BioC 3.4: CHECK report for TRONCO on zin1

Package: TRONCO

Version: 2.5.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.5.2.tar.gz

StartedAt: 2016-09-20 13:34:09 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:37:17 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 188.6 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_2.5.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-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 ‘2.5.2’
* 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 0.212  0.028  15.637
* 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	0.015
TCGA.remove.multiple.samples	0.024	0.000	0.021
TCGA.shorten.barcodes	0.012	0.000	0.014
annotate.description	0.012	0.000	0.013
annotate.stages	0.008	0.000	0.009
as.adj.matrix	0.012	0.004	0.013
as.alterations	0.004	0.000	0.005
as.bootstrap.scores	0.060	0.000	0.059
as.colors	0.000	0.000	0.001
as.confidence	0.008	0.008	0.014
as.description	0.000	0.004	0.002
as.events	0.000	0.000	0.003
as.events.in.patterns	0.004	0.000	0.005
as.events.in.sample	0.004	0.000	0.004
as.gene	0.004	0.000	0.003
as.genes	0.004	0.000	0.002
as.genes.in.patterns	0.004	0.000	0.005
as.genotypes	0.008	0.000	0.009
as.hypotheses	0.004	0.000	0.004
as.joint.probs	0.008	0.004	0.012
as.kfold.eloss	0.104	0.000	0.110
as.kfold.posterr	0.072	0.000	0.072
as.kfold.prederr	0.132	0.000	0.133
as.marginal.probs	0.004	0.000	0.004
as.models	0.020	0.000	0.023
as.parameters	0.000	0.000	0.003
as.pathway	0.004	0.000	0.006
as.patterns	0.004	0.000	0.001
as.samples	0.000	0.000	0.002
as.selective.advantage.relations	0.136	0.000	0.132
as.stages	0.004	0.000	0.007
as.types	0.000	0.000	0.001
as.types.in.patterns	0.004	0.000	0.004
change.color	0.000	0.000	0.002
consolidate.data	0.032	0.000	0.031
delete.event	0.008	0.000	0.007
delete.gene	0.008	0.000	0.005
delete.hypothesis	0.032	0.004	0.037
delete.model	0.000	0.004	0.004
delete.pattern	0.016	0.000	0.014
delete.samples	0.004	0.000	0.003
delete.type	0.004	0.000	0.005
duplicates	0.000	0.000	0.002
enforce.numeric	0.004	0.000	0.002
enforce.string	0.004	0.000	0.003
events.selection	0.008	0.000	0.006
export.graphml	0.196	0.004	0.199
export.mutex	0.008	0.000	0.008
has.duplicates	0.004	0.000	0.002
has.model	0.000	0.000	0.002
has.stages	0.004	0.000	0.007
import.GISTIC	0.008	0.000	0.005
import.MAF	0.088	0.000	0.087
intersect.datasets	0.000	0.000	0.001
is.compliant	0.004	0.000	0.002
join.events	0.004	0.000	0.005
join.types	0.064	0.000	0.064
keysToNames	0.004	0.000	0.005
nameToKey	0.004	0.000	0.003
nevents	0.000	0.000	0.002
ngenes	0.000	0.000	0.001
nhypotheses	0.004	0.000	0.001
npatterns	0.000	0.000	0.001
nsamples	0.004	0.000	0.001
ntypes	0.000	0.000	0.001
oncoprint.cbio	0.008	0.000	0.008
order.frequency	0.008	0.000	0.009
pheatmap	0.048	0.000	0.050
rank.recurrents	0.004	0.000	0.003
rename.gene	0.000	0.000	0.003
rename.type	0.004	0.000	0.005
samples.selection	0.004	0.000	0.003
trim	0.004	0.000	0.004
tronco.bootstrap	0.212	0.028	15.637
tronco.caprese	0.128	0.008	0.134
tronco.capri	1.900	0.000	1.902
tronco.kfold.eloss	0.188	0.008	0.195
tronco.kfold.posterr	0.136	0.048	3.627
tronco.kfold.prederr	0.132	0.016	3.635
tronco.mst.chowliu	1.552	0.004	1.556
tronco.mst.edmonds	1.656	0.004	1.661
tronco.mst.prim	2.340	0.008	2.349
tronco.plot	0.276	0.008	0.283
view	0.004	0.000	0.004
which.samples	0.000	0.000	0.002