BioC 3.5: CHECK report for CGHbase on oaxaca

Package: CGHbase

Version: 1.35.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CGHbase_1.35.0.tar.gz

StartedAt: 2017-03-04 00:15:55 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:16:35 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 40.0 seconds

RetCode: 0

Status:  OK

CheckDir: CGHbase.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CGHbase_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CGHbase.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGHbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHbase’ version ‘1.35.0’
* 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 ‘CGHbase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘Biobase:::assayDataElement’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataDims’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.makeEmptyFeatureData: no visible global function definition for ‘is’
.makeEmptyFeatureData: no visible global function definition for ‘new’
.makeEmptyFeatureDataForRegions: no visible global function definition
  for ‘is’
.makeEmptyFeatureDataForRegions: no visible global function definition
  for ‘new’
frequencyPlotCalls: no visible global function definition for ‘rect’
frequencyPlotCalls: no visible global function definition for ‘box’
frequencyPlotCalls: no visible global function definition for ‘abline’
frequencyPlotCalls: no visible global function definition for ‘axis’
frequencyPlotCalls: no visible global function definition for ‘mtext’
frequencyPlotCalls: no visible global function definition for ‘median’
make_cghRaw: no visible global function definition for ‘read.table’
make_cghRaw: no visible global function definition for ‘new’
summaryPlot: no visible global function definition for ‘rect’
summaryPlot: no visible global function definition for ‘box’
summaryPlot: no visible global function definition for ‘abline’
summaryPlot: no visible global function definition for ‘axis’
summaryPlot: no visible global function definition for ‘mtext’
summaryPlot: no visible global function definition for ‘median’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘par’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘barplot’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘segments’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘gray’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘box’
frequencyPlot,cghRegions-missing: no visible global function definition
  for ‘axis’
initialize,cghCall: no visible global function definition for ‘new’
initialize,cghCall: no visible global function definition for
  ‘callNextMethod’
initialize,cghRaw: no visible global function definition for ‘new’
initialize,cghRaw: no visible global function definition for
  ‘callNextMethod’
initialize,cghRegions: no visible global function definition for ‘new’
initialize,cghRegions: no visible global function definition for
  ‘callNextMethod’
initialize,cghSeg: no visible global function definition for ‘new’
initialize,cghSeg: no visible global function definition for
  ‘callNextMethod’
plot.cghRegions,cghRegions-missing: no visible global function
  definition for ‘layout’
plot.cghRegions,cghRegions-missing: no visible global function
  definition for ‘par’
plot.cghRegions,cghRegions-missing: no visible global function
  definition for ‘segments’
plot.cghRegions,cghRegions-missing: no visible global function
  definition for ‘axis’
plot,cghCall-missing: no visible global function definition for ‘par’
plot,cghCall-missing: no visible global function definition for ‘rect’
plot,cghCall-missing: no visible global function definition for ‘axis’
plot,cghCall-missing: no visible global function definition for ‘box’
plot,cghCall-missing: no visible global function definition for
  ‘abline’
plot,cghCall-missing: no visible global function definition for ‘mtext’
plot,cghCall-missing: no visible global function definition for ‘title’
plot,cghCall-missing: no visible global function definition for
  ‘segments’
plot,cghCall-missing: no visible global function definition for
  ‘median’
plot,cghCall-missing : <anonymous>: no visible global function
  definition for ‘mad’
plot,cghRaw-missing: no visible global function definition for ‘mtext’
plot,cghRaw-missing: no visible global function definition for ‘abline’
plot,cghRaw-missing: no visible global function definition for ‘axis’
plot,cghRaw-missing: no visible global function definition for ‘median’
plot,cghRaw-missing : <anonymous>: no visible global function
  definition for ‘mad’
plot,cghSeg-missing: no visible global function definition for ‘mtext’
plot,cghSeg-missing: no visible global function definition for ‘abline’
plot,cghSeg-missing: no visible global function definition for ‘axis’
plot,cghSeg-missing: no visible global function definition for
  ‘segments’
plot,cghSeg-missing: no visible global function definition for ‘median’
plot,cghSeg-missing : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  abline axis barplot box callNextMethod gray is layout mad median
  mtext new par read.table rect segments title
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "barplot", "box", "layout",
             "mtext", "par", "rect", "segments", "title")
  importFrom("methods", "callNextMethod", "is", "new")
  importFrom("stats", "mad", "median")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/CGHbase.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
class.cghCall	0.236	0.005	0.242
class.cghRaw	0.690	0.023	0.725
class.cghRegions	0.329	0.002	0.358
class.cghSeg	0.034	0.001	0.034
copynumber	0.039	0.005	0.056
frequencyPlot	0	0	0
frequencyPlotCalls	0.001	0.000	0.001
make_cghRaw	0.193	0.003	0.195
summaryPlot	0.001	0.000	0.001