BioC 3.5: CHECK report for TRONCO on veracruz2

Package: TRONCO

Version: 2.8.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.8.2.tar.gz

StartedAt: 2017-10-18 09:55:08 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:59:40 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 272.2 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_2.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TRONCO.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TRONCO/DESCRIPTION’ ... OK
* this is package ‘TRONCO’ version ‘2.8.2’
* 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.kfold.posterr 0.581  0.060   6.566
tronco.bootstrap     0.158  0.019  18.881
tronco.kfold.prederr 0.123  0.046   5.779
* 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	0.017	0.002	0.020
TCGA.remove.multiple.samples	0.112	0.007	0.123
TCGA.shorten.barcodes	0.016	0.006	0.023
annotate.description	0.014	0.006	0.021
annotate.stages	0.010	0.002	0.012
as.adj.matrix	0.056	0.007	0.066
as.alterations	0.004	0.000	0.005
as.bootstrap.scores	0.221	0.003	0.229
as.colors	0.002	0.001	0.003
as.confidence	0.068	0.009	0.079
as.description	0.002	0.001	0.003
as.events	0.003	0.002	0.004
as.events.in.patterns	0.030	0.001	0.032
as.events.in.sample	0.005	0.001	0.006
as.gene	0.004	0.001	0.006
as.genes	0.002	0.001	0.001
as.genes.in.patterns	0.006	0.001	0.007
as.genotypes	0.010	0.005	0.016
as.hypotheses	0.006	0.002	0.009
as.joint.probs	0.030	0.007	0.038
as.kfold.eloss	0.174	0.005	0.184
as.kfold.posterr	0.293	0.012	0.314
as.kfold.prederr	0.147	0.012	0.172
as.marginal.probs	0.024	0.001	0.031
as.models	0.021	0.019	0.041
as.parameters	0.002	0.001	0.004
as.pathway	0.005	0.001	0.007
as.patterns	0.002	0.001	0.004
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.241	0.006	0.252
as.stages	0.037	0.001	0.041
as.types	0.001	0.000	0.002
as.types.in.patterns	0.005	0.001	0.006
change.color	0.002	0.001	0.003
consolidate.data	0.046	0.002	0.049
delete.event	0.006	0.001	0.007
delete.gene	0.007	0.001	0.007
delete.hypothesis	0.098	0.015	0.114
delete.model	0.004	0.001	0.004
delete.pattern	0.017	0.005	0.023
delete.samples	0.020	0.001	0.021
delete.type	0.005	0.001	0.006
duplicates	0.002	0.001	0.003
enforce.numeric	0.003	0.001	0.004
enforce.string	0.003	0.000	0.005
events.selection	0.072	0.001	0.075
export.graphml	0.749	0.009	0.777
export.mutex	0.086	0.001	0.104
has.duplicates	0.002	0.001	0.002
has.model	0.001	0.000	0.002
has.stages	0.005	0.000	0.006
import.GISTIC	0.196	0.001	0.209
import.MAF	0.196	0.004	0.211
intersect.datasets	0.001	0.001	0.002
is.compliant	0.002	0.000	0.002
join.events	0.033	0.001	0.037
join.types	0.117	0.008	0.130
keysToNames	0.009	0.002	0.010
nameToKey	0.004	0.001	0.005
nevents	0.002	0.001	0.002
ngenes	0.001	0.000	0.002
nhypotheses	0.001	0.001	0.003
npatterns	0.001	0.001	0.001
nsamples	0.001	0.000	0.002
ntypes	0.001	0.001	0.001
oncoprint.cbio	0.007	0.000	0.009
order.frequency	0.010	0.005	0.016
pheatmap	1.103	0.007	1.171
rank.recurrents	0.004	0.001	0.004
rename.gene	0.003	0.001	0.003
rename.type	0.025	0.001	0.026
samples.selection	0.004	0.001	0.005
trim	0.003	0.000	0.004
tronco.bootstrap	0.158	0.019	18.881
tronco.caprese	0.352	0.004	0.359
tronco.capri	3.360	0.040	3.525
tronco.chowliu	2.636	0.037	2.814
tronco.edmonds	1.663	0.015	1.734
tronco.gabow	1.665	0.014	1.718
tronco.kfold.eloss	0.447	0.031	0.501
tronco.kfold.posterr	0.581	0.060	6.566
tronco.kfold.prederr	0.123	0.046	5.779
tronco.plot	0.999	0.005	1.031
tronco.prim	2.961	0.046	3.087
view	0.005	0.001	0.006
which.samples	0.004	0.001	0.005