Luca De Sano
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/TRONCO |
| Branch: RELEASE_3_10 |
| Last Commit: fe36bcd |
| Last Changed Date: 2019-10-29 13:09:08 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:09:37 -0400 (Wed, 15 Apr 2020).
| Package 1761/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TRONCO 2.18.0 Luca De Sano
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TRONCO |
| Version: 2.18.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TRONCO_2.18.0.tar.gz |
| StartedAt: 2020-04-15 02:44:24 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:49:13 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 288.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TRONCO.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:TRONCO.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings TRONCO_2.18.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/TRONCO.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.18.0’
* 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
tronco.kfold.posterr 0.236 0.260 10.191
tronco.kfold.prederr 0.200 0.232 9.723
tronco.bootstrap 0.152 0.176 17.032
* 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
TRONCO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL TRONCO ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)
TRONCO.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 4 edges out of 49 (8%)
*** Performing likelihood-fit with regularization: no_reg and score: pmi .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s
*** 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 55 (13%)
*** Performing likelihood-fit with regularization: no_reg .
*** Evaluating BIC / AIC / LogLik informations.
The reconstruction has been successfully completed in 00h:00m:03s
*** 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 10 edges out of 54 (19%)
*** 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 11 edges out of 47 (23%)
*** 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: 225 | SKIPPED: 0 | WARNINGS: 28 | FAILED: 0 ]
>
> proc.time()
user system elapsed
62.540 2.204 159.408
TRONCO.Rcheck/TRONCO-Ex.timings
| name | user | system | elapsed | |
| TCGA.multiple.samples | 0.008 | 0.004 | 0.013 | |
| TCGA.remove.multiple.samples | 0.008 | 0.004 | 0.015 | |
| TCGA.shorten.barcodes | 0.016 | 0.000 | 0.019 | |
| annotate.description | 0.008 | 0.004 | 0.010 | |
| annotate.stages | 0.004 | 0.004 | 0.007 | |
| as.adj.matrix | 0.004 | 0.008 | 0.010 | |
| as.alterations | 0.004 | 0.000 | 0.003 | |
| as.bootstrap.scores | 0.028 | 0.004 | 0.035 | |
| as.colors | 0.000 | 0.000 | 0.001 | |
| as.confidence | 0.012 | 0.000 | 0.012 | |
| as.description | 0.000 | 0.000 | 0.001 | |
| as.events | 0.008 | 0.000 | 0.006 | |
| as.events.in.patterns | 0.004 | 0.000 | 0.003 | |
| as.events.in.sample | 0.004 | 0.000 | 0.003 | |
| as.gene | 0.004 | 0.000 | 0.004 | |
| as.genes | 0.000 | 0.000 | 0.001 | |
| as.genes.in.patterns | 0.000 | 0.000 | 0.004 | |
| as.genotypes | 0.004 | 0.004 | 0.008 | |
| as.hypotheses | 0.004 | 0.000 | 0.003 | |
| as.joint.probs | 0.004 | 0.004 | 0.009 | |
| as.kfold.eloss | 0.032 | 0.004 | 0.035 | |
| as.kfold.posterr | 0.052 | 0.004 | 0.054 | |
| as.kfold.prederr | 0.080 | 0.008 | 0.087 | |
| as.marginal.probs | 0.000 | 0.000 | 0.003 | |
| as.models | 0.000 | 0.016 | 0.019 | |
| as.parameters | 0.004 | 0.000 | 0.001 | |
| as.pathway | 0.004 | 0.000 | 0.004 | |
| as.patterns | 0.004 | 0.000 | 0.002 | |
| as.samples | 0.000 | 0.000 | 0.001 | |
| as.selective.advantage.relations | 0.216 | 0.016 | 0.233 | |
| as.stages | 0.008 | 0.000 | 0.011 | |
| as.types | 0.000 | 0.000 | 0.002 | |
| as.types.in.patterns | 0.004 | 0.004 | 0.006 | |
| change.color | 0.004 | 0.000 | 0.002 | |
| consolidate.data | 0.036 | 0.012 | 0.050 | |
| delete.event | 0.004 | 0.000 | 0.006 | |
| delete.gene | 0.004 | 0.000 | 0.004 | |
| delete.hypothesis | 0.024 | 0.008 | 0.030 | |
| delete.model | 0.000 | 0.004 | 0.003 | |
| delete.pattern | 0.008 | 0.004 | 0.012 | |
| delete.samples | 0.004 | 0.000 | 0.003 | |
| delete.type | 0.008 | 0.000 | 0.009 | |
| duplicates | 0.000 | 0.004 | 0.002 | |
| enforce.numeric | 0.000 | 0.000 | 0.002 | |
| enforce.string | 0.004 | 0.000 | 0.002 | |
| events.selection | 0.004 | 0.000 | 0.003 | |
| export.graphml | 0.076 | 0.000 | 0.171 | |
| export.mutex | 0.008 | 0.000 | 0.012 | |
| has.duplicates | 0.000 | 0.000 | 0.001 | |
| has.model | 0.000 | 0.004 | 0.002 | |
| has.stages | 0.008 | 0.000 | 0.008 | |
| import.GISTIC | 0.004 | 0.000 | 0.006 | |
| import.MAF | 0.104 | 0.004 | 0.108 | |
| intersect.datasets | 0.004 | 0.000 | 0.002 | |
| is.compliant | 0.000 | 0.000 | 0.002 | |
| join.events | 0.020 | 0.000 | 0.017 | |
| join.types | 0.064 | 0.000 | 0.064 | |
| keysToNames | 0.008 | 0.000 | 0.006 | |
| nameToKey | 0.004 | 0.000 | 0.004 | |
| nevents | 0.000 | 0.000 | 0.001 | |
| ngenes | 0.000 | 0.000 | 0.001 | |
| nhypotheses | 0.000 | 0.000 | 0.001 | |
| npatterns | 0.000 | 0.000 | 0.001 | |
| nsamples | 0.004 | 0.000 | 0.002 | |
| ntypes | 0.000 | 0.000 | 0.001 | |
| oncoprint.cbio | 0.008 | 0.000 | 0.008 | |
| order.frequency | 0.004 | 0.008 | 0.012 | |
| pheatmap | 0.060 | 0.000 | 0.064 | |
| rank.recurrents | 0.004 | 0.000 | 0.005 | |
| rename.gene | 0.000 | 0.004 | 0.003 | |
| rename.type | 0.004 | 0.000 | 0.003 | |
| samples.selection | 0.004 | 0.000 | 0.004 | |
| trim | 0.004 | 0.000 | 0.004 | |
| tronco.bootstrap | 0.152 | 0.176 | 17.032 | |
| tronco.caprese | 0.172 | 0.004 | 0.211 | |
| tronco.capri | 2.368 | 0.028 | 2.402 | |
| tronco.chowliu | 1.544 | 0.000 | 1.548 | |
| tronco.edmonds | 2.096 | 0.000 | 2.101 | |
| tronco.gabow | 1.388 | 0.000 | 1.388 | |
| tronco.kfold.eloss | 0.196 | 0.012 | 0.207 | |
| tronco.kfold.posterr | 0.236 | 0.260 | 10.191 | |
| tronco.kfold.prederr | 0.200 | 0.232 | 9.723 | |
| tronco.plot | 0.252 | 0.004 | 0.270 | |
| tronco.prim | 3.672 | 0.040 | 3.738 | |
| view | 0.004 | 0.000 | 0.006 | |
| which.samples | 0.004 | 0.000 | 0.003 | |