
as.confidence	0.049	0.020	0.069
as.description	0.001	0.001	0.002
as.events	0.001	0.002	0.003
as.events.in.patterns	0.004	0.001	0.005
as.events.in.sample	0.005	0.001	0.005
as.gene	0.004	0.003	0.006
as.genes	0.001	0.001	0.003
as.genes.in.patterns	0.004	0.002	0.005
as.genotypes	0.011	0.010	0.021
as.hypotheses	0.005	0.006	0.010
as.joint.probs	0.012	0.019	0.031
as.kfold.eloss	0.053	0.003	0.056
as.kfold.posterr	0.154	0.006	0.160
as.kfold.prederr	0.068	0.008	0.077
as.marginal.probs	0.004	0.002	0.005
as.models	0.021	0.044	0.066
as.parameters	0.002	0.001	0.003
as.pathway	0.006	0.001	0.007
as.patterns	0.002	0.001	0.003
as.samples	0.001	0.001	0.002
as.selective.advantage.relations	0.130	0.021	0.152
as.stages	0.011	0.005	0.015
as.types	0.001	0.002	0.004
as.types.in.patterns	0.005	0.002	0.007
change.color	0.003	0.002	0.006
consolidate.data	0.055	0.007	0.061
delete.event	0.006	0.001	0.007
delete.gene	0.004	0.001	0.005
delete.hypothesis	0.037	0.031	0.069
delete.model	0.005	0.002	0.007
delete.pattern	0.016	0.010	0.026
delete.samples	0.004	0.002	0.006
delete.type	0.006	0.002	0.007
duplicates	0.002	0.001	0.003
enforce.numeric	0.002	0.001	0.004
enforce.string	0.004	0.002	0.006
events.selection	0.005	0.002	0.007
export.graphml	0.107	0.005	0.112
export.mutex	0.009	0.002	0.011
has.duplicates	0.001	0.001	0.002
has.model	0.001	0.001	0.002
has.stages	0.006	0.002	0.008
import.GISTIC	0.005	0.001	0.006
import.MAF	0.077	0.008	0.084
intersect.datasets	0.001	0.001	0.003
is.compliant	0.002	0.001	0.004
join.events	0.004	0.001	0.006
join.types	0.073	0.024	0.098
keysToNames	0.005	0.004	0.009
nameToKey	0.002	0.001	0.003
nevents	0.001	0.001	0.002
ngenes	0.001	0.000	0.002
nhypotheses	0.001	0.001	0.002
npatterns	0.001	0.001	0.002
nsamples	0.001	0.001	0.001
ntypes	0.001	0.001	0.002
oncoprint.cbio	0.006	0.001	0.008
order.frequency	0.008	0.011	0.018
pheatmap	0.035	0.002	0.036
rank.recurrents	0.004	0.001	0.004
rename.gene	0.002	0.001	0.003
rename.type	0.002	0.001	0.003
samples.selection	0.004	0.001	0.004
trim	0.003	0.001	0.004
tronco.bootstrap	0.162	0.016	12.203
tronco.caprese	0.139	0.003	0.142
tronco.capri	2.805	0.101	2.907
tronco.chowliu	2.031	0.025	2.057
tronco.edmonds	1.822	0.015	1.837
tronco.gabow	1.794	0.022	1.817
tronco.kfold.eloss	0.199	0.067	0.266
tronco.kfold.posterr	0.221	0.109	5.203
tronco.kfold.prederr	0.155	0.095	5.420
tronco.plot	0.222	0.006	0.229
tronco.prim	2.748	0.053	2.803
view	0.006	0.001	0.006
which.samples	0.003	0.002	0.005

CHECK results for TRONCO on machv2

Summary

Command output

Installation output

Tests output

Example timings