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BioC 3.0: CHECK report for trackViewer on oaxaca

This page was generated on 2015-04-10 10:08:34 -0700 (Fri, 10 Apr 2015).

Package 895/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trackViewer 1.2.0
Jianhong Ou
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/trackViewer
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK 

Summary

Package: trackViewer
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch trackViewer_1.2.0.tar.gz
StartedAt: 2015-04-10 03:54:04 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:02:32 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 508.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: trackViewer.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch trackViewer_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/trackViewer.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.0’
* 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 ‘trackViewer’ can be installed ... [40s/42s] 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
coverageGR : <anonymous> : <anonymous>: no visible global function
  definition for ‘IRanges’
geneModelFromTxdb: 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 ... [65s/74s] WARNING
Found the following significant warnings:

  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
  Warning: 'dbBeginTransaction' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                      user system elapsed
geneModelFromTxdb   14.503  0.891  23.392
trackViewer-package 14.258  0.896  15.242
viewTracks           9.304  0.512  10.309
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [20s/21s]
 [20s/21s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/trackViewer.Rcheck/00check.log’
for details.

trackViewer.Rcheck/00install.out:

* 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)

trackViewer.Rcheck/trackViewer-Ex.timings:

nameusersystemelapsed
addArrowMark0.0120.0010.012
addGuideLine0.0080.0000.008
coverageGR0.9070.0400.954
geneModelFromTxdb14.503 0.89123.392
getCurTrackViewport0.0070.0000.007
importBam0.5690.0410.624
importScore1.2680.0711.440
interactiveViewer0.0000.0000.001
optimizeStyle1.2930.0701.371
track0.0920.0080.100
trackViewer-package14.258 0.89615.242
trackViewerStyle0.0010.0000.001
viewTracks 9.304 0.51210.309