BioC 3.4: CHECK report for TRONCO on morelia

Package: TRONCO

Version: 2.5.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.5.2.tar.gz

StartedAt: 2016-09-20 14:07:09 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 14:10:38 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 208.4 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.5.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-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 ‘2.5.2’
* 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 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.bootstrap 0.143  0.026  15.736
* 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	0.019	0.003	0.022
TCGA.remove.multiple.samples	0.024	0.005	0.029
TCGA.shorten.barcodes	0.014	0.004	0.019
annotate.description	0.016	0.006	0.023
annotate.stages	0.011	0.002	0.013
as.adj.matrix	0.013	0.007	0.020
as.alterations	0.004	0.001	0.005
as.bootstrap.scores	0.090	0.003	0.093
as.colors	0.001	0.000	0.002
as.confidence	0.014	0.009	0.022
as.description	0.002	0.001	0.002
as.events	0.003	0.001	0.004
as.events.in.patterns	0.006	0.000	0.007
as.events.in.sample	0.005	0.000	0.006
as.gene	0.005	0.001	0.006
as.genes	0.001	0.000	0.003
as.genes.in.patterns	0.006	0.001	0.006
as.genotypes	0.009	0.003	0.012
as.hypotheses	0.005	0.002	0.006
as.joint.probs	0.010	0.005	0.015
as.kfold.eloss	0.132	0.004	0.136
as.kfold.posterr	0.065	0.004	0.070
as.kfold.prederr	0.121	0.002	0.124
as.marginal.probs	0.003	0.000	0.004
as.models	0.015	0.012	0.025
as.parameters	0.002	0.000	0.003
as.pathway	0.005	0.001	0.005
as.patterns	0.002	0.000	0.002
as.samples	0.001	0.000	0.001
as.selective.advantage.relations	0.118	0.005	0.123
as.stages	0.007	0.001	0.008
as.types	0.002	0.001	0.002
as.types.in.patterns	0.004	0.000	0.004
change.color	0.002	0.001	0.003
consolidate.data	0.028	0.000	0.029
delete.event	0.007	0.000	0.007
delete.gene	0.004	0.001	0.005
delete.hypothesis	0.037	0.012	0.049
delete.model	0.003	0.000	0.003
delete.pattern	0.012	0.003	0.016
delete.samples	0.003	0.000	0.003
delete.type	0.004	0.001	0.005
duplicates	0.002	0.000	0.002
enforce.numeric	0.002	0.001	0.003
enforce.string	0.002	0.000	0.002
events.selection	0.005	0.001	0.006
export.graphml	0.165	0.003	0.168
export.mutex	0.007	0.001	0.008
has.duplicates	0.001	0.001	0.002
has.model	0.002	0.000	0.002
has.stages	0.006	0.001	0.006
import.GISTIC	0.005	0.000	0.005
import.MAF	0.081	0.002	0.083
intersect.datasets	0.001	0.001	0.002
is.compliant	0.002	0.000	0.003
join.events	0.005	0.001	0.004
join.types	0.053	0.005	0.058
keysToNames	0.005	0.001	0.006
nameToKey	0.003	0.000	0.003
nevents	0.001	0.001	0.002
ngenes	0.002	0.000	0.002
nhypotheses	0.002	0.000	0.002
npatterns	0.001	0.001	0.002
nsamples	0.001	0.000	0.002
ntypes	0.002	0.001	0.002
oncoprint.cbio	0.006	0.001	0.007
order.frequency	0.008	0.003	0.011
pheatmap	0.109	0.000	0.111
rank.recurrents	0.003	0.001	0.003
rename.gene	0.002	0.000	0.002
rename.type	0.002	0.001	0.003
samples.selection	0.004	0.000	0.005
trim	0.003	0.000	0.004
tronco.bootstrap	0.143	0.026	15.736
tronco.caprese	0.116	0.003	0.119
tronco.capri	1.869	0.023	1.891
tronco.kfold.eloss	0.207	0.028	0.253
tronco.kfold.posterr	0.230	0.056	4.572
tronco.kfold.prederr	0.125	0.039	4.282
tronco.mst.chowliu	1.771	0.021	1.811
tronco.mst.edmonds	1.893	0.014	1.932
tronco.mst.prim	2.187	0.025	2.212
tronco.plot	0.233	0.009	0.242
view	0.003	0.000	0.004
which.samples	0.003	0.001	0.003