BioC experimental data: CHECK report for RforProteomics on perceval

Package: RforProteomics

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RforProteomics_1.7.0.tar.gz

StartedAt: 2015-06-10 09:47:24 -0700 (Wed, 10 Jun 2015)

EndedAt: 2015-06-10 09:52:52 -0700 (Wed, 10 Jun 2015)

EllapsedTime: 328.3 seconds

RetCode: 0

Status:  OK

CheckDir: RforProteomics.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RforProteomics_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/RforProteomics.Rcheck’
* using R version 3.2.1 beta (2015-06-08 r68489)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.7.0’
* 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 ... [24s/25s] OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.6Mb
* 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
shinyMA : <anonymous>: no visible global function definition for
  ‘exprs’
* 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 ... [67s/75s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
id                 35.524  0.397  42.174
proteomicsPackages 17.753  0.437  18.948
* 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
  ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/RforProteomics.Rcheck/00check.log’
for details.

* installing *source* package ‘RforProteomics’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
* DONE (RforProteomics)

name	user	system	elapsed
getThermoHelaPRTC	0.003	0.002	0.698
id	35.524	0.397	42.174
proteomicsPackages	17.753	0.437	18.948
qnt	0.026	0.002	0.108
shinyMA	0.000	0.000	0.001