BioC 3.6: CHECK report for joda on malbec1

Package: joda

Version: 1.25.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings joda_1.25.0.tar.gz

StartedAt: 2017-08-16 00:13:49 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:14:52 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 63.4 seconds

RetCode: 0

Status:  OK

CheckDir: joda.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings joda_1.25.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/joda.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘joda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘joda’ version ‘1.25.0’
* 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 ‘joda’ 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
* 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘RBGL’ ‘bgmm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
infer.probabilities: no visible global function definition for ‘par’
infer.probabilities : getProbs: no visible global function definition
  for ‘unsupervised’
infer.probabilities : getProbs: no visible global function definition
  for ‘DEprobs’
infer.probabilities : getProbs: no visible global function definition
  for ‘belief’
infer.probabilities : getProbs: no visible global function definition
  for ‘plot’
infer.probabilities : getProbs: no visible global function definition
  for ‘title’
infer.probabilities : getProbs: no visible global function definition
  for ‘legend’
regulation.scores: no visible global function definition for ‘as’
regulation.scores: no visible global function definition for
  ‘transitive.closure’
Undefined global functions or variables:
  DEprobs as belief legend par plot title transitive.closure
  unsupervised
Consider adding
  importFrom("graphics", "legend", "par", "plot", "title")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
regulation.scores 5.324  0.004    5.33
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/joda.Rcheck/00check.log’
for details.

* installing *source* package ‘joda’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (joda)

name	user	system	elapsed
damage	0.032	0.004	0.036
deregulation.p.values	0.000	0.000	0.001
deregulation.scores	1.292	0.020	1.314
differential.probs	1.732	0.000	1.749
regulation.scores	5.324	0.004	5.330