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BioC 3.0: CHECK report for pepStat on perceval

This page was generated on 2015-04-10 10:00:00 -0700 (Fri, 10 Apr 2015).

Package 653/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pepStat 1.0.0
Gregory C Imholte
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/pepStat
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: pepStat
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pepStat_1.0.0.tar.gz
StartedAt: 2015-04-10 04:44:21 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:49:35 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 314.1 seconds
RetCode: 0
Status:  OK 
CheckDir: pepStat.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pepStat_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/pepStat.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pepStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pepStat’ version ‘1.0.0’
* 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 ‘pepStat’ can be installed ... [24s/26s] 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 loading without being on the library search path ... 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
coerce,peptideSet-ExpressionSet: no visible global function definition
  for ‘annotation’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [66s/66s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
makeCalls         9.091  0.146   9.401
normalizeArray    8.594  0.090   8.731
plotArray         8.155  0.065   8.261
summarizePeptides 7.993  0.052   8.096
slidingMean       7.985  0.059   8.107
restab            7.976  0.052   8.070
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/pepStat.Rcheck/00check.log’
for details.

pepStat.Rcheck/00install.out:

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

pepStat.Rcheck/pepStat-Ex.timings:

nameusersystemelapsed
create_db0.1040.0010.106
makeCalls9.0910.1469.401
makePeptideSet3.5210.0513.572
normalizeArray8.5940.0908.731
plotArray8.1550.0658.261
restab7.9760.0528.070
shinyPepStat0.0010.0000.001
slidingMean7.9850.0598.107
summarizePeptides7.9930.0528.096