BioC 3.5: CHECK report for TRONCO on malbec2

Package: TRONCO

Version: 2.8.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.8.2.tar.gz

StartedAt: 2017-10-18 02:59:57 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 03:04:00 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 242.2 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.8.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/TRONCO.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.8.2’
* 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 0.492  0.128   8.999
tronco.kfold.prederr 0.172  0.124   8.598
tronco.bootstrap     0.168  0.104  19.898
* 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	0.012	0.000	0.014
TCGA.remove.multiple.samples	0.076	0.000	0.077
TCGA.shorten.barcodes	0.012	0.000	0.010
annotate.description	0.008	0.000	0.009
annotate.stages	0.008	0.000	0.008
as.adj.matrix	0.040	0.000	0.041
as.alterations	0.004	0.000	0.004
as.bootstrap.scores	0.16	0.00	0.16
as.colors	0.000	0.000	0.001
as.confidence	0.048	0.000	0.047
as.description	0.004	0.000	0.002
as.events	0.000	0.000	0.002
as.events.in.patterns	0.016	0.000	0.019
as.events.in.sample	0.000	0.000	0.003
as.gene	0.000	0.004	0.004
as.genes	0.000	0.000	0.002
as.genes.in.patterns	0.008	0.000	0.006
as.genotypes	0.008	0.000	0.008
as.hypotheses	0.000	0.004	0.003
as.joint.probs	0.020	0.004	0.022
as.kfold.eloss	0.152	0.004	0.157
as.kfold.posterr	0.236	0.004	0.243
as.kfold.prederr	0.096	0.008	0.107
as.marginal.probs	0.016	0.000	0.016
as.models	0.008	0.008	0.016
as.parameters	0.004	0.000	0.002
as.pathway	0.004	0.000	0.005
as.patterns	0.000	0.004	0.001
as.samples	0.000	0.000	0.001
as.selective.advantage.relations	0.172	0.004	0.175
as.stages	0.020	0.004	0.025
as.types	0.000	0.000	0.002
as.types.in.patterns	0.004	0.000	0.004
change.color	0.004	0.000	0.002
consolidate.data	0.028	0.000	0.028
delete.event	0.004	0.000	0.005
delete.gene	0.004	0.000	0.004
delete.hypothesis	0.088	0.000	0.089
delete.model	0.000	0.004	0.004
delete.pattern	0.020	0.000	0.019
delete.samples	0.028	0.000	0.027
delete.type	0.008	0.000	0.008
duplicates	0.004	0.000	0.003
enforce.numeric	0.004	0.000	0.004
enforce.string	0.008	0.000	0.004
events.selection	0.052	0.000	0.053
export.graphml	0.568	0.004	0.571
export.mutex	0.064	0.000	0.063
has.duplicates	0.000	0.004	0.001
has.model	0.000	0.000	0.002
has.stages	0.004	0.000	0.006
import.GISTIC	0.156	0.000	0.156
import.MAF	0.144	0.000	0.141
intersect.datasets	0.000	0.000	0.001
is.compliant	0.004	0.000	0.001
join.events	0.024	0.000	0.025
join.types	0.076	0.008	0.083
keysToNames	0.004	0.000	0.004
nameToKey	0.000	0.000	0.002
nevents	0.004	0.000	0.001
ngenes	0.000	0.000	0.001
nhypotheses	0.004	0.000	0.001
npatterns	0.000	0.000	0.002
nsamples	0.004	0.000	0.002
ntypes	0.000	0.000	0.002
oncoprint.cbio	0.008	0.000	0.007
order.frequency	0.004	0.004	0.008
pheatmap	0.864	0.000	0.863
rank.recurrents	0.004	0.000	0.003
rename.gene	0.004	0.000	0.002
rename.type	0.020	0.000	0.021
samples.selection	0.004	0.000	0.003
trim	0.004	0.000	0.003
tronco.bootstrap	0.168	0.104	19.898
tronco.caprese	0.480	0.000	0.482
tronco.capri	2.952	0.000	2.954
tronco.chowliu	1.680	0.004	1.681
tronco.edmonds	1.084	0.000	1.087
tronco.gabow	1.488	0.012	1.499
tronco.kfold.eloss	0.484	0.012	0.498
tronco.kfold.posterr	0.492	0.128	8.999
tronco.kfold.prederr	0.172	0.124	8.598
tronco.plot	0.868	0.004	0.877
tronco.prim	2.368	0.020	2.390
view	0.004	0.000	0.003
which.samples	0.008	0.000	0.009