BioC 3.2: CHECK report for TRONCO on oaxaca

Package: TRONCO

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.2.0.tar.gz

StartedAt: 2015-10-27 08:42:22 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:44:00 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 97.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TRONCO.Rcheck

Warnings: 2

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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_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/TRONCO.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.2.0’
* 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 ... [6s/6s] 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 ... WARNING
Error: .onLoad failed in loadNamespace() for 'bnlearn', details:
  call: setMethod("nodes", cl, function(object) .nodes(object))
  error: no existing definition for function ‘nodes’
Execution halted

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... WARNING
Error: .onLoad failed in loadNamespace() for 'bnlearn', details:
  call: setMethod("nodes", cl, function(object) .nodes(object))
  error: no existing definition for function ‘nodes’
Execution halted
* 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 ... NOTE
Error: .onLoad failed in loadNamespace() for 'bnlearn', details:
  call: setMethod("nodes", cl, function(object) .nodes(object))
  error: no existing definition for function ‘nodes’
Execution halted
* 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 ... [20s/31s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
tronco.bootstrap 6.003  0.121  17.036
tronco.capri     5.980  0.087   6.073
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [2s/2s]
 [2s/2s] 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/TRONCO.Rcheck/00check.log’
for details.

* 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
annotate.description	0.014	0.004	0.018
annotate.stages	0.012	0.002	0.014
as.adj.matrix	0.013	0.003	0.015
as.alterations	0.011	0.001	0.012
as.colors	0.002	0.000	0.003
as.confidence	0.009	0.003	0.012
as.description	0.002	0.001	0.002
as.events	0.003	0.001	0.004
as.events.in.patterns	0.008	0.001	0.009
as.events.in.sample	0.004	0.000	0.006
as.gene	0.006	0.002	0.008
as.genes	0.002	0.000	0.003
as.genes.in.patterns	0.008	0.001	0.009
as.genotypes	0.011	0.003	0.014
as.hypotheses	0.006	0.002	0.006
as.joint.probs	0.009	0.002	0.011
as.marginal.probs	0.008	0.001	0.008
as.models	0.009	0.004	0.013
as.pathway	0.008	0.000	0.009
as.patterns	0.002	0.000	0.003
as.samples	0.001	0.000	0.002
as.selective.advantage.relations	0.151	0.003	0.154
as.stages	0.012	0.001	0.013
as.types	0.003	0.001	0.003
as.types.in.patterns	0.011	0.000	0.012
change.color	0.002	0.000	0.002
delete.event	0.009	0.000	0.010
delete.gene	0.010	0.000	0.011
delete.hypothesis	0.041	0.010	0.051
delete.model	0.006	0.001	0.006
delete.pattern	0.013	0.003	0.016
delete.samples	0.006	0.001	0.006
delete.type	0.013	0.001	0.013
duplicates	0.004	0.000	0.004
enforce.numeric	0.003	0.000	0.004
enforce.string	0.003	0.001	0.004
events.selection	0.008	0.000	0.008
export.mutex	0.024	0.003	0.027
has.duplicates	0.003	0.000	0.003
has.model	0.002	0.001	0.002
has.stages	0.008	0.000	0.008
import.GISTIC	0.139	0.003	0.144
import.MAF	0.163	0.001	0.165
intersect.datasets	0.001	0.001	0.002
keysToNames	0.010	0.001	0.010
merge.events	0.006	0.001	0.006
merge.types	0.079	0.012	0.091
nevents	0.002	0.001	0.002
ngenes	0.002	0.001	0.003
nhypotheses	0.001	0.000	0.003
npatterns	0.002	0.000	0.003
nsamples	0.002	0.001	0.003
ntypes	0.002	0.001	0.002
oncoprint.cbio	0.022	0.002	0.024
pheatmap	4.594	0.027	4.630
rank.recurrents	0.005	0.000	0.005
rename.gene	0.003	0.001	0.003
rename.type	0.004	0.000	0.004
samples.selection	0.004	0.001	0.004
show	0.005	0.000	0.006
sort.by.frequency	0.009	0.003	0.012
trim	0.004	0.000	0.005
tronco.bootstrap	6.003	0.121	17.036
tronco.caprese	0.153	0.003	0.157
tronco.capri	5.980	0.087	6.073
tronco.plot	0.113	0.003	0.117
which.samples	0.004	0.000	0.005