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BioC 3.0: CHECK report for MSstats on perceval

This page was generated on 2015-04-10 09:58:50 -0700 (Fri, 10 Apr 2015).

Package 585/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstats 2.4.0
Meena Choi
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/MSstats
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: MSstats
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSstats_2.4.0.tar.gz
StartedAt: 2015-04-10 04:11:47 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:18:45 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 418.0 seconds
RetCode: 0
Status:  OK 
CheckDir: MSstats.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MSstats_2.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MSstats.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 ‘MSstats/DESCRIPTION’ ... OK
* this is package ‘MSstats’ version ‘2.4.0’
* 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 ‘MSstats’ can be installed ... [36s/37s] 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
.fit.model: no visible binding for global variable ‘LABEL’
.fit.model.single: no visible binding for global variable ‘i’
.fit.model.single: no visible binding for global variable ‘LABEL’
.iter.wls.fit.model: no visible binding for global variable ‘weight’
dataProcess: no visible binding for global variable ‘LABEL’
dataProcessPlots: no visible binding for global variable ‘LABEL’
groupComparisonPlots: no visible binding for global variable ‘logFC’
groupComparisonPlots: no visible binding for global variable ‘ciw’
transformMSnSetToMSstats: no visible global function definition for
  ‘pData’
transformMSnSetToMSstats: no visible global function definition for
  ‘fData’
transformMSnSetToMSstats: no visible global function definition for
  ‘exprs’
transformMSstatsToMSnSet: no visible global function definition for
  ‘sampleNames<-’
transformMSstatsToMSnSet: no visible global function definition for
  ‘featureNames<-’
transformMSstatsToMSnSet: no visible global function definition for
  ‘fData’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [48s/46s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
dataProcessPlots     10.524  0.082  10.958
groupComparisonPlots  4.918  0.072   5.116
* 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/MSstats.Rcheck/00check.log’
for details.

MSstats.Rcheck/00install.out:

* installing *source* package ‘MSstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MSstats)

MSstats.Rcheck/MSstats-Ex.timings:

nameusersystemelapsed
QuantData0.1110.0110.145
RawData0.0050.0000.006
dataProcess0.8550.0220.958
dataProcessPlots10.524 0.08210.958
designSampleSize1.1340.0261.227
designSampleSizePlots0.5450.0130.647
groupComparison2.5200.0562.749
groupComparisonPlots4.9180.0725.116
modelBasedQCPlots1.7500.0261.848
quantification1.3670.0151.383
testResultMultiComparisons0.8420.0150.885
testResultOneComparison0.7240.0100.765
transformMSnSetToMSstats1.1851.6631.548
transformMSstatsToMSnSet0.1570.0180.174