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CHECK report for TRONCO on malbec1

This page was generated on 2019-04-16 11:51:03 -0400 (Tue, 16 Apr 2019).

Package 1593/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TRONCO 2.14.2
Luca De Sano
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/TRONCO
Branch: RELEASE_3_8
Last Commit: fe79b24
Last Changed Date: 2018-12-10 12:28:36 -0400 (Mon, 10 Dec 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TRONCO
Version: 2.14.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TRONCO_2.14.2.tar.gz
StartedAt: 2019-04-16 03:33:07 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:37:05 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 237.6 seconds
RetCode: 0
Status:  OK 
CheckDir: TRONCO.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings TRONCO_2.14.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/TRONCO.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.14.2’
* 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.204  0.288   8.683
tronco.kfold.prederr 0.176  0.268   8.585
tronco.bootstrap     0.164  0.140  15.318
* 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

TRONCO.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘TRONCO’ ...
** 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
* DONE (TRONCO)

Tests output

TRONCO.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 13 edges out of 55 (24%)
*** 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 5 edges out of 51 (10%)
*** 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 5 edges out of 48 (10%)
*** 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 7 edges out of 41 (17%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:02s 
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 253 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 51.584   2.188 124.946 

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

nameusersystemelapsed
TCGA.multiple.samples0.0120.0000.014
TCGA.remove.multiple.samples0.0120.0040.014
TCGA.shorten.barcodes0.0040.0080.010
annotate.description0.0120.0040.015
annotate.stages0.0040.0000.007
as.adj.matrix0.0000.0080.010
as.alterations0.0040.0000.003
as.bootstrap.scores0.0280.0000.029
as.colors0.0040.0000.001
as.confidence0.0080.0000.011
as.description0.0000.0000.001
as.events0.0000.0000.001
as.events.in.patterns0.0040.0040.006
as.events.in.sample0.0040.0000.003
as.gene0.0040.0000.003
as.genes0.0000.0000.001
as.genes.in.patterns0.0040.0000.003
as.genotypes0.0080.0000.008
as.hypotheses0.0040.0000.003
as.joint.probs0.0000.0080.008
as.kfold.eloss0.0320.0040.034
as.kfold.posterr0.0480.0040.054
as.kfold.prederr0.0840.0040.091
as.marginal.probs0.0000.0000.003
as.models0.0160.0040.018
as.parameters0.0040.0000.002
as.pathway0.1080.0000.108
as.patterns0.0000.0000.002
as.samples0.0040.0000.002
as.selective.advantage.relations0.0600.0040.064
as.stages0.0040.0000.005
as.types0.0000.0000.001
as.types.in.patterns0.0040.0000.003
change.color0.0040.0000.001
consolidate.data0.0240.0040.030
delete.event0.0040.0000.005
delete.gene0.0040.0000.004
delete.hypothesis0.0240.0080.034
delete.model0.0040.0000.003
delete.pattern0.0160.0040.020
delete.samples0.0000.0000.003
delete.type0.0040.0000.005
duplicates0.0040.0000.002
enforce.numeric0.0040.0000.004
enforce.string0.0000.0040.003
events.selection0.0080.0000.006
export.graphml0.1640.0000.165
export.mutex0.0120.0000.013
has.duplicates0.0000.0000.001
has.model0.0000.0000.002
has.stages0.0120.0000.010
import.GISTIC0.0080.0000.007
import.MAF0.1120.0000.113
intersect.datasets0.0000.0000.001
is.compliant0.0040.0000.002
join.events0.0080.0000.005
join.types0.0680.0040.074
keysToNames0.0040.0000.007
nameToKey0.0040.0000.003
nevents0.0040.0000.002
ngenes0.0000.0000.002
nhypotheses0.0040.0000.002
npatterns0.0000.0000.001
nsamples0.0000.0000.001
ntypes0.0000.0000.001
oncoprint.cbio0.0080.0000.008
order.frequency0.0080.0040.012
pheatmap0.0680.0000.066
rank.recurrents0.0040.0000.005
rename.gene0.0040.0000.003
rename.type0.0040.0000.002
samples.selection0.0040.0000.004
trim0.0040.0000.005
tronco.bootstrap 0.164 0.14015.318
tronco.caprese0.1520.0080.179
tronco.capri2.8680.0162.887
tronco.chowliu1.2400.0041.246
tronco.edmonds1.5760.0001.578
tronco.gabow1.7760.0081.792
tronco.kfold.eloss0.2000.0200.217
tronco.kfold.posterr0.2040.2888.683
tronco.kfold.prederr0.1760.2688.585
tronco.plot0.2840.0040.289
tronco.prim3.4120.0523.468
view0.0040.0000.005
which.samples0.0040.0000.003