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BioC 3.4: CHECK report for Basic4Cseq on zin1

This page was generated on 2016-09-21 03:38:50 -0700 (Wed, 21 Sep 2016).

Package 81/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Basic4Cseq 1.9.0
Carolin Walter
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Basic4Cseq
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 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: Basic4Cseq
Version: 1.9.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Basic4Cseq_1.9.0.tar.gz
StartedAt: 2016-09-20 03:28:49 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:31:23 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 154.4 seconds
RetCode: 0
Status:  OK 
CheckDir: Basic4Cseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Basic4Cseq_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Basic4Cseq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Basic4Cseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Basic4Cseq’ version ‘1.9.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  inst/extdata/veryShortReference.fasta.sa
Object files/libraries should not be included in a source package.
* 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 ‘Basic4Cseq’ 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 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 ... OK
* checking R code for possible problems ... NOTE
.basic4CPlot: no visible global function definition for ‘loess’
.basic4CPlot: no visible global function definition for ‘predict’
.basic4CPlot: no visible global function definition for ‘polygon’
.basic4CPlot: no visible global function definition for ‘lines’
.basic4CPlot: no visible global function definition for ‘points’
.createVirtualFragmentLibraryMain: no visible global function
  definition for ‘write.table’
.drawDigestionFragmentHistogram: no visible global function definition
  for ‘plot’
.drawHeatmapMain: no visible global function definition for ‘runmed’
.drawHeatmapMain: no visible global function definition for ‘pdf’
.drawHeatmapMain: no visible global function definition for ‘tiff’
.drawHeatmapMain: no visible global function definition for ‘plot’
.drawHeatmapMain: no visible global function definition for ‘axis’
.drawHeatmapMain: no visible global function definition for ‘rect’
.drawHeatmapMain: no visible global function definition for
  ‘heat.colors’
.drawHeatmapMain: no visible global function definition for ‘dev.off’
.drawHeatmapMain: no visible global function definition for ‘par’
.drawMetaData: no visible global function definition for ‘points’
.drawMetaData: no visible global function definition for ‘text’
.drawMetaData: no visible global function definition for ‘axis’
.exportVisualizationFragmentData: no visible global function definition
  for ‘write.table’
.giveEnzymeSequence: no visible global function definition for
  ‘read.table’
.importVisualizationFragmentData: no visible global function definition
  for ‘read.table’
.plotTransInteractionsMain: no visible global function definition for
  ‘pdf’
.plotTransInteractionsMain: no visible global function definition for
  ‘tiff’
.plotTransInteractionsMain: no visible global function definition for
  ‘plot.window’
.plotTransInteractionsMain: no visible global function definition for
  ‘dev.off’
.plotTransInteractions_Character: no visible global function definition
  for ‘read.table’
.printBEDFragmentLibrary: no visible global function definition for
  ‘read.table’
.printBEDFragmentLibrary: no visible global function definition for
  ‘write.table’
.readPointsOfInterestFile: no visible global function definition for
  ‘read.table’
.readsToFragments: no visible global function definition for
  ‘read.table’
.visualizeViewpointMain: no visible global function definition for
  ‘runmed’
.visualizeViewpointMain: no visible global function definition for
  ‘pdf’
.visualizeViewpointMain: no visible global function definition for
  ‘tiff’
.visualizeViewpointMain: no visible global function definition for
  ‘plot’
.visualizeViewpointMain: no visible global function definition for
  ‘dev.off’
.visualizeViewpointMain: no visible global function definition for
  ‘axis’
.visualizeViewpointMain: no visible global function definition for
  ‘rect’
.visualizeViewpointMain: no visible global function definition for
  ‘lines’
basic4CPlot,numeric-numeric-numeric-numeric-numeric-numeric-character:
  no visible global function definition for ‘loess’
basic4CPlot,numeric-numeric-numeric-numeric-numeric-numeric-character:
  no visible global function definition for ‘predict’
basic4CPlot,numeric-numeric-numeric-numeric-numeric-numeric-character:
  no visible global function definition for ‘polygon’
basic4CPlot,numeric-numeric-numeric-numeric-numeric-numeric-character:
  no visible global function definition for ‘lines’
