BioC 3.5: CHECK report for TRONCO on toluca2

Package: TRONCO

Version: 2.7.10

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.7.10.tar.gz

StartedAt: 2017-04-23 10:58:11 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 11:03:26 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 314.8 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_2.7.10.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘2.7.10’
* 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 0.697  0.058   7.492
tronco.bootstrap     0.218  0.015  18.433
tronco.kfold.prederr 0.173  0.045   7.107
* 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	0.020	0.002	0.022
TCGA.remove.multiple.samples	0.135	0.005	0.141
TCGA.shorten.barcodes	0.017	0.005	0.022
annotate.description	0.016	0.006	0.021
annotate.stages	0.012	0.001	0.013
as.adj.matrix	0.072	0.007	0.080
as.alterations	0.006	0.001	0.007
as.bootstrap.scores	0.287	0.003	0.303
as.colors	0.001	0.000	0.002
as.confidence	0.076	0.008	0.085
as.description	0.001	0.000	0.003
as.events	0.003	0.001	0.004
as.events.in.patterns	0.034	0.001	0.034
as.events.in.sample	0.006	0.001	0.006
as.gene	0.006	0.002	0.007
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.007	0.001	0.008
as.genotypes	0.016	0.004	0.020
as.hypotheses	0.006	0.002	0.008
as.joint.probs	0.037	0.006	0.045
as.kfold.eloss	0.186	0.005	0.195
as.kfold.posterr	0.335	0.011	0.348
as.kfold.prederr	0.176	0.013	0.189
as.marginal.probs	0.027	0.001	0.028
as.models	0.023	0.017	0.040
as.parameters	0.003	0.000	0.004
as.pathway	0.007	0.001	0.008
as.patterns	0.003	0.001	0.003
as.samples	0.002	0.001	0.002
as.selective.advantage.relations	0.316	0.005	0.322
as.stages	0.044	0.001	0.045
as.types	0.002	0.001	0.003
as.types.in.patterns	0.006	0.001	0.006
change.color	0.003	0.000	0.003
consolidate.data	0.054	0.001	0.056
delete.event	0.008	0.001	0.009
delete.gene	0.008	0.000	0.008
delete.hypothesis	0.127	0.014	0.141
delete.model	0.004	0.001	0.006
delete.pattern	0.018	0.004	0.023
delete.samples	0.035	0.002	0.038
delete.type	0.007	0.001	0.007
duplicates	0.003	0.001	0.003
enforce.numeric	0.004	0.000	0.004
enforce.string	0.004	0.000	0.005
events.selection	0.093	0.002	0.102
export.graphml	0.961	0.016	1.004
export.mutex	0.111	0.002	0.117
has.duplicates	0.002	0.000	0.003
has.model	0.002	0.000	0.003
has.stages	0.009	0.002	0.010
import.GISTIC	0.268	0.001	0.280
import.MAF	0.222	0.004	0.229
intersect.datasets	0.001	0.001	0.002
is.compliant	0.002	0.000	0.003
join.events	0.046	0.001	0.047
join.types	0.134	0.007	0.142
keysToNames	0.009	0.002	0.010
nameToKey	0.003	0.000	0.004
nevents	0.002	0.000	0.003
ngenes	0.002	0.001	0.003
nhypotheses	0.002	0.000	0.003
npatterns	0.003	0.000	0.003
nsamples	0.002	0.001	0.002
ntypes	0.002	0.001	0.003
oncoprint.cbio	0.010	0.001	0.012
order.frequency	0.012	0.005	0.019
pheatmap	1.524	0.005	1.560
rank.recurrents	0.006	0.001	0.006
rename.gene	0.003	0.000	0.004
rename.type	0.029	0.001	0.030
samples.selection	0.005	0.001	0.006
trim	0.011	0.001	0.011
tronco.bootstrap	0.218	0.015	18.433
tronco.caprese	0.280	0.003	0.283
tronco.capri	3.942	0.032	3.977
tronco.chowliu	2.850	0.025	2.877
tronco.edmonds	1.965	0.015	1.988
tronco.gabow	2.281	0.017	2.351
tronco.kfold.eloss	0.520	0.028	0.562
tronco.kfold.posterr	0.697	0.058	7.492
tronco.kfold.prederr	0.173	0.045	7.107
tronco.plot	1.270	0.005	1.282
tronco.prim	3.678	0.042	3.845
view	0.006	0.001	0.006
which.samples	0.004	0.001	0.005