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This page was generated on 2023-10-16 11:35:51 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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

Package 2151/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TRONCO 2.32.0  (landing page)
Luca De Sano
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/TRONCO
git_branch: RELEASE_3_17
git_last_commit: f8dde58
git_last_commit_date: 2023-04-25 10:37:08 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for TRONCO on nebbiolo1


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: 2.32.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TRONCO_2.32.0.tar.gz
StartedAt: 2023-10-16 01:56:12 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 01:59:53 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 220.5 seconds
RetCode: 0
Status:   OK  
CheckDir: TRONCO.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings TRONCO_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/TRONCO.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.32.0’
* 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 loading without being on the library search path ... OK
* checking 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.bootstrap 0.132  0.005   9.532
* 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 ...
  ‘f1_introduction.rmd’ using ‘UTF-8’... OK
  ‘f2_loading_data.Rmd’ using ‘UTF-8’... OK
  ‘f3_data_visualization.Rmd’ using ‘UTF-8’... OK
  ‘f4_data_manipulation.Rmd’ using ‘UTF-8’... OK
  ‘f5_model_inference.Rmd’ using ‘UTF-8’... OK
  ‘f6_post_reconstruction.Rmd’ using ‘UTF-8’... OK
  ‘f7_import_export.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

TRONCO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL TRONCO
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 52 (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 5 edges out of 48 (10%)
*** 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 8 edges out of 47 (17%)
*** 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 9 edges out of 57 (16%)
*** 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 14 | SKIP 0 | PASS 225 ]

[ FAIL 0 | WARN 14 | SKIP 0 | PASS 225 ]
> 
> proc.time()
   user  system elapsed 
 34.323   1.227  76.610 

Example timings

TRONCO.Rcheck/TRONCO-Ex.timings

nameusersystemelapsed
TCGA.multiple.samples0.0120.0040.017
TCGA.remove.multiple.samples0.0590.0080.067
TCGA.shorten.barcodes0.0050.0120.016
annotate.description0.0030.0120.016
annotate.stages0.0060.0000.007
as.adj.matrix0.0080.0120.020
as.alterations0.1220.0000.122
as.bootstrap.scores0.0330.0000.033
as.colors0.0010.0000.002
as.confidence0.0070.0160.024
as.description0.0010.0000.001
as.events0.0030.0000.002
as.events.in.patterns0.0040.0000.004
as.events.in.sample0.0040.0000.004
as.gene0.0000.0050.004
as.genes0.0000.0020.001
as.genes.in.patterns0.0030.0010.004
as.genotypes0.0100.0040.014
as.hypotheses0.0020.0040.006
as.joint.probs0.0080.0120.020
as.kfold.eloss0.0650.0040.070
as.kfold.posterr0.0710.0160.087
as.kfold.prederr0.0790.0080.087
as.marginal.probs0.0050.0000.005
as.models0.0240.0240.048
as.parameters0.0030.0000.003
as.pathway0.0060.0000.006
as.patterns0.0020.0000.002
as.samples0.0010.0000.002
as.selective.advantage.relations0.0890.0120.101
as.stages0.0070.0000.007
as.types0.0010.0000.002
as.types.in.patterns0.0010.0030.005
change.color0.0020.0000.002
consolidate.data0.0240.0040.028
delete.event0.0040.0000.005
delete.gene0.0010.0040.004
delete.hypothesis0.0200.0320.052
delete.model0.0030.0000.003
delete.pattern0.0110.0080.018
delete.samples0.0020.0000.003
delete.type0.0040.0000.004
duplicates0.0020.0000.001
enforce.numeric0.0030.0000.002
enforce.string0.0030.0000.003
events.selection0.0050.0000.004
export.graphml0.0730.0160.089
export.mutex0.0060.0030.009
has.duplicates0.0000.0010.002
has.model0.0020.0000.002
has.stages0.0050.0000.004
import.GISTIC0.0050.0000.005
import.MAF0.0630.0000.064
intersect.datasets0.0000.0010.001
is.compliant0.0010.0010.001
join.events0.0030.0000.003
join.types0.0340.0160.050
keysToNames0.0020.0030.005
nameToKey0.0020.0010.002
nevents0.0000.0020.001
ngenes0.0000.0010.001
nhypotheses0.0020.0000.001
npatterns0.0010.0000.002
nsamples0.0010.0000.001
ntypes0.0020.0000.001
oncoprint.cbio0.0050.0000.005
order.frequency0.0120.0040.015
pheatmap0.0300.0000.029
rank.recurrents0.0040.0000.003
rename.gene0.0020.0000.002
rename.type0.0020.0000.001
samples.selection0.0030.0000.003
trim0.0030.0000.003
tronco.bootstrap0.1320.0059.532
tronco.caprese0.0860.0000.086
tronco.capri1.5490.0511.600
tronco.chowliu1.1590.0091.167
tronco.edmonds1.2640.0161.280
tronco.gabow1.0560.0071.063
tronco.kfold.eloss0.0770.0490.125
tronco.kfold.posterr0.1560.1013.336
tronco.kfold.prederr0.0950.0772.765
tronco.plot0.1550.0160.171
tronco.prim2.2380.0522.290
view0.0040.0000.004
which.samples0.0030.0000.004