Multiple platform build/check report for BioC 3.11 - CHECK report for TRONCO on tokay2

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CHECK report for TRONCO on tokay2

This page was generated on 2020-10-17 11:57:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TRONCO PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.

TRONCO 2.20.1
Luca De Sano

Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)

URL: https://git.bioconductor.org/packages/TRONCO

Branch: RELEASE_3_11

Last Commit: b94a465

Last Changed Date: 2020-06-20 06:22:00 -0400 (Sat, 20 Jun 2020)

malbec2

Linux (Ubuntu 18.04.4 LTS) / x86_64

tokay2

Windows Server 2012 R2 Standard / x64

[ OK ]

machv2

macOS 10.14.6 Mojave / x86_64

Summary

Package: TRONCO

Version: 2.20.1

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TRONCO.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TRONCO_2.20.1.tar.gz

StartedAt: 2020-10-17 09:03:15 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 09:10:48 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 452.3 seconds

RetCode: 0

Status: OK

CheckDir: TRONCO.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TRONCO.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings TRONCO_2.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/TRONCO.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TRONCO/DESCRIPTION' ... OK
* this is package 'TRONCO' version '2.20.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
tronco.kfold.posterr 0.33   0.11    5.42
tronco.bootstrap     0.25   0.11   14.99
tronco.kfold.prederr 0.23   0.09    5.46
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
tronco.bootstrap     0.33   0.11   18.01
tronco.kfold.posterr 0.19   0.25   11.78
tronco.kfold.prederr 0.22   0.14    6.72
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TRONCO_2.20.1.tar.gz && rm -rf TRONCO.buildbin-libdir && mkdir TRONCO.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TRONCO.buildbin-libdir TRONCO_2.20.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TRONCO_2.20.1.zip && rm TRONCO_2.20.1.tar.gz TRONCO_2.20.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  254k  100  254k    0     0  3886k      0 --:--:-- --:--:-- --:--:-- 4310k

install for i386

* 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
  converting help for package 'TRONCO'
    finding HTML links ... done
    AND                                     html  
    OR                                      html  
    TCGA.map.clinical.data                  html  
    TCGA.multiple.samples                   html  
    TCGA.remove.multiple.samples            html  
    TCGA.shorten.barcodes                   html  
    XOR                                     html  
    aCML                                    html  
    annotate.description                    html  
    annotate.stages                         html  
    as.adj.matrix                           html  
    as.alterations                          html  
    as.bootstrap.scores                     html  
    as.colors                               html  
    as.conditional.probs                    html  
    as.confidence                           html  
    as.description                          html  
    as.events                               html  
    as.events.in.patterns                   html  
    as.events.in.sample                     html  
    as.gene                                 html  
    as.genes                                html  
    as.genes.in.patterns                    html  
    as.genotypes                            html  
    as.hypotheses                           html  
    as.joint.probs                          html  
    as.kfold.eloss                          html  
    as.kfold.posterr                        html  
    as.kfold.prederr                        html  
    as.marginal.probs                       html  
    as.models                               html  
    as.parameters                           html  
    as.pathway                              html  
    as.patterns                             html  
    as.samples                              html  
    as.selective.advantage.relations        html  
    as.stages                               html  
    as.types                                html  
    as.types.in.patterns                    html  
    cbio.query                              html  
    change.color                            html  
    consolidate.data                        html  
    crc_gistic                              html  
    crc_maf                                 html  
    crc_plain                               html  
    delete.event                            html  
    delete.gene                             html  
    delete.hypothesis                       html  
    delete.model                            html  
    delete.pattern                          html  
    delete.samples                          html  
    delete.type                             html  
    duplicates                              html  
    ebind                                   html  
    enforce.numeric                         html  
    enforce.string                          html  
    events.selection                        html  
    export.graphml                          html  
    export.mutex                            html  
    export.nbs.input                        html  
    extract.MAF.HuGO.Entrez.map             html  
    genes.table.report                      html  
    has.duplicates                          html  
    has.model                               html  
    has.stages                              html  
    hypothesis.add                          html  
    hypothesis.add.group                    html  
    hypothesis.add.homologous               html  
    import.GISTIC                           html  
    import.MAF                              html  
    import.genotypes                        html  
    import.model                            html  
    import.mutex.groups                     html  
    intersect.datasets                      html  
    is.compliant                            html  
    join.events                             html  
    join.types                              html  
    keysToNames                             html  
    maf                                     html  
    muts                                    html  
    nameToKey                               html  
    nevents                                 html  
    ngenes                                  html  
    nhypotheses                             html  
    npatterns                               html  
    nsamples                                html  
    ntypes                                  html  
    oncoprint                               html  
    oncoprint.cbio                          html  
    order.frequency                         html  
    pathway.visualization                   html  
    pheatmap                                html  
    rank.recurrents                         html  
    rename.gene                             html  
    rename.type                             html  
    samples.selection                       html  
    sbind                                   html  
    ssplit                                  html  
    stage                                   html  
    test_dataset                            html  
    test_dataset_no_hypos                   html  
    test_model                              html  
    test_model_kfold                        html  
    trim                                    html  
    tronco.bootstrap                        html  
    tronco.caprese                          html  
    tronco.capri                            html  
    tronco.chowliu                          html  
    tronco.edmonds                          html  
    tronco.gabow                            html  
    tronco.kfold.eloss                      html  
    tronco.kfold.posterr                    html  
    tronco.kfold.prederr                    html  
    tronco.pattern.plot                     html  
    tronco.plot                             html  
    tronco.prim                             html  
    view                                    html  
    which.samples                           html  
** 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

