BioC 3.3: CHECK report for TRONCO on morelia

Package: TRONCO

Version: 2.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings TRONCO_2.3.0.tar.gz

StartedAt: 2015-10-22 12:15:16 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 12:16:32 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 76.5 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_2.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/TRONCO.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘2.3.0’
* 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/23s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
tronco.bootstrap 4.725  0.132  13.651
* 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
  ‘/Users/biocbuild/bbs-3.3-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	0.010	0.002	0.012
annotate.stages	0.009	0.001	0.010
as.adj.matrix	0.006	0.002	0.008
as.alterations	0.004	0.001	0.005
as.colors	0.001	0.001	0.002
as.confidence	0.005	0.002	0.008
as.description	0.001	0.001	0.002
as.events	0.002	0.000	0.002
as.events.in.patterns	0.004	0.001	0.005
as.events.in.sample	0.003	0.000	0.003
as.gene	0.004	0.002	0.005
as.genes	0.002	0.000	0.002
as.genes.in.patterns	0.005	0.001	0.005
as.genotypes	0.006	0.003	0.008
as.hypotheses	0.003	0.001	0.004
as.joint.probs	0.006	0.001	0.007
as.marginal.probs	0.006	0.001	0.006
as.models	0.007	0.004	0.011
as.pathway	0.007	0.000	0.008
as.patterns	0.003	0.001	0.003
as.samples	0.002	0.000	0.003
as.selective.advantage.relations	0.112	0.001	0.114
as.stages	0.006	0.001	0.006
as.types	0.001	0.000	0.002
as.types.in.patterns	0.004	0.001	0.004
change.color	0.001	0.000	0.002
delete.event	0.004	0.000	0.004
delete.gene	0.005	0.001	0.005
delete.hypothesis	0.021	0.006	0.027
delete.model	0.003	0.000	0.003
delete.pattern	0.010	0.002	0.012
delete.samples	0.002	0.000	0.002
delete.type	0.005	0.000	0.005
duplicates	0.001	0.000	0.002
enforce.numeric	0.002	0.000	0.002
enforce.string	0.002	0.000	0.003
events.selection	0.005	0.000	0.005
export.mutex	0.014	0.002	0.015
has.duplicates	0.001	0.000	0.002
has.model	0.002	0.000	0.002
has.stages	0.007	0.000	0.007
import.GISTIC	0.085	0.001	0.087
import.MAF	0.061	0.001	0.062
intersect.datasets	0.000	0.000	0.001
keysToNames	0.006	0.001	0.006
merge.events	0.003	0.000	0.004
merge.types	0.049	0.005	0.054
nevents	0.001	0.001	0.002
ngenes	0.001	0.000	0.001
nhypotheses	0.001	0.000	0.001
npatterns	0.002	0.001	0.002
nsamples	0.002	0.000	0.001
ntypes	0.001	0.000	0.002
oncoprint.cbio	0.013	0.001	0.014
pheatmap	3.338	0.030	3.375
rank.recurrents	0.004	0.000	0.004
rename.gene	0.003	0.001	0.004
rename.type	0.002	0.000	0.003
samples.selection	0.003	0.001	0.003
show	0.003	0.000	0.004
sort.by.frequency	0.005	0.002	0.007
trim	0.003	0.001	0.003
tronco.bootstrap	4.725	0.132	13.651
tronco.caprese	0.195	0.003	0.199
tronco.capri	3.741	0.062	3.808
tronco.plot	0.128	0.003	0.131
which.samples	0.004	0.000	0.005