Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:21:01 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


To the developers/maintainers of the TRONCO package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2063/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TRONCO 2.28.0  (landing page)
Luca De Sano
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/TRONCO
git_branch: RELEASE_3_15
git_last_commit: 962edc7
git_last_commit_date: 2022-04-26 11:23:23 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: TRONCO
Version: 2.28.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TRONCO_2.28.0.tar.gz
StartedAt: 2022-10-18 22:14:57 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:18:05 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 187.7 seconds
RetCode: 0
Status:   OK  
CheckDir: TRONCO.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings TRONCO_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/TRONCO.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.28.0’
* 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 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.prederr 0.160  0.099   6.045
tronco.bootstrap     0.103  0.013   7.526
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/TRONCO.Rcheck/00check.log’
for details.



Installation output

TRONCO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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

TRONCO.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 6 edges out of 49 (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:01s 
*** 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:01s 
*** 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 44 (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:01s 
*** 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 49 (14%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:01s 
[ FAIL 0 | WARN 16 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 16 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 35.538   1.138  75.152 

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

nameusersystemelapsed
TCGA.multiple.samples0.0070.0080.015
TCGA.remove.multiple.samples0.0120.0120.024
TCGA.shorten.barcodes0.0130.0080.020
annotate.description0.0070.0120.019
annotate.stages0.0060.0000.006
as.adj.matrix0.0080.0180.026
as.alterations0.0030.0000.004
as.bootstrap.scores0.1330.0000.132
as.colors0.0010.0000.002
as.confidence0.0140.0160.030
as.description0.0010.0000.002
as.events0.0010.0010.003
as.events.in.patterns0.0020.0010.004
as.events.in.sample0.0030.0010.003
as.gene0.0050.0000.005
as.genes0.0020.0000.001
as.genes.in.patterns0.0030.0000.003
as.genotypes0.0060.0070.014
as.hypotheses0.0010.0060.007
as.joint.probs0.0050.0180.024
as.kfold.eloss0.0620.0040.067
as.kfold.posterr0.0740.0120.086
as.kfold.prederr0.0760.0120.088
as.marginal.probs0.0050.0000.005
as.models0.0140.0440.057
as.parameters0.0030.0000.003
as.pathway0.0060.0000.006
as.patterns0.0020.0000.002
as.samples0.0000.0020.002
as.selective.advantage.relations0.0690.0160.086
as.stages0.0050.0000.006
as.types0.0010.0000.002
as.types.in.patterns0.0030.0000.004
change.color0.0020.0000.002
consolidate.data0.0230.0000.023
delete.event0.0040.0000.004
delete.gene0.0040.0000.004
delete.hypothesis0.0170.0400.058
delete.model0.0000.0030.003
delete.pattern0.0070.0120.020
delete.samples0.0030.0000.003
delete.type0.0040.0000.004
duplicates0.0010.0000.002
enforce.numeric0.0020.0000.002
enforce.string0.0020.0000.003
events.selection0.0000.0040.004
export.graphml0.0550.0080.062
export.mutex0.0090.0000.008
has.duplicates0.0020.0000.002
has.model0.0020.0000.002
has.stages0.0050.0000.005
import.GISTIC0.0020.0040.005
import.MAF0.0660.0000.067
intersect.datasets0.0010.0000.002
is.compliant0.0020.0000.001
join.events0.0000.0030.003
join.types0.0420.0080.049
keysToNames0.0050.0000.005
nameToKey0.0030.0000.002
nevents0.0020.0000.002
ngenes0.0010.0000.002
nhypotheses0.0000.0020.002
npatterns0.0000.0010.002
nsamples0.0010.0000.002
ntypes0.0010.0000.001
oncoprint.cbio0.0050.0000.005
order.frequency0.0010.0160.017
pheatmap0.0280.0000.028
rank.recurrents0.0000.0040.004
rename.gene0.0030.0000.002
rename.type0.0020.0000.002
samples.selection0.0020.0000.003
trim0.0000.0030.002
tronco.bootstrap0.1030.0137.526
tronco.caprese0.0850.0010.086
tronco.capri1.7870.0671.855
tronco.chowliu1.1920.0321.224
tronco.edmonds1.0560.0121.068
tronco.gabow1.2380.0201.258
tronco.kfold.eloss0.0860.0600.147
tronco.kfold.posterr0.1640.1364.081
tronco.kfold.prederr0.1600.0996.045
tronco.plot0.2250.0030.230
tronco.prim4.1980.0914.457
view0.0030.0040.007
which.samples0.0050.0000.005