install for x64

* installing *source* package 'TRONCO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TRONCO' as TRONCO_2.20.1.zip
* DONE (TRONCO)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TRONCO' successfully unpacked and MD5 sums checked

Tests output

TRONCO.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 7 edges out of 47 (15%)
*** 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 8 edges out of 49 (16%)
*** 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 6 edges out of 44 (14%)
*** 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 13 edges out of 57 (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 
  49.57    0.96  114.50

TRONCO.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 7 edges out of 48 (15%)
*** 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 51 (18%)
*** 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 10 edges out of 55 (18%)
*** 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 51 (14%)
*** 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 
  52.23    0.76  118.14

Example timings

TRONCO.Rcheck/examples_i386/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.03	0.00	0.03
TCGA.remove.multiple.samples	0.03	0.00	0.03
TCGA.shorten.barcodes	0.03	0.00	0.03
annotate.description	0.02	0.00	0.02
annotate.stages	0.01	0.02	0.03
as.adj.matrix	0.03	0.00	0.03
as.alterations	0	0	0
as.bootstrap.scores	0.08	0.00	0.08
as.colors	0	0	0
as.confidence	0.03	0.00	0.03
as.description	0.01	0.00	0.01
as.events	0	0	0
as.events.in.patterns	0.02	0.00	0.02
as.events.in.sample	0.02	0.00	0.01
as.gene	0.01	0.00	0.02
as.genes	0	0	0
as.genes.in.patterns	0.02	0.00	0.02
as.genotypes	0.01	0.00	0.01
as.hypotheses	0	0	0
as.joint.probs	0.01	0.01	0.03
as.kfold.eloss	0.08	0.00	0.08
as.kfold.posterr	0.10	0.02	0.11
as.kfold.prederr	0.15	0.01	0.17
as.marginal.probs	0	0	0
as.models	0.00	0.03	0.03
as.parameters	0.00	0.02	0.02
as.pathway	0	0	0
as.patterns	0	0	0
as.samples	0.12	0.00	0.12
as.selective.advantage.relations	0.14	0.03	0.17
as.stages	0.00	0.01	0.02
as.types	0	0	0
as.types.in.patterns	0.01	0.00	0.02
change.color	0	0	0
consolidate.data	0.02	0.02	0.05
delete.event	0	0	0
delete.gene	0.01	0.00	0.02
delete.hypothesis	0.08	0.00	0.11
delete.model	0.00	0.00	0.11
delete.pattern	0.00	0.01	0.09
delete.samples	0	0	0
delete.type	0.02	0.00	0.01
duplicates	0.00	0.02	0.10
enforce.numeric	0	0	0
enforce.string	0.02	0.00	0.01
events.selection	0.01	0.00	0.09
export.graphml	0.17	0.00	0.96
export.mutex	0.03	0.00	0.03
has.duplicates	0.00	0.00	0.03
has.model	0.00	0.02	0.02
has.stages	0.02	0.00	0.04
import.GISTIC	0	0	0
import.MAF	0.08	0.03	0.16
intersect.datasets	0	0	0
is.compliant	0.01	0.00	0.03
join.events	0.02	0.00	0.02
join.types	0.06	0.00	0.26
keysToNames	0.02	0.00	0.02
nameToKey	0.01	0.00	0.05
nevents	0	0	0
ngenes	0.00	0.00	0.04
nhypotheses	0	0	0
npatterns	0.02	0.00	0.08
nsamples	0	0	0
ntypes	0.00	0.00	0.03
oncoprint.cbio	0.00	0.00	0.04
order.frequency	0.02	0.00	0.02
pheatmap	0.08	0.00	0.12
rank.recurrents	0	0	0
rename.gene	0	0	0
rename.type	0.01	0.00	0.02
samples.selection	0	0	0
trim	0.00	0.00	0.09
tronco.bootstrap	0.25	0.11	14.99
tronco.caprese	0.21	0.00	0.20
tronco.capri	2.84	0.06	2.90
tronco.chowliu	1.58	0.00	1.63
tronco.edmonds	1.89	0.02	1.91
tronco.gabow	2.09	0.02	2.12
tronco.kfold.eloss	0.24	0.01	0.28
tronco.kfold.posterr	0.33	0.11	5.42
tronco.kfold.prederr	0.23	0.09	5.46
tronco.plot	0.27	0.02	0.28
tronco.prim	3.84	0.03	3.87
view	0.02	0.00	0.02
which.samples	0	0	0

