BioC 3.6: CHECK report for TRONCO on malbec1

Package: TRONCO

Version: 2.9.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.9.0.tar.gz

StartedAt: 2017-08-16 02:53:55 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:57:49 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 233.7 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.9.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/TRONCO.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.9.0’
* 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 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 0.564  0.132   8.303
tronco.bootstrap     0.208  0.148  20.163
tronco.kfold.prederr 0.128  0.160   8.036
* 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	0.000	0.015
TCGA.remove.multiple.samples	0.076	0.004	0.079
TCGA.shorten.barcodes	0.012	0.000	0.011
annotate.description	0.004	0.004	0.009
annotate.stages	0.004	0.000	0.007
as.adj.matrix	0.044	0.000	0.044
as.alterations	0.004	0.000	0.004
as.bootstrap.scores	0.164	0.000	0.164
as.colors	0.000	0.000	0.001
as.confidence	0.048	0.000	0.048
as.description	0.000	0.004	0.001
as.events	0.000	0.000	0.001
as.events.in.patterns	0.020	0.000	0.021
as.events.in.sample	0.004	0.000	0.004
as.gene	0.004	0.000	0.005
as.genes	0.004	0.000	0.002
as.genes.in.patterns	0.004	0.000	0.004
as.genotypes	0.004	0.004	0.008
as.hypotheses	0.000	0.004	0.004
as.joint.probs	0.020	0.004	0.025
as.kfold.eloss	0.148	0.000	0.148
as.kfold.posterr	0.228	0.008	0.235
as.kfold.prederr	0.092	0.012	0.104
as.marginal.probs	0.016	0.000	0.015
as.models	0.016	0.000	0.016
as.parameters	0.000	0.004	0.002
as.pathway	0.004	0.000	0.005
as.patterns	0.004	0.000	0.002
as.samples	0.004	0.000	0.002
as.selective.advantage.relations	0.172	0.000	0.173
as.stages	0.028	0.000	0.025
as.types	0.000	0.000	0.002
as.types.in.patterns	0.004	0.000	0.004
change.color	0.000	0.000	0.002
consolidate.data	0.028	0.000	0.026
delete.event	0.004	0.000	0.005
delete.gene	0.004	0.000	0.005
delete.hypothesis	0.068	0.000	0.067
delete.model	0.004	0.000	0.003
delete.pattern	0.016	0.000	0.017
delete.samples	0.016	0.000	0.013
delete.type	0.004	0.000	0.004
duplicates	0.004	0.000	0.002
enforce.numeric	0.000	0.000	0.002
enforce.string	0.000	0.000	0.002
events.selection	0.052	0.000	0.052
export.graphml	0.544	0.000	0.545
export.mutex	0.064	0.000	0.064
has.duplicates	0.004	0.000	0.002
has.model	0.000	0.000	0.002
has.stages	0.008	0.000	0.005
import.GISTIC	0.152	0.000	0.154
import.MAF	0.136	0.000	0.138
intersect.datasets	0.000	0.004	0.001
is.compliant	0.000	0.000	0.001
join.events	0.024	0.000	0.023
join.types	0.072	0.008	0.080
keysToNames	0.004	0.000	0.004
nameToKey	0.000	0.000	0.002
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	0.002
nsamples	0.004	0.000	0.001
ntypes	0.000	0.000	0.001
oncoprint.cbio	0.008	0.000	0.006
order.frequency	0.008	0.000	0.007
pheatmap	0.864	0.000	0.864
rank.recurrents	0.004	0.000	0.003
rename.gene	0.004	0.000	0.002
rename.type	0.016	0.000	0.016
samples.selection	0.004	0.000	0.002
trim	0.004	0.000	0.003
tronco.bootstrap	0.208	0.148	20.163
tronco.caprese	0.264	0.004	0.268
tronco.capri	2.700	0.024	2.725
tronco.chowliu	1.692	0.000	1.693
tronco.edmonds	1.092	0.000	1.093
tronco.gabow	1.304	0.004	1.309
tronco.kfold.eloss	0.320	0.008	0.327
tronco.kfold.posterr	0.564	0.132	8.303
tronco.kfold.prederr	0.128	0.160	8.036
tronco.plot	0.808	0.004	0.814
tronco.prim	2.396	0.016	2.413
view	0.000	0.004	0.004
which.samples	0.000	0.000	0.002