BioC 3.4: CHECK report for goTools on malbec1

Package: goTools

Version: 1.48.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings goTools_1.48.0.tar.gz

StartedAt: 2017-04-14 23:00:34 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:01:35 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 61.4 seconds

RetCode: 0

Status:  OK

CheckDir: goTools.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings goTools_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/goTools.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 ‘goTools/DESCRIPTION’ ... OK
* this is package ‘goTools’ version ‘1.48.0’
* 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 ‘goTools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GO.db’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
EndNodeList: warning in get("GO:0003674", env = GOMFCHILDREN): partial
  argument match of 'env' to 'envir'
EndNodeList: warning in get("GO:0005575", env = GOCCCHILDREN): partial
  argument match of 'env' to 'envir'
EndNodeList: warning in get("GO:0008150", env = GOBPCHILDREN): partial
  argument match of 'env' to 'envir'
getGOID: warning in mget(x, env = GOenv): partial argument match of
  'env' to 'envir'
goChildren: warning in get(id, env = envi): partial argument match of
  'env' to 'envir'
goParents: warning in get(paste("GO", cat, "PARENTS", sep = ""), env =
  as.environment("package:GO.db")): partial argument match of 'env' to
  'envir'
goParents: warning in get(goid, env = envi): partial argument match of
  'env' to 'envir'
* 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
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/goTools.Rcheck/00check.log’
for details.

* installing *source* package ‘goTools’ ...
** 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 (goTools)

name	user	system	elapsed
EndNodeList	0.000	0.000	0.001
ontoCompare	0	0	0