BioC 3.2: CHECK report for TRONCO on zin1

Package: TRONCO

Version: 2.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.2.0.tar.gz

StartedAt: 2016-04-23 06:18:29 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 06:19:34 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 65.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TRONCO.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings TRONCO_2.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/TRONCO.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ... [4s/4s] 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 ... [14s/22s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
tronco.bootstrap 3.976  0.055   12.54
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [1s/1s]
 [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
  ‘/home/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	0.009	0.005	0.013
annotate.stages	0.01	0.00	0.01
as.adj.matrix	0.005	0.004	0.009
as.alterations	0.005	0.000	0.004
as.colors	0.002	0.000	0.002
as.confidence	0.004	0.003	0.008
as.description	0.002	0.001	0.001
as.events	0.002	0.000	0.003
as.events.in.patterns	0.006	0.000	0.006
as.events.in.sample	0.003	0.000	0.004
as.gene	0.008	0.000	0.007
as.genes	0.001	0.000	0.002
as.genes.in.patterns	0.005	0.000	0.005
as.genotypes	0.007	0.000	0.007
as.hypotheses	0.004	0.000	0.003
as.joint.probs	0.002	0.004	0.006
as.marginal.probs	0.004	0.000	0.005
as.models	0.003	0.004	0.006
as.pathway	0.003	0.001	0.006
as.patterns	0.003	0.000	0.002
as.samples	0.002	0.000	0.002
as.selective.advantage.relations	0.093	0.000	0.092
as.stages	0.007	0.000	0.008
as.types	0.002	0.000	0.002
as.types.in.patterns	0.005	0.000	0.004
change.color	0.002	0.000	0.003
delete.event	0.005	0.000	0.005
delete.gene	0.003	0.001	0.005
delete.hypothesis	0.016	0.012	0.028
delete.model	0.003	0.000	0.004
delete.pattern	0.011	0.000	0.010
delete.samples	0.003	0.000	0.003
delete.type	0.002	0.001	0.006
duplicates	0.003	0.000	0.002
enforce.numeric	0.002	0.000	0.003
enforce.string	0.003	0.000	0.003
events.selection	0.006	0.000	0.006
export.mutex	0.018	0.000	0.019
has.duplicates	0.002	0.000	0.002
has.model	0.002	0.000	0.003
has.stages	0.007	0.000	0.007
import.GISTIC	0.102	0.000	0.102
import.MAF	0.070	0.000	0.069
intersect.datasets	0.001	0.000	0.001
keysToNames	0.002	0.001	0.006
merge.events	0.004	0.000	0.004
merge.types	0.053	0.007	0.061
nevents	0.001	0.000	0.001
ngenes	0.002	0.000	0.002
nhypotheses	0.001	0.000	0.001
npatterns	0.002	0.000	0.002
nsamples	0.002	0.000	0.001
ntypes	0.001	0.000	0.002
oncoprint.cbio	0.010	0.001	0.013
pheatmap	3.572	0.024	3.603
rank.recurrents	0.005	0.000	0.004
rename.gene	0.003	0.000	0.003
rename.type	0.003	0.000	0.003
samples.selection	0.004	0.000	0.004
show	0.004	0.000	0.005
sort.by.frequency	0.008	0.000	0.008
trim	0.004	0.000	0.004
tronco.bootstrap	3.976	0.055	12.540
tronco.caprese	0.170	0.000	0.169
tronco.capri	3.915	0.008	3.920
tronco.plot	0.087	0.000	0.087
which.samples	0.003	0.000	0.003