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BioC 3.2: CHECK report for msmsEDA on perceval

This page was generated on 2015-11-10 14:48:16 -0800 (Tue, 10 Nov 2015).

Package 678/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msmsEDA 1.8.0
Josep Gregori
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/msmsEDA
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: msmsEDA
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings msmsEDA_1.8.0.tar.gz
StartedAt: 2015-11-10 07:24:39 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 07:26:45 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 125.9 seconds
RetCode: 0
Status:  OK 
CheckDir: msmsEDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings msmsEDA_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/msmsEDA.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msmsEDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msmsEDA’ version ‘1.8.0’
* package encoding: latin1
* 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 ‘msmsEDA’ can be installed ... [13s/14s] 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘MSnbase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘MSnbase:::logging’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
count.stats: no visible global function definition for ‘exprs’
counts.hc: no visible global function definition for ‘exprs’
counts.hc: no visible global function definition for ‘pData’
counts.heatmap: no visible global function definition for ‘exprs’
counts.pca: no visible global function definition for ‘exprs’
counts.pca: no visible global function definition for ‘pData’
disp.estimates: no visible global function definition for ‘exprs’
disp.estimates: no visible global function definition for ‘pData’
norm.counts: no visible global function definition for ‘exprs’
norm.counts: no visible global function definition for ‘exprs<-’
pp.msms.data: no visible global function definition for ‘exprs’
pp.msms.data: 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [10s/10s] OK
* 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-bioc/meat/msmsEDA.Rcheck/00check.log’
for details.


msmsEDA.Rcheck/00install.out:

* installing *source* package ‘msmsEDA’ ...
** 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 (msmsEDA)

msmsEDA.Rcheck/msmsEDA-Ex.timings:

nameusersystemelapsed
batch.neutralize0.1350.0050.140
count.stats0.2890.0050.294
counts.hc0.1250.0080.134
counts.heatmap1.0990.0281.151
counts.pca0.0930.0040.099
disp.estimates0.8210.0050.828
filter.flags0.0610.0010.062
gene.table0.0120.0010.012
msms.dataset0.0150.0010.016
norm.counts0.0680.0020.069
pnms0.0130.0010.013
pp.msms.data0.0540.0010.054
spc.barplots0.0080.0010.011
spc.boxplots0.0290.0020.053
spc.densityplots0.0480.0040.053
spc.scatterplot0.1970.0020.201