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BioC experimental data: CHECK report for RforProteomics on malbec2

This page was generated on 2017-08-15 15:07:51 -0400 (Tue, 15 Aug 2017).

Package 243/316HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RforProteomics 1.14.0
Laurent Gatto
Snapshot Date: 2017-08-15 09:00:06 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_5/experiment/pkgs/RforProteomics
Last Changed Rev: 4155 / Revision: 4227
Last Changed Date: 2017-04-24 16:09:26 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: RforProteomics
Version: 1.14.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RforProteomics_1.14.0.tar.gz
StartedAt: 2017-08-15 11:01:28 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 11:04:38 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 189.8 seconds
RetCode: 0
Status:  OK 
CheckDir: RforProteomics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RforProteomics_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-data-experiment/meat/RforProteomics.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 ‘RforProteomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RforProteomics’ version ‘1.14.0’
* 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 ‘RforProteomics’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
* 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 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                 9.448  0.044  14.322
proteomicsPackages 4.940  0.012   5.649
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘AnnotationDbi’
* 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-3.5-data-experiment/meat/RforProteomics.Rcheck/00check.log’
for details.


RforProteomics.Rcheck/00install.out:

* 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)

RforProteomics.Rcheck/RforProteomics-Ex.timings:

nameusersystemelapsed
getThermoHelaPRTC0.0040.0001.103
id 9.448 0.04414.322
proteomicsPackages4.9400.0125.649
qnt0.0160.0000.017
shinyMA000