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BioC experimental data: CHECK report for RforProteomics on zin2

This page was generated on 2015-10-07 16:20:57 -0700 (Wed, 07 Oct 2015).

Package 190/241HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RforProteomics 1.6.0
Laurent Gatto
Snapshot Date: 2015-10-07 07:15:35 -0700 (Wed, 07 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_1/experiment/pkgs/RforProteomics
Last Changed Rev: 3279 / Revision: 3442
Last Changed Date: 2015-04-16 13:16:53 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: RforProteomics
Version: 1.6.0
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RforProteomics_1.6.0.tar.gz
StartedAt: 2015-10-07 10:29:36 -0700 (Wed, 07 Oct 2015)
EndedAt: 2015-10-07 10:35:00 -0700 (Wed, 07 Oct 2015)
EllapsedTime: 323.6 seconds
RetCode: 0
Status:  OK 
CheckDir: RforProteomics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings RforProteomics_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-data-experiment/meat/RforProteomics.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.0’
* 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 ... [16s/29s] OK
* checking installed package size ... NOTE
  installed size is  7.5Mb
  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 ... [34s/63s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
id                 15.424  0.542  32.165
proteomicsPackages 10.102  0.073  15.391
* 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-3.1-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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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)

RforProteomics.Rcheck/RforProteomics-Ex.timings:

nameusersystemelapsed
getThermoHelaPRTC0.0010.0040.316
id15.424 0.54232.165
proteomicsPackages10.102 0.07315.391
qnt0.0190.0000.039
shinyMA0.0000.0000.005