BioC experimental data: CHECK report for RforProteomics on zin1

Package: RforProteomics

Version: 1.11.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RforProteomics_1.11.2.tar.gz

StartedAt: 2016-08-17 12:17:13 -0700 (Wed, 17 Aug 2016)

EndedAt: 2016-08-17 12:20:09 -0700 (Wed, 17 Aug 2016)

EllapsedTime: 176.3 seconds

RetCode: 0

Status:  OK

CheckDir: RforProteomics.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 RforProteomics_1.11.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/RforProteomics.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RforProteomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RforProteomics’ version ‘1.11.2’
* 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 ‘RforProteomics’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
RProtVis: no visible global function definition for ‘vignette’
RProtViz: no visible global function definition for ‘vignette’
RforProteomics: no visible global function definition for ‘vignette’
downloadData: no visible global function definition for ‘download.file’
getPackagesInBiocView: no visible global function definition for ‘data’
shinyMA: no visible global function definition for ‘data’
shinyMA : <anonymous>: no visible global function definition for ‘par’
shinyMA : <anonymous>: no visible global function definition for ‘grid’
shinyMA : <anonymous>: no visible global function definition for
  ‘abline’
shinyMA : <anonymous>: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  abline data download.file grid par points vignette
Consider adding
  importFrom("graphics", "abline", "grid", "par", "points")
  importFrom("utils", "data", "download.file", "vignette")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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
Examples with CPU or elapsed time > 5s
                     user system elapsed
id                 14.132  0.104  20.702
proteomicsPackages  5.608  0.000   6.165
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘AnnotationDbi’
'library' or 'require' calls not declared from:
  ‘dplyr’ ‘jsonlite’
* 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-data-experiment/meat/RforProteomics.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
getThermoHelaPRTC	0.000	0.004	0.585
id	14.132	0.104	20.702
proteomicsPackages	5.608	0.000	6.165
qnt	0.016	0.000	0.018
shinyMA	0	0	0