BioC 3.5: CHECK report for TRONCO on malbec2

Package: TRONCO

Version: 2.8.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.8.0.tar.gz

StartedAt: 2017-08-16 02:46:21 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:50:14 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 232.5 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_2.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-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 ‘2.8.0’
* 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 0.580  0.132   8.798
tronco.bootstrap     0.200  0.164  20.125
tronco.kfold.prederr 0.176  0.168   8.238
* 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	0.008	0.004	0.013
TCGA.remove.multiple.samples	0.076	0.000	0.077
TCGA.shorten.barcodes	0.012	0.000	0.010
annotate.description	0.004	0.004	0.009
annotate.stages	0.008	0.000	0.008
as.adj.matrix	0.040	0.000	0.041
as.alterations	0.000	0.000	0.004
as.bootstrap.scores	0.160	0.000	0.162
as.colors	0.004	0.000	0.001
as.confidence	0.044	0.004	0.048
as.description	0.004	0.000	0.001
as.events	0.000	0.000	0.002
as.events.in.patterns	0.024	0.000	0.022
as.events.in.sample	0.004	0.000	0.003
as.gene	0.004	0.000	0.004
as.genes	0.000	0.004	0.001
as.genes.in.patterns	0.000	0.004	0.004
as.genotypes	0.008	0.000	0.007
as.hypotheses	0.004	0.000	0.003
as.joint.probs	0.024	0.000	0.024
as.kfold.eloss	0.152	0.004	0.153
as.kfold.posterr	0.236	0.008	0.242
as.kfold.prederr	0.096	0.004	0.102
as.marginal.probs	0.016	0.000	0.015
as.models	0.008	0.008	0.015
as.parameters	0.004	0.000	0.002
as.pathway	0.004	0.000	0.005
as.patterns	0.000	0.000	0.002
as.samples	0.000	0.000	0.001
as.selective.advantage.relations	0.164	0.004	0.166
as.stages	0.024	0.000	0.024
as.types	0.000	0.000	0.002
as.types.in.patterns	0.000	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	0.004
delete.gene	0.004	0.000	0.004
delete.hypothesis	0.072	0.000	0.069
delete.model	0.004	0.000	0.003
delete.pattern	0.008	0.008	0.018
delete.samples	0.012	0.000	0.012
delete.type	0.004	0.000	0.005
duplicates	0.004	0.000	0.001
enforce.numeric	0.000	0.000	0.002
enforce.string	0.000	0.000	0.002
events.selection	0.052	0.000	0.050
export.graphml	0.544	0.004	0.584
export.mutex	0.064	0.000	0.064
has.duplicates	0.004	0.000	0.002
has.model	0.000	0.000	0.001
has.stages	0.004	0.004	0.005
import.GISTIC	0.148	0.000	0.148
import.MAF	0.128	0.004	0.131
intersect.datasets	0.000	0.000	0.001
is.compliant	0.000	0.000	0.001
join.events	0.024	0.000	0.024
join.types	0.084	0.000	0.081
keysToNames	0.004	0.000	0.005
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	0.001
npatterns	0.000	0.000	0.001
nsamples	0.000	0.000	0.001
ntypes	0.000	0.000	0.001
oncoprint.cbio	0.008	0.000	0.005
order.frequency	0.008	0.000	0.007
pheatmap	0.888	0.000	0.891
rank.recurrents	0.000	0.000	0.004
rename.gene	0.000	0.000	0.002
rename.type	0.016	0.004	0.018
samples.selection	0.004	0.000	0.003
trim	0.004	0.000	0.003
tronco.bootstrap	0.200	0.164	20.125
tronco.caprese	0.284	0.000	0.288
tronco.capri	2.688	0.016	2.706
tronco.chowliu	1.588	0.000	1.590
tronco.edmonds	1.164	0.004	1.171
tronco.gabow	1.284	0.000	1.286
tronco.kfold.eloss	0.300	0.004	0.303
tronco.kfold.posterr	0.580	0.132	8.798
tronco.kfold.prederr	0.176	0.168	8.238
tronco.plot	0.760	0.004	0.764
tronco.prim	2.416	0.032	2.449
view	0.004	0.000	0.004
which.samples	0.004	0.000	0.003