BioC experimental data: CHECK report for Fletcher2013a on malbec1

Package: Fletcher2013a

Version: 1.10.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Fletcher2013a_1.10.0.tar.gz

StartedAt: 2017-04-15 10:53:31 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 10:54:11 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 40.5 seconds

RetCode: 0

Status:  OK

CheckDir: Fletcher2013a.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Fletcher2013a_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/Fletcher2013a.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Fletcher2013a/DESCRIPTION’ ... OK
* this is package ‘Fletcher2013a’ version ‘1.10.0’
* 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 ‘Fletcher2013a’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 70.0Mb
  sub-directories of 1Mb or more:
    data  69.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Exp1signatures: no visible global function definition for ‘data’
Exp2signatures: no visible global function definition for ‘data’
Exp3signatures: no visible global function definition for ‘data’
Fletcher2013pipeline.limma: no visible global function definition for
  ‘model.matrix’
Fletcher2013pipeline.pca: no visible global function definition for
  ‘data’
Fletcher2013pipeline.pca: no visible global function definition for
  ‘na.omit’
Fletcher2013pipeline.pca: no visible global function definition for
  ‘prcomp’
PlotGroups: no visible global function definition for ‘dist’
PlotGroups: no visible binding for global variable ‘median’
PlotGroups: no visible binding for global variable ‘sd’
PlotGroups: no visible global function definition for ‘par’
PlotGroups: no visible global function definition for ‘plot’
PlotGroups: no visible global function definition for ‘axis’
PlotGroups: no visible global function definition for ‘mtext’
PlotGroups: no visible global function definition for ‘points’
PlotGroups: no visible global function definition for ‘lines’
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for ‘pdf’
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for ‘layout’
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for ‘par’
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for ‘barplot’
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for ‘mtext’
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for ‘legend’
plotExpDeg : plot.deg.exp1 : plotendsum: no visible global function
  definition for ‘dev.off’
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for ‘pdf’
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for ‘layout’
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for ‘par’
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for ‘barplot’
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for ‘mtext’
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for ‘legend’
plotExpDeg : plot.deg.exp2 : plotendsum: no visible global function
  definition for ‘dev.off’
plotExpDeg : plot.deg.exp3 : plotendsum: no visible global function
  definition for ‘par’
plotExpDeg : plot.deg.exp3 : plotendsum: no visible global function
  definition for ‘barplot’
plotExpDeg : plot.deg.exp3 : plotendsum: no visible global function
  definition for ‘mtext’
plotExpDeg : plot.deg.exp3 : plotendsum: no visible global function
  definition for ‘legend’
plotExpDeg : plot.deg.exp3: no visible global function definition for
  ‘pdf’
plotExpDeg : plot.deg.exp3: no visible global function definition for
  ‘layout’
plotExpDeg : plot.deg.exp3: no visible global function definition for
  ‘dev.off’
plotExpPca : plot.pca.exp1: no visible global function definition for
  ‘pdf’
plotExpPca : plot.pca.exp1: no visible global function definition for
  ‘plot’
plotExpPca : plot.pca.exp1: no visible global function definition for
  ‘legend’
plotExpPca : plot.pca.exp1: no visible global function definition for
  ‘mtext’
plotExpPca : plot.pca.exp1: no visible global function definition for
  ‘dev.off’
plotExpPca : plot.pca.exp2: no visible global function definition for
  ‘pdf’
plotExpPca : plot.pca.exp2: no visible global function definition for
  ‘plot’
plotExpPca : plot.pca.exp2: no visible global function definition for
  ‘text’
plotExpPca : plot.pca.exp2: no visible global function definition for
  ‘legend’
plotExpPca : plot.pca.exp2: no visible global function definition for
  ‘mtext’
plotExpPca : plot.pca.exp2: no visible global function definition for
  ‘dev.off’
plotExpPca : plot.pca.exp3: no visible global function definition for
  ‘pdf’
plotExpPca : plot.pca.exp3: no visible global function definition for
  ‘plot’
plotExpPca : plot.pca.exp3: no visible global function definition for
  ‘legend’
plotExpPca : plot.pca.exp3: no visible global function definition for
  ‘mtext’
plotExpPca : plot.pca.exp3: no visible global function definition for
  ‘dev.off’
plotFollowup: no visible global function definition for ‘data’
plotFollowup: no visible global function definition for ‘pdf’
plotFollowup: no visible global function definition for ‘layout’
plotFollowup: no visible global function definition for ‘palette’
plotFollowup: no visible global function definition for ‘plot’
plotFollowup: no visible global function definition for ‘axis’
plotFollowup: no visible global function definition for ‘lines’
plotFollowup: no visible global function definition for ‘legend’
plotFollowup: no visible global function definition for ‘dev.off’
plotOverlap: no visible global function definition for ‘pdf’
plotOverlap: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  axis barplot data dev.off dist layout legend lines median
  model.matrix mtext na.omit palette par pdf plot points prcomp sd text
Consider adding
  importFrom("grDevices", "dev.off", "palette", "pdf")
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "plot", "points", "text")
  importFrom("stats", "dist", "median", "model.matrix", "na.omit",
             "prcomp", "sd")
  importFrom("utils", "data")
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 ... 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-data-experiment/meat/Fletcher2013a.Rcheck/00check.log’
for details.

* installing *source* package ‘Fletcher2013a’ ...
** 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 (Fletcher2013a)

name	user	system	elapsed
Exp1	0.700	0.084	0.785
Exp2	0.840	0.128	0.972
Exp3	1.032	0.212	1.247
Fletcher2013a.pipelines	0.004	0.000	0.000
siESR1	0.204	0.016	0.222
siOTHERS	0.520	0.072	0.589