BioC 3.3: CHECK report for TRONCO on morelia

Package: TRONCO

Version: 2.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.3.0.tar.gz

StartedAt: 2016-04-21 08:19:34 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 08:24:02 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 267.6 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_2.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/TRONCO.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘2.3.0’
* 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 ... [5s/6s] 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 ... [16s/48s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
tronco.kfold.posterr 0.248  0.056   5.465
tronco.bootstrap     0.239  0.024  21.220
tronco.kfold.prederr 0.168  0.049   5.809
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [52s/142s]
 [52s/142s] 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	0.021	0.004	0.024
TCGA.remove.multiple.samples	0.030	0.007	0.037
TCGA.shorten.barcodes	0.015	0.004	0.019
annotate.description	0.015	0.005	0.020
annotate.stages	0.011	0.002	0.013
as.adj.matrix	0.009	0.005	0.014
as.alterations	0.004	0.001	0.005
as.bootstrap.scores	0.074	0.002	0.076
as.colors	0.002	0.001	0.002
as.confidence	0.014	0.008	0.022
as.description	0.002	0.001	0.002
as.events	0.003	0.001	0.004
as.events.in.patterns	0.007	0.001	0.009
as.events.in.sample	0.006	0.001	0.007
as.gene	0.005	0.002	0.006
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.007	0.001	0.007
as.genotypes	0.013	0.004	0.018
as.hypotheses	0.006	0.003	0.009
as.joint.probs	0.013	0.008	0.021
as.kfold.eloss	0.128	0.005	0.133
as.kfold.posterr	0.070	0.003	0.073
as.kfold.prederr	0.165	0.003	0.169
as.marginal.probs	0.007	0.002	0.008
as.models	0.022	0.017	0.038
as.parameters	0.003	0.001	0.004
as.pathway	0.008	0.001	0.008
as.patterns	0.003	0.001	0.003
as.samples	0.003	0.001	0.003
as.selective.advantage.relations	0.214	0.009	0.223
as.stages	0.011	0.001	0.012
as.types	0.002	0.001	0.003
as.types.in.patterns	0.008	0.001	0.009
change.color	0.004	0.001	0.005
consolidate.data	0.050	0.001	0.051
delete.event	0.012	0.001	0.013
delete.gene	0.007	0.000	0.008
delete.hypothesis	0.052	0.018	0.070
delete.model	0.005	0.001	0.005
delete.pattern	0.024	0.006	0.030
delete.samples	0.005	0.000	0.006
delete.type	0.008	0.000	0.009
duplicates	0.003	0.000	0.003
enforce.numeric	0.002	0.001	0.003
enforce.string	0.004	0.000	0.004
events.selection	0.007	0.001	0.008
export.graphml	0.263	0.005	0.298
export.mutex	0.013	0.001	0.014
has.duplicates	0.003	0.000	0.003
has.model	0.002	0.001	0.003
has.stages	0.009	0.002	0.011
import.GISTIC	0.009	0.000	0.009
import.MAF	0.119	0.003	0.122
intersect.datasets	0.002	0.001	0.003
is.compliant	0.003	0.001	0.003
join.events	0.008	0.000	0.008
join.types	0.078	0.008	0.086
keysToNames	0.009	0.002	0.011
nameToKey	0.004	0.001	0.005
nevents	0.002	0.001	0.003
ngenes	0.003	0.001	0.002
nhypotheses	0.002	0.001	0.003
npatterns	0.003	0.001	0.003
nsamples	0.002	0.000	0.002
ntypes	0.002	0.000	0.003
oncoprint.cbio	0.012	0.001	0.013
order.frequency	0.013	0.006	0.019
pheatmap	0.071	0.000	0.072
rank.recurrents	0.003	0.000	0.004
rename.gene	0.003	0.000	0.004
rename.type	0.003	0.001	0.003
samples.selection	0.009	0.001	0.009
trim	0.005	0.000	0.004
tronco.bootstrap	0.239	0.024	21.220
tronco.caprese	0.153	0.009	0.162
tronco.capri	2.531	0.028	2.562
tronco.kfold.eloss	0.252	0.021	0.273
tronco.kfold.posterr	0.248	0.056	5.465
tronco.kfold.prederr	0.168	0.049	5.809
tronco.mst.chowliu	2.099	0.016	2.143
tronco.mst.edmonds	2.334	0.020	2.480
tronco.mst.prim	3.616	0.044	3.671
tronco.plot	0.374	0.004	0.378
view	0.006	0.001	0.007
which.samples	0.005	0.001	0.005