TRONCO.Rcheck/examples_x64/TRONCO-Ex.timings

name	user	system	elapsed
TCGA.multiple.samples	0.03	0.02	0.05
TCGA.remove.multiple.samples	0.03	0.00	0.03
TCGA.shorten.barcodes	0.02	0.01	0.03
annotate.description	0.02	0.00	0.01
annotate.stages	0.03	0.00	0.03
as.adj.matrix	0.00	0.02	0.14
as.alterations	0.01	0.00	0.02
as.bootstrap.scores	0.10	0.00	0.22
as.colors	0	0	0
as.confidence	0.01	0.01	0.03
as.description	0	0	0
as.events	0.00	0.00	0.06
as.events.in.patterns	0.02	0.00	0.02
as.events.in.sample	0.01	0.00	0.01
as.gene	0	0	0
as.genes	0	0	0
as.genes.in.patterns	0.01	0.00	0.02
as.genotypes	0.02	0.00	0.01
as.hypotheses	0.00	0.02	0.02
as.joint.probs	0.02	0.00	0.01
as.kfold.eloss	0.07	0.00	0.08
as.kfold.posterr	0.10	0.01	0.11
as.kfold.prederr	0.18	0.00	0.20
as.marginal.probs	0	0	0
as.models	0.02	0.04	0.05
as.parameters	0	0	0
as.pathway	0.00	0.01	0.02
as.patterns	0.17	0.00	0.17
as.samples	0.00	0.00	0.09
as.selective.advantage.relations	0.13	0.02	0.52
as.stages	0.00	0.00	0.04
as.types	0.00	0.01	0.02
as.types.in.patterns	0.01	0.00	0.05
change.color	0	0	0
consolidate.data	0.08	0.00	0.28
delete.event	0	0	0
delete.gene	0.02	0.00	0.01
delete.hypothesis	0.06	0.00	0.11
delete.model	0	0	0
delete.pattern	0.03	0.00	0.05
delete.samples	0.00	0.02	0.01
delete.type	0.02	0.00	0.02
duplicates	0.00	0.00	0.06
enforce.numeric	0	0	0
enforce.string	0.02	0.00	0.01
events.selection	0.00	0.00	0.08
export.graphml	0.22	0.00	0.64
export.mutex	0.01	0.00	0.02
has.duplicates	0	0	0
has.model	0	0	0
has.stages	0.00	0.01	0.02
import.GISTIC	0.01	0.00	0.02
import.MAF	0.11	0.00	0.10
intersect.datasets	0	0	0
is.compliant	0.00	0.02	0.02
join.events	0	0	0
join.types	0.06	0.02	0.20
keysToNames	0.02	0.00	0.02
nameToKey	0.02	0.00	0.01
nevents	0	0	0
ngenes	0	0	0
nhypotheses	0.00	0.01	0.02
npatterns	0	0	0
nsamples	0	0	0
ntypes	0	0	0
oncoprint.cbio	0.02	0.00	0.01
order.frequency	0.00	0.02	0.02
pheatmap	0.04	0.00	0.12
rank.recurrents	0.02	0.00	0.02
rename.gene	0	0	0
rename.type	0.00	0.01	0.01
samples.selection	0	0	0
trim	0.00	0.02	0.02
tronco.bootstrap	0.33	0.11	18.01
tronco.caprese	0.20	0.00	0.21
tronco.capri	2.74	0.01	2.75
tronco.chowliu	2.01	0.02	2.08
tronco.edmonds	1.86	0.00	1.86
tronco.gabow	2.42	0.00	2.87
tronco.kfold.eloss	0.22	0.03	0.77
tronco.kfold.posterr	0.19	0.25	11.78
tronco.kfold.prederr	0.22	0.14	6.72
tronco.plot	0.25	0.00	0.25
tronco.prim	3.59	0.05	3.65
view	0.02	0.00	0.02
which.samples	0	0	0