Multiple platform build/check report for BioC 3.21 - CHECK results for TRONCO on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4609
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4393
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3839
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3835
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
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*

CHECK results for TRONCO on lconway

To the developers/maintainers of the TRONCO package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TRONCO.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: TRONCO

Version: 2.39.0

Command: /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_2.39.0.tar.gz

StartedAt: 2025-01-23 20:46:30 -0500 (Thu, 23 Jan 2025)

EndedAt: 2025-01-23 20:50:34 -0500 (Thu, 23 Jan 2025)

EllapsedTime: 243.9 seconds

RetCode: 0

Status: OK

CheckDir: TRONCO.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_2.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.39.0’
* 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 code 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 whether 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.kfold.posterr 0.155  0.088   8.122
tronco.kfold.prederr 0.114  0.076   6.701
tronco.bootstrap     0.095  0.019   9.909
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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

TRONCO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘TRONCO’ ...
** this is package ‘TRONCO’ version ‘2.39.0’
** 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

TRONCO.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 9 edges out of 53 (17%)
*** 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 52 (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 57 (11%)
*** 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 23 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 23 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 44.724   1.362 112.728

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.030	0.011	0.050
TCGA.remove.multiple.samples	0.025	0.043	0.185
TCGA.shorten.barcodes	0.012	0.024	0.043
annotate.description	0.010	0.024	0.046
annotate.stages	0.007	0.003	0.012
as.adj.matrix	0.010	0.025	0.040
as.alterations	0.003	0.002	0.009
as.bootstrap.scores	0.087	0.005	0.094
as.colors	0.002	0.002	0.005
as.confidence	0.010	0.033	0.080
as.description	0.001	0.002	0.007
as.events	0.002	0.003	0.005
as.events.in.patterns	0.004	0.003	0.012
as.events.in.sample	0.004	0.002	0.006
as.gene	0.004	0.005	0.010
as.genes	0.002	0.003	0.005
as.genes.in.patterns	0.004	0.001	0.006
as.genotypes	0.008	0.014	0.026
as.hypotheses	0.004	0.007	0.011
as.joint.probs	0.008	0.024	0.032
as.kfold.eloss	0.211	0.004	0.217
as.kfold.posterr	0.098	0.010	0.113
as.kfold.prederr	0.098	0.008	0.107
as.marginal.probs	0.004	0.005	0.015
as.models	0.014	0.058	0.077
as.parameters	0.003	0.001	0.005
as.pathway	0.005	0.002	0.007
as.patterns	0.002	0.002	0.003
as.samples	0.002	0.001	0.004
as.selective.advantage.relations	0.074	0.021	0.097
as.stages	0.007	0.004	0.012
as.types	0.002	0.001	0.004
as.types.in.patterns	0.004	0.002	0.006
change.color	0.001	0.001	0.003
consolidate.data	0.032	0.006	0.040
delete.event	0.004	0.002	0.007
delete.gene	0.005	0.002	0.008
delete.hypothesis	0.030	0.057	0.086
delete.model	0.003	0.001	0.004
delete.pattern	0.022	0.020	0.055
delete.samples	0.003	0.002	0.005
delete.type	0.004	0.002	0.005
duplicates	0.002	0.001	0.004
enforce.numeric	0.002	0.002	0.004
enforce.string	0.003	0.002	0.004
events.selection	0.004	0.002	0.006
export.graphml	0.118	0.006	0.127
export.mutex	0.008	0.004	0.012
has.duplicates	0.002	0.002	0.004
has.model	0.002	0.001	0.003
has.stages	0.006	0.003	0.009
import.GISTIC	0.006	0.002	0.007
import.MAF	0.070	0.008	0.079
intersect.datasets	0.001	0.002	0.003
is.compliant	0.002	0.002	0.004
join.events	0.003	0.001	0.004
join.types	0.041	0.027	0.076
keysToNames	0.005	0.004	0.012
nameToKey	0.003	0.001	0.005
nevents	0.002	0.002	0.002
ngenes	0.002	0.002	0.003
nhypotheses	0.001	0.001	0.004
npatterns	0.001	0.001	0.003
nsamples	0.002	0.002	0.003
ntypes	0.002	0.002	0.003
oncoprint.cbio	0.006	0.003	0.009
order.frequency	0.007	0.018	0.025
pheatmap	0.050	0.003	0.056
rank.recurrents	0.003	0.001	0.004
rename.gene	0.002	0.001	0.004
rename.type	0.002	0.001	0.003
samples.selection	0.003	0.001	0.004
trim	0.003	0.002	0.004
tronco.bootstrap	0.095	0.019	9.909
tronco.caprese	0.160	0.005	0.166
tronco.capri	2.127	0.076	2.214
tronco.chowliu	1.449	0.026	1.482
tronco.edmonds	1.158	0.016	1.177
tronco.gabow	1.439	0.029	1.809
tronco.kfold.eloss	0.117	0.062	0.321
tronco.kfold.posterr	0.155	0.088	8.122
tronco.kfold.prederr	0.114	0.076	6.701
tronco.plot	0.140	0.006	0.149
tronco.prim	2.579	0.110	3.059
view	0.003	0.001	0.004
which.samples	0.002	0.001	0.004