BioC 3.2: CHECK report for trackViewer on zin1

Package: trackViewer

Version: 1.5.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings trackViewer_1.5.2.tar.gz

StartedAt: 2015-08-24 04:25:59 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:30:57 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 297.7 seconds

RetCode: 0

Status:  OK

CheckDir: trackViewer.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings trackViewer_1.5.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/trackViewer.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.5.2’
* 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 ‘trackViewer’ can be installed ... [23s/24s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
coverageGR : <anonymous> : <anonymous>: no visible global function
  definition for ‘IRanges’
geneModelFromTxdb: no visible global function definition for ‘IRanges’
importScore : filterByRange: no visible global function definition for
  ‘IRanges’
importScore : readWIG: no visible global function definition for
  ‘CharacterList’
importScore : readWIG: no visible global function definition for
  ‘IRanges’
importScore : readBED: no visible global function definition for
  ‘IRanges’
importScore : readFourCols: no visible global function definition for
  ‘IRanges’
interactiveViewer : importData: no visible global function definition
  for ‘gwindow’
interactiveViewer : importData: no visible global function definition
  for ‘ggroup’
interactiveViewer : importData: no visible global function definition
  for ‘glabel’
interactiveViewer : importData: no visible global function definition
  for ‘gfilebrowse’
interactiveViewer : importData : <anonymous>: no visible global
  function definition for ‘ggroup’
interactiveViewer : importData : <anonymous>: no visible global
  function definition for ‘gedit’
interactiveViewer : importData : <anonymous>: no visible global
  function definition for ‘gcheckbox’
interactiveViewer : importData: no visible global function definition
  for ‘gframe’
interactiveViewer : importData: no visible global function definition
  for ‘gedit’
interactiveViewer : importData: no visible global function definition
  for ‘gcheckbox’
interactiveViewer : importData: no visible global function definition
  for ‘gradio’
interactiveViewer : importData: no visible global function definition
  for ‘gbutton’
interactiveViewer : importData : <anonymous>: no visible global
  function definition for ‘IRanges’
interactiveViewer : trackBrowser: no visible global function definition
  for ‘IRanges’
interactiveViewer : saveFile: no visible global function definition for
  ‘gwindow’
interactiveViewer : saveFile: no visible global function definition for
  ‘ggroup’
interactiveViewer : saveFile: no visible global function definition for
  ‘glabel’
interactiveViewer : saveFile: no visible global function definition for
  ‘gfilebrowse’
interactiveViewer : saveFile: no visible global function definition for
  ‘gedit’
interactiveViewer : saveFile: no visible global function definition for
  ‘gbutton’
interactiveViewer : xaxisDialog: no visible global function definition
  for ‘gwindow’
interactiveViewer : xaxisDialog: no visible global function definition
  for ‘ggroup’
interactiveViewer : xaxisDialog: no visible global function definition
  for ‘gframe’
interactiveViewer : xaxisDialog: no visible global function definition
  for ‘glabel’
interactiveViewer : xaxisDialog: no visible global function definition
  for ‘gradio’
interactiveViewer : xaxisDialog: no visible global function definition
  for ‘gedit’
interactiveViewer : xaxisDialog: no visible global function definition
  for ‘gbutton’
interactiveViewer : margintopDialog: no visible global function
  definition for ‘gwindow’
interactiveViewer : margintopDialog: no visible global function
  definition for ‘ggroup’
interactiveViewer : margintopDialog: no visible global function
  definition for ‘gframe’
interactiveViewer : margintopDialog: no visible global function
  definition for ‘glabel’
interactiveViewer : margintopDialog: no visible global function
  definition for ‘gedit’
interactiveViewer : margintopDialog: no visible global function
  definition for ‘gbutton’
interactiveViewer : trackLabelDialog: no visible global function
  definition for ‘gwindow’
interactiveViewer : trackLabelDialog: no visible global function
  definition for ‘ggroup’
interactiveViewer : trackLabelDialog: no visible global function
  definition for ‘gframe’
interactiveViewer : trackLabelDialog: no visible global function
  definition for ‘glabel’
interactiveViewer : trackLabelDialog: no visible global function
  definition for ‘gradio’
interactiveViewer : trackLabelDialog: no visible global function
  definition for ‘gedit’
interactiveViewer : trackLabelDialog: no visible global function
  definition for ‘gbutton’
interactiveViewer : trackDialog: no visible global function definition
  for ‘gwindow’
interactiveViewer : trackDialog: no visible global function definition
  for ‘ggroup’
interactiveViewer : trackDialog: no visible global function definition
  for ‘gframe’
interactiveViewer : trackDialog: no visible global function definition
  for ‘gradio’
interactiveViewer : trackDialog: no visible global function definition
  for ‘glabel’
interactiveViewer : trackDialog: no visible global function definition
  for ‘gedit’
interactiveViewer : trackDialog: no visible global function definition
  for ‘gbutton’
locateScale: no visible global function definition for ‘IRanges’
parseWIG : parser : <anonymous>: no visible global function definition
  for ‘IRanges’
plotDataTrack: no visible global function definition for ‘IRanges’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [69s/69s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
trackViewer-package 19.408  0.474  19.864
parseWIG            12.155  0.338  12.446
viewTracks          11.773  0.299  12.008
geneModelFromTxdb    7.655  0.515   8.350
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [12s/12s]
 [12s/12s] 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/trackViewer.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
GRoperator	0.763	0.072	0.841
addArrowMark	0.009	0.000	0.009
addGuideLine	0.005	0.000	0.006
coverageGR	0.282	0.012	0.295
geneModelFromTxdb	7.655	0.515	8.350
getCurTrackViewport	0.004	0.000	0.004
importBam	0.318	0.004	0.320
importScore	0.912	0.033	0.952
interactiveViewer	0.001	0.000	0.000
optimizeStyle	0.813	0.028	0.839
parseWIG	12.155	0.338	12.446
plotGRanges	1.151	0.048	1.188
track	0.054	0.005	0.058
trackViewer-package	19.408	0.474	19.864
trackViewerStyle	0	0	0
viewTracks	11.773	0.299	12.008