BioC 3.5: CHECK report for TRONCO on veracruz2

Package: TRONCO

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.8.0.tar.gz

StartedAt: 2017-08-16 09:03:22 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 09:07:44 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 262.9 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_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/TRONCO.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.8.0’
* 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 ... 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 0.578  0.054   6.527
tronco.bootstrap     0.189  0.020  17.040
tronco.kfold.prederr 0.138  0.048   6.411
* 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	0.018	0.003	0.021
TCGA.remove.multiple.samples	0.105	0.006	0.112
TCGA.shorten.barcodes	0.016	0.006	0.023
annotate.description	0.011	0.003	0.015
annotate.stages	0.008	0.001	0.009
as.adj.matrix	0.044	0.006	0.055
as.alterations	0.005	0.001	0.006
as.bootstrap.scores	0.188	0.001	0.200
as.colors	0.001	0.000	0.002
as.confidence	0.058	0.010	0.071
as.description	0.001	0.000	0.002
as.events	0.002	0.000	0.004
as.events.in.patterns	0.028	0.000	0.028
as.events.in.sample	0.004	0.001	0.005
as.gene	0.005	0.002	0.007
as.genes	0.002	0.001	0.003
as.genes.in.patterns	0.005	0.001	0.007
as.genotypes	0.008	0.003	0.011
as.hypotheses	0.004	0.002	0.008
as.joint.probs	0.027	0.006	0.039
as.kfold.eloss	0.164	0.004	0.175
as.kfold.posterr	0.271	0.010	0.291
as.kfold.prederr	0.133	0.011	0.143
as.marginal.probs	0.016	0.001	0.018
as.models	0.018	0.015	0.033
as.parameters	0.003	0.001	0.004
as.pathway	0.007	0.001	0.008
as.patterns	0.002	0.000	0.002
as.samples	0.002	0.001	0.003
as.selective.advantage.relations	0.232	0.006	0.240
as.stages	0.030	0.002	0.032
as.types	0.002	0.000	0.003
as.types.in.patterns	0.006	0.000	0.007
change.color	0.002	0.001	0.003
consolidate.data	0.030	0.001	0.031
delete.event	0.004	0.000	0.005
delete.gene	0.004	0.001	0.005
delete.hypothesis	0.083	0.011	0.094
delete.model	0.002	0.000	0.004
delete.pattern	0.030	0.005	0.040
delete.samples	0.017	0.001	0.017
delete.type	0.004	0.001	0.005
duplicates	0.003	0.001	0.004
enforce.numeric	0.002	0.000	0.003
enforce.string	0.004	0.000	0.006
events.selection	0.065	0.003	0.069
export.graphml	0.639	0.008	0.672
export.mutex	0.069	0.001	0.075
has.duplicates	0.002	0.000	0.003
has.model	0.001	0.001	0.001
has.stages	0.005	0.001	0.006
import.GISTIC	0.186	0.001	0.198
import.MAF	0.144	0.002	0.148
intersect.datasets	0.001	0.000	0.002
is.compliant	0.003	0.000	0.003
join.events	0.029	0.001	0.030
join.types	0.097	0.007	0.106
keysToNames	0.008	0.002	0.010
nameToKey	0.003	0.001	0.004
nevents	0.001	0.001	0.002
ngenes	0.002	0.000	0.002
nhypotheses	0.001	0.000	0.002
npatterns	0.001	0.000	0.002
nsamples	0.002	0.000	0.002
ntypes	0.001	0.000	0.001
oncoprint.cbio	0.008	0.001	0.009
order.frequency	0.010	0.005	0.019
pheatmap	1.060	0.003	1.077
rank.recurrents	0.005	0.001	0.005
rename.gene	0.002	0.000	0.002
rename.type	0.018	0.001	0.020
samples.selection	0.004	0.001	0.004
trim	0.003	0.000	0.003
tronco.bootstrap	0.189	0.020	17.040
tronco.caprese	0.296	0.002	0.310
tronco.capri	2.719	0.036	2.795
tronco.chowliu	1.997	0.021	2.041
tronco.edmonds	1.171	0.011	1.198
tronco.gabow	1.474	0.018	1.514
tronco.kfold.eloss	0.343	0.027	0.382
tronco.kfold.posterr	0.578	0.054	6.527
tronco.kfold.prederr	0.138	0.048	6.411
tronco.plot	0.986	0.004	1.009
tronco.prim	3.141	0.042	3.276
view	0.013	0.001	0.014
which.samples	0.002	0.001	0.003