BioC 3.5: CHECK report for TRONCO on oaxaca

Package: TRONCO

Version: 2.7.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.7.3.tar.gz

StartedAt: 2017-01-31 08:41:30 -0800 (Tue, 31 Jan 2017)

EndedAt: 2017-01-31 08:45:37 -0800 (Tue, 31 Jan 2017)

EllapsedTime: 246.9 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_2.7.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2016-10-26 r71594)
* 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 ‘2.7.3’
* 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     0.302  0.023  21.477
tronco.kfold.posterr 0.218  0.048   5.334
tronco.kfold.prederr 0.171  0.047   5.548
* 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	0.021	0.002	0.025
TCGA.remove.multiple.samples	0.026	0.004	0.031
TCGA.shorten.barcodes	0.019	0.006	0.025
annotate.description	0.016	0.006	0.021
annotate.stages	0.012	0.001	0.014
as.adj.matrix	0.089	0.007	0.096
as.alterations	0.006	0.001	0.007
as.bootstrap.scores	0.049	0.006	0.055
as.colors	0.002	0.001	0.003
as.confidence	0.015	0.010	0.024
as.description	0.001	0.001	0.002
as.events	0.002	0.001	0.003
as.events.in.patterns	0.005	0.001	0.006
as.events.in.sample	0.004	0.001	0.005
as.gene	0.004	0.001	0.005
as.genes	0.001	0.001	0.002
as.genes.in.patterns	0.004	0.000	0.004
as.genotypes	0.012	0.004	0.016
as.hypotheses	0.006	0.002	0.008
as.joint.probs	0.012	0.008	0.020
as.kfold.eloss	0.055	0.004	0.059
as.kfold.posterr	0.145	0.002	0.146
as.kfold.prederr	0.076	0.003	0.079
as.marginal.probs	0.004	0.001	0.005
as.models	0.017	0.014	0.031
as.parameters	0.003	0.001	0.004
as.pathway	0.006	0.000	0.007
as.patterns	0.002	0.001	0.003
as.samples	0.007	0.001	0.008
as.selective.advantage.relations	0.163	0.009	0.171
as.stages	0.010	0.001	0.011
as.types	0.003	0.001	0.003
as.types.in.patterns	0.006	0.000	0.006
change.color	0.002	0.000	0.003
consolidate.data	0.030	0.001	0.030
delete.event	0.005	0.000	0.005
delete.gene	0.005	0.001	0.005
delete.hypothesis	0.034	0.010	0.044
delete.model	0.003	0.001	0.003
delete.pattern	0.016	0.004	0.020
delete.samples	0.002	0.001	0.003
delete.type	0.005	0.000	0.006
duplicates	0.002	0.001	0.002
enforce.numeric	0.003	0.000	0.003
enforce.string	0.002	0.001	0.003
events.selection	0.004	0.000	0.005
export.graphml	0.224	0.005	0.230
export.mutex	0.013	0.002	0.013
has.duplicates	0.002	0.000	0.003
has.model	0.003	0.000	0.003
has.stages	0.008	0.001	0.009
import.GISTIC	0.007	0.000	0.006
import.MAF	0.104	0.004	0.108
intersect.datasets	0.001	0.001	0.003
is.compliant	0.003	0.001	0.004
join.events	0.005	0.001	0.006
join.types	0.050	0.005	0.055
keysToNames	0.006	0.001	0.006
nameToKey	0.002	0.000	0.003
nevents	0.002	0.001	0.003
ngenes	0.002	0.001	0.003
nhypotheses	0.002	0.000	0.003
npatterns	0.002	0.000	0.003
nsamples	0.002	0.001	0.003
ntypes	0.002	0.001	0.003
oncoprint.cbio	0.011	0.001	0.012
order.frequency	0.012	0.005	0.016
pheatmap	0.071	0.001	0.071
rank.recurrents	0.006	0.001	0.006
rename.gene	0.003	0.001	0.004
rename.type	0.004	0.001	0.004
samples.selection	0.004	0.000	0.004
trim	0.005	0.000	0.006
tronco.bootstrap	0.302	0.023	21.477
tronco.caprese	0.217	0.014	0.232
tronco.capri	2.311	0.028	2.339
tronco.chowliu	2.128	0.013	2.159
tronco.edmonds	2.342	0.017	2.360
tronco.gabow	2.531	0.025	2.557
tronco.kfold.eloss	0.225	0.018	0.242
tronco.kfold.posterr	0.218	0.048	5.334
tronco.kfold.prederr	0.171	0.047	5.548
tronco.plot	0.189	0.003	0.192
tronco.prim	3.084	0.024	3.109
view	0.006	0.001	0.007
which.samples	0.004	0.001	0.005