Package: msmsEDA

Version: 1.16.0

Command: rm -rf msmsEDA.buildbin-libdir msmsEDA.Rcheck && mkdir msmsEDA.buildbin-libdir msmsEDA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msmsEDA.buildbin-libdir msmsEDA_1.16.0.tar.gz >msmsEDA.Rcheck\00install.out 2>&1 && cp msmsEDA.Rcheck\00install.out msmsEDA-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=msmsEDA.buildbin-libdir --install="check:msmsEDA-install.out" --force-multiarch --no-vignettes --timings msmsEDA_1.16.0.tar.gz

StartedAt: 2018-04-12 01:39:01 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:41:30 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 148.5 seconds

RetCode: 0

Status:  OK

CheckDir: msmsEDA.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf msmsEDA.buildbin-libdir msmsEDA.Rcheck && mkdir msmsEDA.buildbin-libdir msmsEDA.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=msmsEDA.buildbin-libdir msmsEDA_1.16.0.tar.gz >msmsEDA.Rcheck\00install.out 2>&1 && cp msmsEDA.Rcheck\00install.out msmsEDA-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=msmsEDA.buildbin-libdir --install="check:msmsEDA-install.out" --force-multiarch --no-vignettes --timings msmsEDA_1.16.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/msmsEDA.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'msmsEDA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'msmsEDA' version '1.16.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/msmsEDA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'msmsEDA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'msmsEDA'
    finding HTML links ... done
    batch.neutralize                        html  
    finding level-2 HTML links ... done

    count.stats                             html  
    counts.hc                               html  
    counts.heatmap                          html  
    counts.pca                              html  
    disp.estimates                          html  
    filter.flags                            html  
    gene.table                              html  
    msms.dataset                            html  
    msmsEDA-package                         html  
    norm.counts                             html  
    pnms                                    html  
    pp.msms.data                            html  
    spc.barplots                            html  
    spc.boxplots                            html  
    spc.densityplots                        html  
    spc.scatterplot                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'msmsEDA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'msmsEDA' as msmsEDA_1.16.0.zip
* DONE (msmsEDA)
In R CMD INSTALL
In R CMD INSTALL