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CHECK report for msmsEDA on merida2

This page was generated on 2018-10-17 08:51:47 -0400 (Wed, 17 Oct 2018).

Package 952/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msmsEDA 1.18.0
Josep Gregori
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/msmsEDA
Branch: RELEASE_3_7
Last Commit: 792fa71
Last Changed Date: 2018-04-30 10:35:30 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: msmsEDA
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msmsEDA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msmsEDA_1.18.0.tar.gz
StartedAt: 2018-10-16 22:48:02 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:50:09 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 127.1 seconds
RetCode: 0
Status:  OK 
CheckDir: msmsEDA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msmsEDA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msmsEDA_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/msmsEDA.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.0’
* 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 ... 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
batch.neutralize: no visible global function definition for
  ‘model.matrix’
count.stats: no visible global function definition for ‘exprs’
count.stats: no visible binding for global variable ‘fivenum’
counts.hc: no visible global function definition for ‘exprs’
counts.hc: no visible global function definition for ‘hclust’
counts.hc: no visible global function definition for ‘dist’
counts.hc: no visible global function definition for ‘par’
counts.hc: no visible global function definition for ‘pData’
counts.hc: no visible global function definition for ‘as.dendrogram’
counts.hc: no visible global function definition for ‘dendrapply’
counts.hc: no visible global function definition for ‘plot’
counts.hc: no visible global function definition for ‘title’
counts.heatmap: no visible global function definition for ‘exprs’
counts.heatmap: no visible global function definition for ‘pdf’
counts.heatmap: no visible global function definition for ‘heatmap’
counts.heatmap: no visible global function definition for ‘dev.off’
counts.pca: no visible global function definition for ‘exprs’
counts.pca: no visible global function definition for ‘prcomp’
counts.pca: no visible global function definition for ‘pData’
counts.pca: no visible global function definition for ‘text’
counts.pca: no visible global function definition for ‘abline’
counts.pca: no visible global function definition for ‘title’
disp.estimates: no visible global function definition for ‘exprs’
disp.estimates: no visible global function definition for ‘pData’
disp.estimates: no visible global function definition for ‘pdf’
disp.estimates: no visible global function definition for ‘par’
disp.estimates: no visible global function definition for ‘quantile’
disp.estimates: no visible global function definition for ‘plot’
disp.estimates: no visible global function definition for ‘density’
disp.estimates: no visible global function definition for ‘abline’
disp.estimates: no visible global function definition for ‘title’
disp.estimates: no visible global function definition for ‘dev.off’
edgeCol: no visible global function definition for ‘is.leaf’
filter.flags: no visible binding for global variable ‘var’
filter.flags: no visible global function definition for ‘quantile’
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<-’
residual.var : ss: no visible global function definition for ‘var’
spc.barplots: no visible global function definition for ‘median’
spc.barplots: no visible global function definition for ‘par’
spc.barplots: no visible global function definition for ‘barplot’
spc.barplots: no visible global function definition for ‘abline’
spc.boxplots: no visible global function definition for ‘par’
spc.boxplots: no visible global function definition for ‘boxplot’
spc.boxplots: no visible global function definition for ‘axis’
spc.boxplots: no visible global function definition for ‘legend’
spc.densityplots: no visible global function definition for ‘density’
spc.densityplots: no visible global function definition for ‘par’
spc.densityplots: no visible global function definition for ‘plot’
spc.densityplots: no visible global function definition for ‘abline’
spc.densityplots: no visible global function definition for ‘lines’
spc.densityplots: no visible global function definition for ‘legend’
spc.scatterplot: no visible global function definition for ‘par’
spc.scatterplot: no visible global function definition for ‘plot’
spc.scatterplot: no visible global function definition for ‘points’
spc.scatterplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline as.dendrogram axis barplot boxplot dendrapply density dev.off
  dist exprs exprs<- fivenum hclust heatmap is.leaf legend lines median
  model.matrix pData par pdf plot points prcomp quantile text title var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "barplot", "boxplot",
             "legend", "lines", "par", "plot", "points", "text", "title")
  importFrom("stats", "as.dendrogram", "dendrapply", "density", "dist",
             "fivenum", "hclust", "heatmap", "is.leaf", "median",
             "model.matrix", "prcomp", "quantile", "var")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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-3.7-bioc/meat/msmsEDA.Rcheck/00check.log’
for details.



Installation output

msmsEDA.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msmsEDA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘msmsEDA’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (msmsEDA)

Tests output


Example timings

msmsEDA.Rcheck/msmsEDA-Ex.timings

nameusersystemelapsed
batch.neutralize0.1520.0060.160
count.stats0.0580.0030.060
counts.hc0.1290.0040.135
counts.heatmap1.2640.0121.291
counts.pca0.0940.0030.099
disp.estimates0.8090.0050.823
filter.flags0.1000.0020.105
gene.table0.0150.0020.018
msms.dataset0.0200.0030.024
norm.counts0.0760.0030.079
pnms0.0210.0020.023
pp.msms.data0.0550.0020.058
spc.barplots0.0090.0010.011
spc.boxplots0.0340.0020.036
spc.densityplots0.0510.0030.056
spc.scatterplot0.1280.0020.132