BioC 3.2: CHECK report for TRONCO on windows1.bioconductor.org

Package: TRONCO

Version: 2.2.0

Command: rm -rf TRONCO.buildbin-libdir TRONCO.Rcheck && mkdir TRONCO.buildbin-libdir TRONCO.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TRONCO.buildbin-libdir TRONCO_2.2.0.tar.gz >TRONCO.Rcheck\00install.out 2>&1 && cp TRONCO.Rcheck\00install.out TRONCO-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=TRONCO.buildbin-libdir --install="check:TRONCO-install.out" --force-multiarch --no-vignettes --timings TRONCO_2.2.0.tar.gz

StartedAt: 2015-10-27 06:20:07 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:22:09 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 122.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TRONCO.Rcheck

Warnings: 4

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### Running command:
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###   rm -rf TRONCO.buildbin-libdir TRONCO.Rcheck && mkdir TRONCO.buildbin-libdir TRONCO.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TRONCO.buildbin-libdir TRONCO_2.2.0.tar.gz >TRONCO.Rcheck\00install.out 2>&1 && cp TRONCO.Rcheck\00install.out TRONCO-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=TRONCO.buildbin-libdir --install="check:TRONCO-install.out" --force-multiarch --no-vignettes --timings TRONCO_2.2.0.tar.gz
###
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/TRONCO.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [24s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
tronco.bootstrap 4.86   0.03   14.19
** running examples for arch 'x64' ... [31s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
tronco.bootstrap 5.83   0.08   17.86
tronco.capri     5.31   0.02    5.35
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [1s]
 [1s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [1s]
 [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: 4 WARNINGs, 1 NOTE
See
  'C:/biocbld/bbs-3.2-bioc/meat/TRONCO.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'TRONCO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TRONCO' as TRONCO_2.2.0.zip
* DONE (TRONCO)

name	user	system	elapsed
annotate.description	0.01	0.00	0.01
annotate.stages	0.02	0.00	0.02
as.adj.matrix	0	0	0
as.alterations	0.01	0.00	0.02
as.colors	0	0	0
as.confidence	0.02	0.00	0.01
as.description	0	0	0
as.events	0	0	0
as.events.in.patterns	0.01	0.00	0.02
as.events.in.sample	0	0	0
as.gene	0	0	0
as.genes	0.00	0.02	0.01
as.genes.in.patterns	0	0	0
as.genotypes	0.00	0.01	0.02
as.hypotheses	0	0	0
as.joint.probs	0	0	0
as.marginal.probs	0.00	0.02	0.01
as.models	0	0	0
as.pathway	0.02	0.00	0.02
as.patterns	0	0	0
as.samples	0	0	0
as.selective.advantage.relations	0.08	0.00	0.08
as.stages	0	0	0
as.types	0	0	0
as.types.in.patterns	0.02	0.00	0.02
change.color	0	0	0
delete.event	0.01	0.00	0.01
delete.gene	0	0	0
delete.hypothesis	0.02	0.02	0.04
delete.model	0	0	0
delete.pattern	0.00	0.01	0.01
delete.samples	0	0	0
delete.type	0	0	0
duplicates	0.02	0.00	0.02
enforce.numeric	0	0	0
enforce.string	0	0	0
events.selection	0.01	0.00	0.01
export.mutex	0.02	0.00	0.02
has.duplicates	0	0	0
has.model	0.01	0.00	0.01
has.stages	0	0	0
import.GISTIC	0.1	0.0	0.1
import.MAF	0.11	0.00	0.11
intersect.datasets	0.01	0.00	0.01
keysToNames	0	0	0
merge.events	0	0	0
merge.types	0.08	0.00	0.08
nevents	0	0	0
ngenes	0	0	0
nhypotheses	0.02	0.00	0.02
npatterns	0	0	0
nsamples	0	0	0
ntypes	0.01	0.00	0.01
oncoprint.cbio	0.08	0.02	0.10
pheatmap	3.73	0.01	3.75
rank.recurrents	0	0	0
rename.gene	0.02	0.00	0.01
rename.type	0	0	0
samples.selection	0.02	0.00	0.02
show	0	0	0
sort.by.frequency	0	0	0
trim	0.01	0.00	0.01
tronco.bootstrap	4.86	0.03	14.19
tronco.caprese	0.16	0.00	0.16
tronco.capri	4.09	0.00	4.09
tronco.plot	0.08	0.00	0.07
which.samples	0	0	0

name	user	system	elapsed
annotate.description	0	0	0
annotate.stages	0	0	0
as.adj.matrix	0.00	0.02	0.01
as.alterations	0.01	0.00	0.02
as.colors	0	0	0
as.confidence	0	0	0
as.description	0	0	0
as.events	0	0	0
as.events.in.patterns	0	0	0
as.events.in.sample	0	0	0
as.gene	0	0	0
as.genes	0	0	0
as.genes.in.patterns	0	0	0
as.genotypes	0.01	0.00	0.02
as.hypotheses	0	0	0
as.joint.probs	0.02	0.00	0.02
as.marginal.probs	0	0	0
as.models	0.00	0.02	0.01
as.pathway	0	0	0
as.patterns	0.01	0.00	0.02
as.samples	0	0	0
as.selective.advantage.relations	0.14	0.00	0.14
as.stages	0.02	0.00	0.01
as.types	0	0	0
as.types.in.patterns	0.01	0.00	0.02
change.color	0	0	0
delete.event	0	0	0
delete.gene	0.02	0.00	0.01
delete.hypothesis	0.03	0.00	0.04
delete.model	0	0	0
delete.pattern	0.02	0.00	0.01
delete.samples	0	0	0
delete.type	0.01	0.00	0.02
duplicates	0	0	0
enforce.numeric	0	0	0
enforce.string	0.02	0.00	0.01
events.selection	0	0	0
export.mutex	0.01	0.01	0.03
has.duplicates	0	0	0
has.model	0.02	0.00	0.02
has.stages	0	0	0
import.GISTIC	0.14	0.00	0.14
import.MAF	0.2	0.0	0.2
intersect.datasets	0	0	0
keysToNames	0	0	0
merge.events	0.00	0.02	0.01
merge.types	0.08	0.02	0.10
nevents	0	0	0
ngenes	0.01	0.00	0.01
nhypotheses	0	0	0
npatterns	0	0	0
nsamples	0	0	0
ntypes	0	0	0
oncoprint.cbio	0.03	0.00	0.03
pheatmap	4.61	0.00	4.61
rank.recurrents	0	0	0
rename.gene	0	0	0
rename.type	0	0	0
samples.selection	0	0	0
show	0	0	0
sort.by.frequency	0.02	0.00	0.02
trim	0	0	0
tronco.bootstrap	5.83	0.08	17.86
tronco.caprese	0.19	0.00	0.18
tronco.capri	5.31	0.02	5.35
tronco.plot	0.09	0.00	0.09
which.samples	0	0	0