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BioC 3.4: CHECK report for AnnotationFuncs on malbec1

This page was generated on 2017-04-15 16:10:21 -0400 (Sat, 15 Apr 2017).

Package 50/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AnnotationFuncs 1.24.0
Stefan McKinnon Edwards
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/AnnotationFuncs
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AnnotationFuncs
Version: 1.24.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings AnnotationFuncs_1.24.0.tar.gz
StartedAt: 2017-04-14 20:58:20 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 20:59:10 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 50.0 seconds
RetCode: 0
Status:  OK 
CheckDir: AnnotationFuncs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings AnnotationFuncs_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/AnnotationFuncs.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationFuncs/DESCRIPTION’ ... OK
* this is package ‘AnnotationFuncs’ version ‘1.24.0’
* 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 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/AnnotationFuncs.Rcheck/00check.log’
for details.


AnnotationFuncs.Rcheck/00install.out:

* 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)

AnnotationFuncs.Rcheck/AnnotationFuncs-Ex.timings:

nameusersystemelapsed
AnnotationFuncs-package0.3920.0080.452
getEvidenceCodes000
getOrthologs0.3400.0200.379
mapLists0.0000.0000.001
pickGO0.0560.0000.201
pickRefSeq0.1680.0000.170
removeNAs0.0000.0000.001
translate0.1440.0000.145