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BioC 3.4: CHECK report for seqplots on morelia

This page was generated on 2016-09-21 03:53:38 -0700 (Wed, 21 Sep 2016).

Package 1101/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqplots 1.11.2
Przemyslaw Stempor
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqplots
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: seqplots
Version: 1.11.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqplots_1.11.2.tar.gz
StartedAt: 2016-09-20 12:59:21 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:02:44 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 202.6 seconds
RetCode: 0
Status:  OK 
CheckDir: seqplots.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqplots_1.11.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/seqplots.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqplots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqplots’ version ‘1.11.2’
* 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 ‘seqplots’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    seqplots   4.8Mb
* 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 ... NOTE
Foreign function call to a different package:
  .Call("BWGFile_summary", ..., PACKAGE = "rtracklayer")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
getPlotSetArray : <anonymous>: no visible global function definition
  for ‘qt’
getSF : <anonymous>: no visible global function definition for ‘approx’
ggHeatmapPlotWrapper: no visible global function definition for
  ‘colorRampPalette’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var2’
ggHeatmapPlotWrapper: no visible binding for global variable ‘Var1’
ggHeatmapPlotWrapper: no visible binding for global variable ‘value’
heatmapPlotWrapper: no visible global function definition for
  ‘colorRampPalette’
heatmapPlotWrapper: no visible global function definition for ‘layout’
heatmapPlotWrapper: no visible global function definition for
  ‘capture.output’
heatmapPlotWrapper: no visible global function definition for ‘par’
heatmapPlotWrapper: no visible global function definition for ‘abline’
heatmapPlotWrapper: no visible global function definition for ‘axis’
heatmapPlotWrapper: no visible global function definition for ‘image’
heatmapPlotWrapper: no visible global function definition for ‘rect’
heatmapPlotWrapper: no visible global function definition for ‘title’
heatmapPlotWrapper: no visible global function definition for ‘box’
heatmapPlotWrapper: no visible global function definition for
  ‘plot.new’
imPlot2: no visible global function definition for ‘par’
imPlot2: no visible global function definition for ‘image’
imPlot2: no visible global function definition for ‘rect’
imPlot2: no visible global function definition for ‘axis’
imPlot2: no visible global function definition for ‘box’
imPlot2: no visible binding for global variable ‘mtext’
plotMext: no visible global function definition for ‘par’
plotMext: no visible global function definition for ‘rainbow’
plotMext: no visible global function definition for ‘plot.new’
plotMext: no visible global function definition for ‘rgb’
plotMext: no visible global function definition for ‘axis’
plotMext: no visible global function definition for ‘adjustcolor’
plotMext: no visible global function definition for ‘lines’
plotMext: no visible global function definition for ‘abline’
plotAverage,list: no visible global function definition for ‘par’
plotHeatmap,list: no visible global function definition for ‘par’
plotHeatmap,list: no visible global function definition for ‘kmeans’
plotHeatmap,list: no visible global function definition for ‘hclust’
plotHeatmap,list: no visible global function definition for ‘dist’
plotHeatmap,list: no visible global function definition for ‘cutree’
plotHeatmap,list: no visible global function definition for
  ‘as.dendrogram’
plotHeatmap,list: no visible global function definition for ‘title’
Undefined global functions or variables:
  Var1 Var2 abline adjustcolor approx as.dendrogram axis box
  capture.output colorRampPalette cutree dist hclust image kmeans
  layout lines mtext par plot.new qt rainbow rect rgb title value
Consider adding
  importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow",
             "rgb")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "mtext", "par", "plot.new", "rect", "title")
  importFrom("stats", "approx", "as.dendrogram", "cutree", "dist",
             "hclust", "kmeans", "qt")
  importFrom("utils", "capture.output")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getPlotSetArray 3.371  0.133  15.133
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/seqplots.Rcheck/00check.log’
for details.


seqplots.Rcheck/00install.out:

* installing *source* package ‘seqplots’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seqplots)

seqplots.Rcheck/seqplots-Ex.timings:

nameusersystemelapsed
MotifSetup-class0.0050.0000.006
getPlotSetArray 3.371 0.13315.133
plot0.3770.0180.410
plotAverage0.5490.0150.569
plotHeatmap0.5600.0140.581
run0.0010.0000.001