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BioC 3.2: CHECK report for trackViewer on oaxaca

This page was generated on 2015-08-24 10:58:11 -0700 (Mon, 24 Aug 2015).

Package 1028/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trackViewer 1.5.2
Jianhong Ou
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/trackViewer
Last Changed Rev: 105747 / Revision: 107696
Last Changed Date: 2015-07-01 12:10:18 -0700 (Wed, 01 Jul 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: trackViewer
Version: 1.5.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings trackViewer_1.5.2.tar.gz
StartedAt: 2015-08-24 04:28:54 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 04:36:25 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 450.6 seconds
RetCode: 0
Status:  OK 
CheckDir: trackViewer.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings trackViewer_1.5.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/trackViewer.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.5.2’
* 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 ... [33s/35s] 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 ... [99s/116s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
trackViewer-package 27.351  1.627  33.394
parseWIG            17.441  1.088  19.549
viewTracks          17.336  1.011  19.726
geneModelFromTxdb    8.970  0.583  19.042
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/17s]
 [17s/18s] 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
  ‘/Users/biocbuild/bbs-3.2-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
GRoperator0.9660.0701.080
addArrowMark0.0100.0010.011
addGuideLine0.0050.0000.005
coverageGR0.3650.0270.391
geneModelFromTxdb 8.970 0.58319.042
getCurTrackViewport0.0060.0010.008
importBam0.5230.0340.586
importScore1.3890.0941.632
interactiveViewer0.0010.0000.001
optimizeStyle1.1050.0661.200
parseWIG17.441 1.08819.549
plotGRanges1.7070.1091.960
track0.0890.0070.104
trackViewer-package27.351 1.62733.394
trackViewerStyle0.0010.0000.001
viewTracks17.336 1.01119.726