BioC 3.3: CHECK report for TRONCO on oaxaca

Package: TRONCO

Version: 2.4.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.4.3.tar.gz

StartedAt: 2016-10-13 07:02:37 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:07:44 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 306.3 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/TRONCO.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.4.3’
* 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 0.254  0.059   6.078
tronco.kfold.prederr 0.175  0.048   6.130
tronco.bootstrap     0.178  0.029  20.296
* 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	0.020	0.002	0.022
TCGA.remove.multiple.samples	0.024	0.005	0.030
TCGA.shorten.barcodes	0.020	0.005	0.025
annotate.description	0.017	0.006	0.023
annotate.stages	0.008	0.001	0.009
as.adj.matrix	0.013	0.007	0.020
as.alterations	0.004	0.000	0.005
as.bootstrap.scores	0.074	0.003	0.076
as.colors	0.002	0.000	0.002
as.confidence	0.015	0.010	0.024
as.description	0.001	0.000	0.003
as.events	0.002	0.000	0.003
as.events.in.patterns	0.005	0.001	0.006
as.events.in.sample	0.004	0.001	0.005
as.gene	0.005	0.001	0.006
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.006	0.001	0.007
as.genotypes	0.009	0.003	0.012
as.hypotheses	0.006	0.003	0.009
as.joint.probs	0.011	0.006	0.016
as.kfold.eloss	0.103	0.004	0.108
as.kfold.posterr	0.078	0.004	0.082
as.kfold.prederr	0.165	0.003	0.170
as.marginal.probs	0.006	0.001	0.008
as.models	0.025	0.019	0.045
as.parameters	0.003	0.001	0.004
as.pathway	0.008	0.001	0.009
as.patterns	0.003	0.001	0.004
as.samples	0.003	0.001	0.003
as.selective.advantage.relations	0.178	0.006	0.185
as.stages	0.012	0.002	0.014
as.types	0.002	0.000	0.003
as.types.in.patterns	0.007	0.001	0.007
change.color	0.003	0.001	0.003
consolidate.data	0.050	0.001	0.051
delete.event	0.007	0.001	0.008
delete.gene	0.008	0.001	0.009
delete.hypothesis	0.051	0.015	0.064
delete.model	0.005	0.001	0.006
delete.pattern	0.017	0.005	0.022
delete.samples	0.005	0.001	0.005
delete.type	0.007	0.000	0.008
duplicates	0.003	0.000	0.004
enforce.numeric	0.004	0.001	0.005
enforce.string	0.004	0.001	0.005
events.selection	0.007	0.001	0.008
export.graphml	0.274	0.006	0.281
export.mutex	0.012	0.001	0.013
has.duplicates	0.002	0.000	0.003
has.model	0.002	0.001	0.003
has.stages	0.009	0.001	0.010
import.GISTIC	0.009	0.001	0.008
import.MAF	0.108	0.002	0.111
intersect.datasets	0.004	0.001	0.006
is.compliant	0.002	0.001	0.004
join.events	0.007	0.001	0.008
join.types	0.087	0.008	0.096
keysToNames	0.009	0.001	0.011
nameToKey	0.004	0.001	0.004
nevents	0.002	0.000	0.002
ngenes	0.001	0.000	0.002
nhypotheses	0.002	0.001	0.002
npatterns	0.002	0.001	0.002
nsamples	0.001	0.000	0.002
ntypes	0.002	0.000	0.002
oncoprint.cbio	0.010	0.001	0.011
order.frequency	0.010	0.006	0.015
pheatmap	0.140	0.001	0.142
rank.recurrents	0.006	0.001	0.006
rename.gene	0.004	0.001	0.004
rename.type	0.003	0.001	0.004
samples.selection	0.004	0.000	0.004
trim	0.005	0.001	0.006
tronco.bootstrap	0.178	0.029	20.296
tronco.caprese	0.191	0.005	0.195
tronco.capri	2.826	0.027	2.858
tronco.chowliu	2.090	0.014	2.138
tronco.edmonds	2.476	0.018	2.496
tronco.gabow	2.497	0.017	2.518
tronco.kfold.eloss	0.290	0.029	0.320
tronco.kfold.posterr	0.254	0.059	6.078
tronco.kfold.prederr	0.175	0.048	6.130
tronco.plot	0.180	0.003	0.183
tronco.prim	3.515	0.022	3.540
view	0.006	0.000	0.006
which.samples	0.004	0.001	0.005