BioC 3.5: CHECK report for MBCB on oaxaca

Package: MBCB

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MBCB_1.29.0.tar.gz

StartedAt: 2017-03-04 05:19:26 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:19:55 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 29.6 seconds

RetCode: 0

Status:  OK

CheckDir: MBCB.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MBCB_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MBCB.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 ‘MBCB/DESCRIPTION’ ... OK
* this is package ‘MBCB’ version ‘1.29.0’
* 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 ‘MBCB’ 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 ... NOTE
Packages in Depends field not imported from:
  ‘tcltk’ ‘tcltk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bg.mcmc: no visible binding for global variable ‘obsbead’
bg.mcmc: no visible binding for global variable ‘obsnc’
esttruesig: no visible binding for global variable ‘obsbead’
esttruesig: no visible binding for global variable ‘truesignal’
liksig: no visible binding for global variable ‘obsbead’
liksig.all: no visible binding for global variable ‘obsbead’
liksig.all: no visible binding for global variable ‘obsnc’
liksig.gamnoise: no visible binding for global variable ‘nbead’
liksig.gamnoise: no visible binding for global variable ‘sortedObsbead’
liksigall.gamnoise: no visible binding for global variable ‘obsnc’
mbcb.correct: no visible binding for '<<-' assignment to ‘trialNames’
mbcb.correct: no visible binding for '<<-' assignment to ‘n.array’
mbcb.correct: no visible binding for '<<-' assignment to ‘truesignal’
mbcb.correct: no visible binding for '<<-' assignment to ‘truenoise’
mbcb.correct: no visible binding for '<<-' assignment to ‘obsbead’
mbcb.correct: no visible binding for '<<-' assignment to ‘obsnc’
mbcb.correct: no visible binding for '<<-' assignment to ‘nbead’
mbcb.correct: no visible binding for global variable ‘n.array’
mbcb.correct: no visible global function definition for
  ‘setTkProgressBar’
mbcb.correct: no visible binding for global variable ‘mbcbPB’
mbcb.correct: no visible binding for global variable ‘obsbead’
mbcb.correct: no visible binding for '<<-' assignment to ‘nnc’
mbcb.correct: no visible binding for '<<-' assignment to
  ‘sortedObsbead’
mbcb.correct: no visible binding for global variable ‘obsnc’
mbcb.correct: no visible binding for global variable ‘nbead’
mbcb.correct: no visible binding for global variable ‘nnc’
mbcb.correct: no visible binding for global variable ‘sortedObsbead’
mbcb.gui: no visible global function definition for ‘tclVar’
mbcb.gui : import.sig: no visible global function definition for
  ‘tclvalue’
mbcb.gui : import.sig: no visible global function definition for
  ‘tkgetOpenFile’
mbcb.gui : import.sig: no visible global function definition for
  ‘tkconfigure’
mbcb.gui : import.sig: no visible global function definition for
  ‘tclVar’
mbcb.gui : import.negCon: no visible global function definition for
  ‘tclvalue’
mbcb.gui : import.negCon: no visible global function definition for
  ‘tkgetOpenFile’
mbcb.gui : import.negCon: no visible global function definition for
  ‘tkconfigure’
mbcb.gui : import.negCon: no visible global function definition for
  ‘tclVar’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tkmessageBox’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tk2notetab’
mbcb.gui : actions.norm: no visible binding for global variable
  ‘main.nb’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tk2notetab.select’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tclVar’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tkframe’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tkcheckbutton’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tkentry’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tkbutton’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tkconfigure’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tkgrid’
mbcb.gui : actions.norm: no visible global function definition for
  ‘tklabel’
mbcb.gui : actions.norm : initiate: no visible global function
  definition for ‘tclvalue’
mbcb.gui : actions.norm : initiate: no visible global function
  definition for ‘tkmessageBox’
mbcb.gui : actions.norm : updateChecks: no visible global function
  definition for ‘tclvalue’
mbcb.gui : actions.norm : updateChecks: no visible global function
  definition for ‘tkconfigure’
mbcb.gui : normalizeData: no visible global function definition for
  ‘tk2notetab’
mbcb.gui : normalizeData: no visible binding for global variable
  ‘main.nb’
mbcb.gui : normalizeData: no visible global function definition for
  ‘tk2notetab.select’
mbcb.gui : normalizeData: no visible global function definition for
  ‘tclVar’
mbcb.gui : normalizeData: no visible global function definition for
  ‘tkframe’
mbcb.gui : normalizeData: no visible global function definition for
  ‘tkradiobutton’
mbcb.gui : normalizeData: no visible global function definition for
  ‘tkbutton’
mbcb.gui : normalizeData : <anonymous>: no visible global function
