BioC 3.2: CHECK report for TRONCO on moscato1

Package: TRONCO

Version: 2.2.0

Command: rm -rf TRONCO.buildbin-libdir TRONCO.Rcheck && mkdir TRONCO.buildbin-libdir TRONCO.Rcheck && D:\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 && D:\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: 2016-04-23 08:22:53 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 08:26:23 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 210.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: TRONCO.Rcheck

Warnings: 4

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### Running command:
###
###   rm -rf TRONCO.buildbin-libdir TRONCO.Rcheck && mkdir TRONCO.buildbin-libdir TRONCO.Rcheck && D:\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  && D:\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 'D:/biocbld/bbs-3.2-bioc/meat/TRONCO.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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' ... [45s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
tronco.bootstrap 9.93   0.12   27.64
pheatmap         6.54   0.01    7.05
tronco.capri     6.15   0.00    6.15
** running examples for arch 'x64' ... [47s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
tronco.bootstrap 8.63   0.01   27.09
tronco.capri     7.85   0.02    7.87
pheatmap         6.45   0.02    6.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R' [2s]
 [3s] OK
** running tests for arch 'x64' ...
  Running 'testthat.R' [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: 4 WARNINGs, 1 NOTE
See
  'D:/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	0.03	0.00	0.04
annotate.stages	0.01	0.01	0.03
as.adj.matrix	0.02	0.02	0.03
as.alterations	0.01	0.00	0.01
as.colors	0	0	0
as.confidence	0.00	0.02	0.02
as.description	0	0	0
as.events	0.00	0.01	0.01
as.events.in.patterns	0.02	0.00	0.02
as.events.in.sample	0.00	0.02	0.01
as.gene	0.01	0.00	0.02
as.genes	0	0	0
as.genes.in.patterns	0.02	0.00	0.01
as.genotypes	0.01	0.00	0.02
as.hypotheses	0.02	0.00	0.01
as.joint.probs	0.01	0.00	0.02
as.marginal.probs	0.02	0.00	0.02
as.models	0.01	0.00	0.01
as.pathway	0.02	0.00	0.02
as.patterns	0.02	0.00	0.01
as.samples	0.01	0.00	0.02
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	0.00	0.01	0.02
change.color	0	0	0
delete.event	0.01	0.00	0.02
delete.gene	0.02	0.00	0.01
delete.hypothesis	0.03	0.00	0.03
delete.model	0.02	0.00	0.02
delete.pattern	0.01	0.00	0.01
delete.samples	0	0	0
delete.type	0.02	0.00	0.02
duplicates	0	0	0
enforce.numeric	0.00	0.02	0.01
enforce.string	0	0	0
events.selection	0.00	0.01	0.02
export.mutex	0.04	0.00	0.06
has.duplicates	0	0	0
has.model	0.02	0.00	0.02
has.stages	0.00	0.02	0.01
import.GISTIC	0.23	0.00	0.24
import.MAF	0.13	0.01	0.14
intersect.datasets	0	0	0
keysToNames	0.00	0.02	0.02
merge.events	0.01	0.00	0.02
merge.types	0.11	0.00	0.11
nevents	0	0	0
ngenes	0.02	0.00	0.01
nhypotheses	0	0	0
npatterns	0.01	0.00	0.02
nsamples	0	0	0
ntypes	0	0	0
oncoprint.cbio	0.01	0.02	0.03
pheatmap	6.54	0.01	7.05
rank.recurrents	0	0	0
rename.gene	0	0	0
rename.type	0.00	0.01	0.02
samples.selection	0.01	0.00	0.01
show	0.02	0.00	0.02
sort.by.frequency	0.02	0.00	0.01
trim	0.00	0.02	0.02
tronco.bootstrap	9.93	0.12	27.64
tronco.caprese	0.31	0.00	0.31
tronco.capri	6.15	0.00	6.15
tronco.plot	0.11	0.02	0.12
which.samples	0.00	0.01	0.02

name	user	system	elapsed
annotate.description	0.01	0.00	0.02
annotate.stages	0.00	0.01	0.02
as.adj.matrix	0.02	0.00	0.01
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	0.02	0.00	0.01
as.events.in.sample	0	0	0
as.gene	0.02	0.00	0.02
as.genes	0	0	0
as.genes.in.patterns	0.01	0.00	0.02
as.genotypes	0.00	0.02	0.01
as.hypotheses	0	0	0
as.joint.probs	0.02	0.00	0.02
as.marginal.probs	0	0	0
as.models	0	0	0
as.pathway	0.02	0.00	0.02
as.patterns	0	0	0
as.samples	0.00	0.01	0.01
as.selective.advantage.relations	0.11	0.00	0.11
as.stages	0.01	0.00	0.01
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	0.04	0.00	0.04
delete.model	0	0	0
delete.pattern	0.02	0.00	0.02
delete.samples	0	0	0
delete.type	0.00	0.01	0.01
duplicates	0	0	0
enforce.numeric	0	0	0
enforce.string	0	0	0
events.selection	0	0	0
export.mutex	0.02	0.01	0.05
has.duplicates	0.00	0.02	0.02
has.model	0.01	0.00	0.01
has.stages	0.00	0.02	0.02
import.GISTIC	0.21	0.00	0.20
import.MAF	0.12	0.01	0.14
intersect.datasets	0.02	0.00	0.02
keysToNames	0.01	0.00	0.02
merge.events	0.02	0.00	0.01
merge.types	0.08	0.00	0.08
nevents	0.00	0.02	0.02
ngenes	0	0	0
nhypotheses	0	0	0
npatterns	0	0	0
nsamples	0	0	0
ntypes	0.00	0.01	0.02
oncoprint.cbio	0.03	0.00	0.03
pheatmap	6.45	0.02	6.55
rank.recurrents	0.01	0.00	0.02
rename.gene	0	0	0
rename.type	0.02	0.00	0.01
samples.selection	0.01	0.00	0.02
show	0.02	0.00	0.01
sort.by.frequency	0.01	0.00	0.02
trim	0.02	0.00	0.01
tronco.bootstrap	8.63	0.01	27.09
tronco.caprese	0.32	0.00	0.32
tronco.capri	7.85	0.02	7.87
tronco.plot	0.11	0.00	0.11
which.samples	0.01	0.00	0.01