BioC 3.4: CHECK report for AnnotationFuncs on morelia

Package: AnnotationFuncs

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationFuncs_1.23.0.tar.gz

StartedAt: 2016-09-20 03:09:12 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 03:10:00 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 48.1 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_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/AnnotationFuncs.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationFuncs/DESCRIPTION’ ... OK
* this is package ‘AnnotationFuncs’ version ‘1.23.0’
* 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 ... 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-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	0.346	0.017	0.773
getEvidenceCodes	0.001	0.001	0.000
getOrthologs	0.302	0.018	1.082
mapLists	0.001	0.000	0.000
pickGO	0.047	0.001	0.099
pickRefSeq	0.137	0.001	0.152
removeNAs	0	0	0
translate	0.075	0.003	0.078