BioC 3.6: CHECK report for Onassis on veracruz1

Package: Onassis

Version: 0.99.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Onassis_0.99.9.tar.gz

StartedAt: 2017-08-16 06:23:37 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:25:28 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 110.4 seconds

RetCode: 0

Status:  OK

CheckDir: Onassis.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Onassis_0.99.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Onassis.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Onassis/DESCRIPTION’ ... OK
* this is package ‘Onassis’ version ‘0.99.9’
* 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 ‘Onassis’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotate: no visible global function definition for ‘is’
annotateDF,EntityFinder-data.frame-character-CMoptions: no visible
  binding for global variable ‘ID’
annotateDF,EntityFinder-data.frame-character-CMoptions: no visible
  binding for global variable ‘NEW’
multisim,list-list-character-character : <anonymous>: no visible global
  function definition for ‘is’
Undefined global functions or variables:
  ID NEW is
Consider adding
  importFrom("methods", "is")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
EntityFinder-class 8.672  0.516   3.763
Similarity-class   7.921  0.390   4.527
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/Onassis.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
CMdictionary-class	1.460	0.157	1.081
CMoptions-class	0.093	0.014	0.107
EntityFinder-class	8.672	0.516	3.763
GEOHandler-functions	0.002	0.000	0.002
Similarity-class	7.921	0.390	4.527
Similarity-methods	0.068	0.000	0.067
annotate	1.022	0.070	0.540
connectToSRADB	0.003	0.000	0.001
experiment_types	0.002	0.001	0.001
getGEOMetadata	0.016	0.000	0.002
getSRAMetadata	0.004	0.001	0.002
library_sources	0.002	0.001	0.001
library_strategies	0.004	0.000	0.003
organism_types	0.001	0.000	0.001