basic4CPlot,numeric-numeric-numeric-numeric-numeric-numeric-character:
  no visible global function definition for ‘points’
createVirtualFragmentLibraryMain,data.frame-data.frame-character-character-numeric:
  no visible global function definition for ‘write.table’
drawDigestionFragmentHistogram,data.frame: no visible global function
  definition for ‘plot’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘runmed’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘pdf’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘tiff’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘plot’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘axis’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘rect’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘heat.colors’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘dev.off’
drawHeatmapMain,data.frame: no visible global function definition for
  ‘par’
drawMetaData,numeric-numeric-numeric: no visible global function
  definition for ‘points’
drawMetaData,numeric-numeric-numeric: no visible global function
  definition for ‘text’
drawMetaData,numeric-numeric-numeric: no visible global function
  definition for ‘axis’
exportVisualizationFragmentData,Data4Cseq-character: no visible global
  function definition for ‘write.table’
giveEnzymeSequence,character-character: no visible global function
  definition for ‘read.table’
importVisualizationFragmentData,character: no visible global function
  definition for ‘read.table’
plotTransInteractions,character-character-numeric-character: no visible
  global function definition for ‘read.table’
plotTransInteractionsMain,data.frame-character-numeric-data.frame: no
  visible global function definition for ‘pdf’
plotTransInteractionsMain,data.frame-character-numeric-data.frame: no
  visible global function definition for ‘tiff’
plotTransInteractionsMain,data.frame-character-numeric-data.frame: no
  visible global function definition for ‘plot.window’
plotTransInteractionsMain,data.frame-character-numeric-data.frame: no
  visible global function definition for ‘dev.off’
printBEDFragmentLibrary,character-character: no visible global function
  definition for ‘read.table’
printBEDFragmentLibrary,character-character: no visible global function
  definition for ‘write.table’
readPointsOfInterestFile,character: no visible global function
  definition for ‘read.table’
readsToFragments,Data4Cseq-character: no visible global function
  definition for ‘read.table’
visualizeViewpointMain,data.frame: no visible global function
  definition for ‘runmed’
visualizeViewpointMain,data.frame: no visible global function
  definition for ‘pdf’
visualizeViewpointMain,data.frame: no visible global function
  definition for ‘tiff’
visualizeViewpointMain,data.frame: no visible global function
  definition for ‘plot’
visualizeViewpointMain,data.frame: no visible global function
  definition for ‘dev.off’
visualizeViewpointMain,data.frame: no visible global function
  definition for ‘axis’
visualizeViewpointMain,data.frame: no visible global function
  definition for ‘rect’
visualizeViewpointMain,data.frame: no visible global function
  definition for ‘lines’
Undefined global functions or variables:
  axis dev.off heat.colors lines loess par pdf plot plot.window points
  polygon predict read.table rect runmed text tiff write.table
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "tiff")
  importFrom("graphics", "axis", "lines", "par", "plot", "plot.window",
             "points", "polygon", "rect", "text")
  importFrom("stats", "loess", "predict", "runmed")
  importFrom("utils", "read.table", "write.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
readsToFragments 2.336  6.264   8.603
* 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/Basic4Cseq.Rcheck/00check.log’
for details.

Basic4Cseq.Rcheck/00install.out:

* installing *source* package ‘Basic4Cseq’ ...
** 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 (Basic4Cseq)

Basic4Cseq.Rcheck/Basic4Cseq-Ex.timings:

nameusersystemelapsed
Data4Cseq-class0.0000.0000.002
Data4Cseq0.0720.0000.073
checkRestrictionEnzymeSequence0.0000.0000.001
chooseNearCisFragments0.0080.0000.010
createVirtualFragmentLibrary0.0000.0000.001
drawDigestionFragmentHistogram0.0040.0000.006
drawHeatmap000
exportVisualizationFragmentData0.0000.0000.001
getReadDistribution0.1040.0000.103
giveEnzymeSequence0.0040.0000.002
importVisualizationFragmentData0.0080.0000.010
liverData0.0000.0000.004
liverDataRaw0.0000.0000.003
normalizeFragmentData0.0040.0000.007
plotTransInteractions0.0040.0000.000
prepare4CseqData0.0000.0000.001
printBEDFragmentLibrary000
printWigFile0.0000.0000.001
readPointsOfInterestFile0.0040.0000.003
readsToFragments2.3366.2648.603
simulateDigestion0.0000.0000.002
visualizeViewpoint0.0240.0000.025