BioC 3.6: CHECK report for TRONCO on veracruz1

Package: TRONCO

Version: 2.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.9.0.tar.gz

StartedAt: 2017-08-16 09:19:37 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:24:00 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 263.5 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/TRONCO.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.9.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.519  0.050   6.245
tronco.bootstrap     0.193  0.019  18.201
tronco.kfold.prederr 0.131  0.044   6.210
* 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

* installing *source* package ‘TRONCO’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TRONCO)

name	user	system	elapsed
TCGA.multiple.samples	0.016	0.002	0.018
TCGA.remove.multiple.samples	0.098	0.004	0.103
TCGA.shorten.barcodes	0.013	0.005	0.022
annotate.description	0.013	0.005	0.022
annotate.stages	0.009	0.002	0.010
as.adj.matrix	0.049	0.006	0.056
as.alterations	0.005	0.001	0.006
as.bootstrap.scores	0.184	0.001	0.194
as.colors	0.002	0.001	0.002
as.confidence	0.055	0.008	0.065
as.description	0.002	0.000	0.001
as.events	0.002	0.000	0.002
as.events.in.patterns	0.019	0.001	0.020
as.events.in.sample	0.005	0.001	0.006
as.gene	0.004	0.001	0.005
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.004	0.001	0.004
as.genotypes	0.011	0.004	0.015
as.hypotheses	0.004	0.002	0.006
as.joint.probs	0.022	0.005	0.027
as.kfold.eloss	0.155	0.005	0.160
as.kfold.posterr	0.250	0.008	0.259
as.kfold.prederr	0.104	0.008	0.112
as.marginal.probs	0.019	0.001	0.020
as.models	0.014	0.012	0.027
as.parameters	0.003	0.001	0.004
as.pathway	0.005	0.001	0.005
as.patterns	0.002	0.000	0.002
as.samples	0.001	0.001	0.002
as.selective.advantage.relations	0.197	0.004	0.213
as.stages	0.025	0.001	0.027
as.types	0.002	0.000	0.001
as.types.in.patterns	0.004	0.001	0.004
change.color	0.002	0.000	0.002
consolidate.data	0.031	0.001	0.037
delete.event	0.005	0.001	0.006
delete.gene	0.005	0.001	0.006
delete.hypothesis	0.075	0.011	0.094
delete.model	0.004	0.001	0.003
delete.pattern	0.020	0.003	0.023
delete.samples	0.011	0.001	0.011
delete.type	0.005	0.001	0.006
duplicates	0.001	0.000	0.002
enforce.numeric	0.002	0.000	0.002
enforce.string	0.002	0.000	0.002
events.selection	0.064	0.002	0.072
export.graphml	0.621	0.008	0.637
export.mutex	0.068	0.001	0.070
has.duplicates	0.001	0.001	0.002
has.model	0.001	0.000	0.002
has.stages	0.006	0.001	0.007
import.GISTIC	0.162	0.001	0.175
import.MAF	0.151	0.002	0.160
intersect.datasets	0.002	0.001	0.003
is.compliant	0.002	0.001	0.001
join.events	0.022	0.000	0.022
join.types	0.090	0.007	0.107
keysToNames	0.008	0.002	0.010
nameToKey	0.003	0.001	0.004
nevents	0.002	0.001	0.002
ngenes	0.002	0.000	0.002
nhypotheses	0.001	0.000	0.001
npatterns	0.001	0.001	0.002
nsamples	0.001	0.000	0.001
ntypes	0.001	0.001	0.001
oncoprint.cbio	0.007	0.001	0.009
order.frequency	0.009	0.004	0.013
pheatmap	1.111	0.003	1.142
rank.recurrents	0.004	0.001	0.005
rename.gene	0.003	0.001	0.003
rename.type	0.024	0.001	0.025
samples.selection	0.004	0.001	0.006
trim	0.004	0.000	0.005
tronco.bootstrap	0.193	0.019	18.201
tronco.caprese	0.284	0.003	0.295
tronco.capri	3.348	0.034	3.457
tronco.chowliu	2.278	0.016	2.373
tronco.edmonds	1.473	0.014	1.519
tronco.gabow	1.653	0.011	1.691
tronco.kfold.eloss	0.308	0.020	0.337
tronco.kfold.posterr	0.519	0.050	6.245
tronco.kfold.prederr	0.131	0.044	6.210
tronco.plot	0.879	0.004	0.904
tronco.prim	3.052	0.033	3.184
view	0.005	0.001	0.008
which.samples	0.004	0.001	0.005