BioC 3.4: CHECK report for TRONCO on malbec1

Package: TRONCO

Version: 2.6.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.6.1.tar.gz

StartedAt: 2017-04-15 01:43:58 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:48:21 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 263.1 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/TRONCO.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.6.1’
* 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 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 0.224  0.100   6.738
tronco.kfold.prederr 0.156  0.132   6.886
tronco.bootstrap     0.212  0.068  19.941
* 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	0.014
TCGA.remove.multiple.samples	0.016	0.004	0.019
TCGA.shorten.barcodes	0.012	0.000	0.011
annotate.description	0.004	0.004	0.009
annotate.stages	0.004	0.000	0.008
as.adj.matrix	0.004	0.004	0.010
as.alterations	0.000	0.004	0.003
as.bootstrap.scores	0.056	0.000	0.055
as.colors	0.000	0.000	0.001
as.confidence	0.004	0.004	0.010
as.description	0.004	0.000	0.002
as.events	0.000	0.000	0.002
as.events.in.patterns	0.004	0.000	0.004
as.events.in.sample	0.004	0.000	0.004
as.gene	0.004	0.000	0.003
as.genes	0.000	0.000	0.001
as.genes.in.patterns	0.004	0.000	0.004
as.genotypes	0.000	0.004	0.007
as.hypotheses	0.000	0.000	0.003
as.joint.probs	0.008	0.000	0.009
as.kfold.eloss	0.108	0.000	0.110
as.kfold.posterr	0.056	0.008	0.064
as.kfold.prederr	0.128	0.004	0.133
as.marginal.probs	0.004	0.000	0.004
as.models	0.004	0.012	0.016
as.parameters	0.004	0.000	0.003
as.pathway	0.004	0.000	0.005
as.patterns	0.000	0.000	0.002
as.samples	0.004	0.000	0.001
as.selective.advantage.relations	0.096	0.004	0.102
as.stages	0.004	0.000	0.006
as.types	0.004	0.000	0.001
as.types.in.patterns	0.004	0.000	0.004
change.color	0.000	0.000	0.002
consolidate.data	0.024	0.000	0.024
delete.event	0.004	0.000	0.005
delete.gene	0.008	0.000	0.007
delete.hypothesis	0.020	0.008	0.027
delete.model	0.004	0.000	0.003
delete.pattern	0.012	0.000	0.011
delete.samples	0.004	0.000	0.003
delete.type	0.004	0.000	0.005
duplicates	0.000	0.004	0.002
enforce.numeric	0.000	0.000	0.002
enforce.string	0.000	0.000	0.002
events.selection	0.004	0.000	0.004
export.graphml	0.172	0.000	0.175
export.mutex	0.008	0.000	0.008
has.duplicates	0.000	0.000	0.001
has.model	0.004	0.000	0.001
has.stages	0.000	0.004	0.006
import.GISTIC	0.008	0.000	0.004
import.MAF	0.080	0.000	0.083
intersect.datasets	0.000	0.000	0.001
is.compliant	0.000	0.000	0.002
join.events	0.000	0.000	0.004
join.types	0.052	0.000	0.053
keysToNames	0.004	0.000	0.004
nameToKey	0.004	0.000	0.002
nevents	0.000	0.000	0.001
ngenes	0.000	0.000	0.001
nhypotheses	0.000	0.000	0.002
npatterns	0.000	0.000	0.001
nsamples	0.000	0.000	0.001
ntypes	0.004	0.000	0.001
oncoprint.cbio	0.008	0.000	0.006
order.frequency	0.004	0.000	0.007
pheatmap	0.120	0.000	0.121
rank.recurrents	0.004	0.000	0.003
rename.gene	0.004	0.000	0.002
rename.type	0.000	0.000	0.001
samples.selection	0.000	0.000	0.003
trim	0.004	0.000	0.003
tronco.bootstrap	0.212	0.068	19.941
tronco.caprese	0.260	0.000	0.259
tronco.capri	2.240	0.000	2.239
tronco.chowliu	1.696	0.000	1.699
tronco.edmonds	1.568	0.000	1.571
tronco.gabow	1.648	0.008	1.655
tronco.kfold.eloss	0.128	0.012	0.140
tronco.kfold.posterr	0.224	0.100	6.738
tronco.kfold.prederr	0.156	0.132	6.886
tronco.plot	0.132	0.000	0.136
tronco.prim	2.520	0.020	2.543
view	0.004	0.000	0.004
which.samples	0.004	0.000	0.003