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: 2016-04-23 05:08:55 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:10:29 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 93.8 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 3.2.4 (2016-03-10)
* 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/32s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
tronco.capri     6.152  0.086   6.245
tronco.bootstrap 5.429  0.118  17.690
* 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	0.016	0.005	0.022
annotate.stages	0.010	0.003	0.013
as.adj.matrix	0.013	0.002	0.015
as.alterations	0.007	0.001	0.008
as.colors	0.002	0.001	0.003
as.confidence	0.008	0.004	0.011
as.description	0.002	0.001	0.003
as.events	0.003	0.002	0.005
as.events.in.patterns	0.005	0.001	0.007
as.events.in.sample	0.004	0.001	0.005
as.gene	0.004	0.001	0.006
as.genes	0.001	0.000	0.002
as.genes.in.patterns	0.007	0.001	0.007
as.genotypes	0.009	0.002	0.012
as.hypotheses	0.005	0.002	0.007
as.joint.probs	0.008	0.002	0.011
as.marginal.probs	0.006	0.001	0.008
as.models	0.009	0.005	0.013
as.pathway	0.008	0.001	0.009
as.patterns	0.003	0.001	0.004
as.samples	0.003	0.002	0.004
as.selective.advantage.relations	0.141	0.003	0.144
as.stages	0.011	0.002	0.012
as.types	0.003	0.001	0.003
as.types.in.patterns	0.006	0.001	0.007
change.color	0.003	0.001	0.005
delete.event	0.008	0.001	0.009
delete.gene	0.009	0.001	0.010
delete.hypothesis	0.035	0.010	0.045
delete.model	0.003	0.001	0.003
delete.pattern	0.014	0.003	0.016
delete.samples	0.003	0.001	0.005
delete.type	0.008	0.001	0.008
duplicates	0.003	0.001	0.003
enforce.numeric	0.003	0.001	0.004
enforce.string	0.003	0.001	0.004
events.selection	0.011	0.001	0.013
export.mutex	0.024	0.003	0.028
has.duplicates	0.002	0.001	0.004
has.model	0.002	0.001	0.003
has.stages	0.010	0.001	0.011
import.GISTIC	0.140	0.004	0.144
import.MAF	0.099	0.003	0.102
intersect.datasets	0.002	0.000	0.002
keysToNames	0.010	0.001	0.011
merge.events	0.006	0.001	0.007
merge.types	0.079	0.008	0.087
nevents	0.002	0.001	0.003
ngenes	0.002	0.001	0.003
nhypotheses	0.002	0.001	0.002
npatterns	0.002	0.001	0.003
nsamples	0.002	0.001	0.003
ntypes	0.002	0.001	0.003
oncoprint.cbio	0.022	0.001	0.023
pheatmap	4.525	0.028	4.559
rank.recurrents	0.005	0.001	0.005
rename.gene	0.004	0.001	0.004
rename.type	0.003	0.001	0.004
samples.selection	0.004	0.001	0.004
show	0.005	0.001	0.007
sort.by.frequency	0.009	0.004	0.013
trim	0.005	0.001	0.006
tronco.bootstrap	5.429	0.118	17.690
tronco.caprese	0.226	0.005	0.231
tronco.capri	6.152	0.086	6.245
tronco.plot	0.106	0.002	0.109
which.samples	0.005	0.001	0.006