BioC 3.5: CHECK report for AnnotationFuncs on veracruz2

Package: AnnotationFuncs

Version: 1.26.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationFuncs_1.26.0.tar.gz

StartedAt: 2017-08-15 23:42:54 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 23:43:50 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 55.9 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationFuncs.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 AnnotationFuncs_1.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationFuncs.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 ‘AnnotationFuncs/DESCRIPTION’ ... OK
* this is package ‘AnnotationFuncs’ version ‘1.26.0’
* 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 ‘AnnotationFuncs’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
BugReports field should not be empty
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘AnnotationDbi’
  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
getOrthologs: no visible global function definition for ‘dbmeta’
getOrthologs: no visible global function definition for ‘dbconn’
getOrthologs: no visible global function definition for ‘dbfile’
getOrthologs: no visible global function definition for ‘direction’
translate: no visible global function definition for ‘dbmeta’
translate: no visible global function definition for ‘dbconn’
translate: no visible global function definition for ‘stack’
Undefined global functions or variables:
  dbconn dbfile dbmeta direction stack
Consider adding
  importFrom("utils", "stack")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/AnnotationFuncs.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
AnnotationFuncs-package	0.701	0.020	0.739
getEvidenceCodes	0	0	0
getOrthologs	0.618	0.014	0.650
mapLists	0.001	0.000	0.001
pickGO	0.051	0.002	0.056
pickRefSeq	0.053	0.001	0.064
removeNAs	0.000	0.000	0.001
translate	0.190	0.003	0.202