BioC 3.5: CHECK report for mygene on malbec2

Package: mygene

Version: 1.12.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings mygene_1.12.0.tar.gz

StartedAt: 2017-08-16 00:54:17 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:57:07 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 169.5 seconds

RetCode: 0

Status:  OK

CheckDir: mygene.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings mygene_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/mygene.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mygene/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mygene’ version ‘1.12.0’
* 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 ‘mygene’ 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 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.df2DF: no visible binding for global variable ‘as’
.unnest.df : <anonymous>: no visible global function definition for
  ‘is’
.unnest.df : <anonymous>: no visible global function definition for
  ‘setNames’
MyGene: no visible global function definition for ‘new’
index.tx.id: no visible global function definition for
  ‘installed.packages’
validMyGeneObject: no visible global function definition for ‘slot’
.request.get,MyGene: no visible global function definition for
  ‘capture.output’
.request.post,MyGene: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  as capture.output installed.packages is new setNames slot
Consider adding
  importFrom("methods", "as", "is", "new", "slot")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output", "installed.packages")
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
* 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-3.5-bioc/meat/mygene.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
MyGene-class	0.000	0.000	0.001
MyGene	0.000	0.000	0.002
getGene	0.364	0.020	0.798
getGenes	0.392	0.000	0.793
makeTxDbFromMyGene	1.176	0.048	1.429
metadata	0.032	0.000	0.221
query	0.076	0.000	0.445
queryMany	0.116	0.000	0.727