BioC 3.4: CHECK report for TRONCO on morelia

Package: TRONCO

Version: 2.6.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.6.1.tar.gz

StartedAt: 2017-04-15 09:04:30 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 09:09:04 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 273.8 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_2.6.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/TRONCO.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.6.1’
* 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 0.239  0.056   5.163
tronco.kfold.prederr 0.166  0.048   5.264
tronco.bootstrap     0.182  0.029  21.537
* 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	0.019	0.004	0.022
TCGA.remove.multiple.samples	0.019	0.004	0.022
TCGA.shorten.barcodes	0.012	0.003	0.016
annotate.description	0.010	0.003	0.014
annotate.stages	0.008	0.001	0.009
as.adj.matrix	0.014	0.009	0.023
as.alterations	0.006	0.001	0.007
as.bootstrap.scores	0.070	0.002	0.071
as.colors	0.001	0.001	0.002
as.confidence	0.012	0.008	0.020
as.description	0.001	0.001	0.002
as.events	0.002	0.000	0.003
as.events.in.patterns	0.005	0.000	0.005
as.events.in.sample	0.005	0.001	0.005
as.gene	0.004	0.001	0.005
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.006	0.000	0.007
as.genotypes	0.010	0.003	0.013
as.hypotheses	0.007	0.003	0.010
as.joint.probs	0.014	0.007	0.020
as.kfold.eloss	0.091	0.003	0.095
as.kfold.posterr	0.118	0.002	0.120
as.kfold.prederr	0.059	0.004	0.064
as.marginal.probs	0.004	0.002	0.006
as.models	0.016	0.012	0.028
as.parameters	0.002	0.000	0.003
as.pathway	0.005	0.001	0.005
as.patterns	0.002	0.000	0.002
as.samples	0.001	0.000	0.002
as.selective.advantage.relations	0.140	0.004	0.144
as.stages	0.010	0.001	0.012
as.types	0.002	0.001	0.003
as.types.in.patterns	0.007	0.001	0.007
change.color	0.003	0.001	0.004
consolidate.data	0.052	0.001	0.054
delete.event	0.008	0.001	0.009
delete.gene	0.008	0.001	0.008
delete.hypothesis	0.046	0.014	0.059
delete.model	0.005	0.001	0.006
delete.pattern	0.018	0.004	0.022
delete.samples	0.004	0.000	0.005
delete.type	0.005	0.000	0.005
duplicates	0.002	0.001	0.002
enforce.numeric	0.007	0.000	0.008
enforce.string	0.004	0.000	0.005
events.selection	0.006	0.001	0.007
export.graphml	0.208	0.005	0.258
export.mutex	0.012	0.002	0.013
has.duplicates	0.003	0.000	0.003
has.model	0.003	0.000	0.003
has.stages	0.009	0.001	0.011
import.GISTIC	0.009	0.000	0.008
import.MAF	0.109	0.002	0.123
intersect.datasets	0.001	0.001	0.002
is.compliant	0.003	0.001	0.004
join.events	0.007	0.001	0.008
join.types	0.072	0.008	0.081
keysToNames	0.010	0.002	0.011
nameToKey	0.004	0.001	0.005
nevents	0.002	0.001	0.003
ngenes	0.002	0.000	0.003
nhypotheses	0.002	0.001	0.003
npatterns	0.002	0.001	0.002
nsamples	0.002	0.000	0.002
ntypes	0.001	0.000	0.002
oncoprint.cbio	0.010	0.001	0.011
order.frequency	0.011	0.005	0.017
pheatmap	0.136	0.001	0.138
rank.recurrents	0.005	0.001	0.005
rename.gene	0.003	0.000	0.003
rename.type	0.003	0.000	0.003
samples.selection	0.005	0.001	0.005
trim	0.006	0.001	0.006
tronco.bootstrap	0.182	0.029	21.537
tronco.caprese	0.224	0.005	0.229
tronco.capri	2.344	0.023	2.367
tronco.chowliu	1.869	0.016	1.900
tronco.edmonds	2.332	0.016	2.350
tronco.gabow	2.368	0.022	2.390
tronco.kfold.eloss	0.185	0.019	0.204
tronco.kfold.posterr	0.239	0.056	5.163
tronco.kfold.prederr	0.166	0.048	5.264
tronco.plot	0.180	0.002	0.183
tronco.prim	3.240	0.041	3.284
view	0.006	0.000	0.007
which.samples	0.004	0.001	0.004