BioC 3.3: CHECK report for TRONCO on zin2

Package: TRONCO

Version: 2.4.3

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.4.3.tar.gz

StartedAt: 2016-10-13 07:37:15 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:41:02 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 227.4 seconds

RetCode: 0

Status:  OK

CheckDir: TRONCO.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.4.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/TRONCO.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.4.3’
* 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.bootstrap 0.231  0.037  18.492
* 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	0.018	0.000	0.019
TCGA.remove.multiple.samples	0.021	0.004	0.025
TCGA.shorten.barcodes	0.012	0.004	0.016
annotate.description	0.014	0.000	0.014
annotate.stages	0.010	0.000	0.009
as.adj.matrix	0.016	0.000	0.015
as.alterations	0.002	0.000	0.006
as.bootstrap.scores	0.071	0.000	0.070
as.colors	0.001	0.000	0.002
as.confidence	0.018	0.000	0.017
as.description	0.002	0.000	0.002
as.events	0.001	0.004	0.003
as.events.in.patterns	0.003	0.000	0.005
as.events.in.sample	0.005	0.000	0.004
as.gene	0.004	0.000	0.004
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.005	0.000	0.005
as.genotypes	0.01	0.00	0.01
as.hypotheses	0.005	0.000	0.004
as.joint.probs	0.012	0.000	0.013
as.kfold.eloss	0.104	0.004	0.108
as.kfold.posterr	0.066	0.008	0.073
as.kfold.prederr	0.129	0.000	0.130
as.marginal.probs	0.005	0.000	0.004
as.models	0.024	0.000	0.024
as.parameters	0.003	0.000	0.003
as.pathway	0.005	0.000	0.005
as.patterns	0.002	0.000	0.002
as.samples	0.002	0.000	0.001
as.selective.advantage.relations	0.124	0.004	0.128
as.stages	0.009	0.000	0.009
as.types	0.002	0.000	0.002
as.types.in.patterns	0.001	0.004	0.004
change.color	0.003	0.000	0.003
consolidate.data	0.033	0.000	0.033
delete.event	0.006	0.000	0.005
delete.gene	0.007	0.000	0.007
delete.hypothesis	0.035	0.004	0.039
delete.model	0.000	0.000	0.003
delete.pattern	0.011	0.004	0.015
delete.samples	0.000	0.000	0.004
delete.type	0.005	0.000	0.005
duplicates	0.003	0.000	0.003
enforce.numeric	0.003	0.000	0.003
enforce.string	0.003	0.000	0.003
events.selection	0.005	0.000	0.005
export.graphml	0.197	0.004	0.216
export.mutex	0.009	0.000	0.009
has.duplicates	0.002	0.000	0.001
has.model	0.002	0.000	0.002
has.stages	0.006	0.000	0.006
import.GISTIC	0.002	0.000	0.006
import.MAF	0.083	0.008	0.090
intersect.datasets	0.001	0.000	0.001
is.compliant	0.004	0.000	0.004
join.events	0.006	0.000	0.006
join.types	0.066	0.008	0.074
keysToNames	0.006	0.000	0.006
nameToKey	0.003	0.000	0.003
nevents	0.002	0.000	0.002
ngenes	0.002	0.000	0.002
nhypotheses	0.001	0.000	0.001
npatterns	0.002	0.000	0.002
nsamples	0.002	0.000	0.002
ntypes	0.002	0.000	0.002
oncoprint.cbio	0.005	0.000	0.009
order.frequency	0.008	0.004	0.012
pheatmap	0.055	0.000	0.055
rank.recurrents	0.000	0.004	0.004
rename.gene	0.003	0.000	0.003
rename.type	0.003	0.000	0.003
samples.selection	0.005	0.000	0.004
trim	0.004	0.000	0.004
tronco.bootstrap	0.231	0.037	18.492
tronco.caprese	0.188	0.004	0.192
tronco.capri	2.030	0.008	2.039
tronco.chowliu	1.772	0.004	1.789
tronco.edmonds	1.760	0.004	1.766
tronco.gabow	2.026	0.003	2.044
tronco.kfold.eloss	0.202	0.008	0.210
tronco.kfold.posterr	0.168	0.065	4.279
tronco.kfold.prederr	0.133	0.067	4.706
tronco.plot	0.170	0.000	0.171
tronco.prim	2.714	0.028	2.801
view	0.005	0.000	0.004
which.samples	0.003	0.000	0.004