  definition for ‘tclvalue’
mbcb.gui : normalizeData: no visible global function definition for
  ‘tkgrid’
mbcb.gui : normalizeData: no visible global function definition for
  ‘tklabel’
mbcb.gui : exportData: no visible global function definition for
  ‘tclVar’
mbcb.gui : exportData: no visible global function definition for
  ‘tk2notetab’
mbcb.gui : exportData: no visible binding for global variable ‘main.nb’
mbcb.gui : exportData: no visible global function definition for
  ‘tk2notetab.select’
mbcb.gui : exportData: no visible global function definition for
  ‘tkentry’
mbcb.gui : exportData: no visible global function definition for
  ‘tkbutton’
mbcb.gui : exportData : <anonymous>: no visible binding for global
  variable ‘outFile’
mbcb.gui : exportData : setOut: no visible binding for '<<-' assignment
  to ‘outFile’
mbcb.gui : exportData : setOut: no visible global function definition
  for ‘tclvalue’
mbcb.gui : exportData : setOut: no visible global function definition
  for ‘tkgetSaveFile’
mbcb.gui : exportData : setOut: no visible binding for global variable
  ‘outFile’
mbcb.gui : exportData : setOut: no visible global function definition
  for ‘tkconfigure’
mbcb.gui : exportData : setOut: no visible global function definition
  for ‘tclVar’
mbcb.gui : exportData : setDetOut: no visible global function
  definition for ‘tclvalue’
mbcb.gui : exportData : setDetOut: no visible global function
  definition for ‘tkgetSaveFile’
mbcb.gui : exportData : setDetOut: no visible global function
  definition for ‘tkconfigure’
mbcb.gui : exportData : setDetOut: no visible global function
  definition for ‘tclVar’
mbcb.gui : exportData: no visible global function definition for
  ‘tkgrid’
mbcb.gui : exportData: no visible global function definition for
  ‘tklabel’
mbcb.gui : exportData : eval: no visible global function definition for
  ‘tkmessageBox’
mbcb.gui : exportData : eval: no visible binding for '<<-' assignment
  to ‘mbcbPB’
mbcb.gui : exportData : eval: no visible global function definition for
  ‘tkProgressBar’
mbcb.gui : exportData : eval: no visible global function definition for
  ‘tkconfigure’
mbcb.gui : exportData : eval: no visible global function definition for
  ‘tclvalue’
mbcb.gui : exportData : eval: no visible global function definition for
  ‘tkdestroy’
mbcb.gui : help.about: no visible global function definition for
  ‘tkmessageBox’
mbcb.gui : removeItem: no visible global function definition for
  ‘tkcurselection’
mbcb.gui : removeItem: no visible binding for global variable
  ‘importTab.f.dataList’
mbcb.gui : removeItem: no visible global function definition for
  ‘tkdelete’
mbcb.gui : Try: no visible global function definition for
  ‘tkmessageBox’
mbcb.gui: no visible global function definition for ‘tktoplevel’
mbcb.gui: no visible global function definition for ‘tkwm.resizable’
mbcb.gui: no visible global function definition for ‘tkfocus’
mbcb.gui: no visible binding for '<<-' assignment to ‘main.nb’
mbcb.gui: no visible global function definition for ‘tk2notebook’
mbcb.gui: no visible global function definition for ‘tk2notetab’
mbcb.gui: no visible binding for global variable ‘main.nb’
mbcb.gui: no visible global function definition for ‘tkframe’
mbcb.gui: no visible global function definition for ‘tklabel’
mbcb.gui: no visible global function definition for ‘tkentry’
mbcb.gui: no visible global function definition for ‘tkbutton’
mbcb.gui: no visible global function definition for ‘tkgrid’
mbcb.main: no visible binding for global variable ‘n.array’
mbcb.main: no visible binding for '<<-' assignment to ‘bgCorrSig’
mbcb.main: no visible binding for global variable ‘bgCorrSig’
mbcb.parseFile: no visible global function definition for
  ‘setTkProgressBar’
mbcb.parseFile: no visible binding for global variable ‘mbcbPB’
mbcb.parseFile: no visible binding for '<<-' assignment to ‘types’
mbcb.parseFile: no visible binding for global variable ‘types’
mbcb.parseFile: no visible binding for '<<-' assignment to ‘sig2’
mbcb.parseFile: no visible binding for global variable ‘sig2’
printMBCBOutput: no visible binding for '<<-' assignment to ‘dete’
printMBCBOutput: no visible global function definition for
  ‘setTkProgressBar’
printMBCBOutput: no visible binding for global variable ‘mbcbPB’
printMBCBOutput: no visible binding for global variable ‘trialNames’
truesig: no visible binding for global variable ‘obsbead’
Undefined global functions or variables:
  bgCorrSig importTab.f.dataList main.nb mbcbPB n.array nbead nnc
  obsbead obsnc outFile setTkProgressBar sig2 sortedObsbead tclVar
  tclvalue tk2notebook tk2notetab tk2notetab.select tkProgressBar
  tkbutton tkcheckbutton tkconfigure tkcurselection tkdelete tkdestroy
  tkentry tkfocus tkframe tkgetOpenFile tkgetSaveFile tkgrid tklabel
  tkmessageBox tkradiobutton tktoplevel tkwm.resizable trialNames
  truesignal types
* 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
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MBCB.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
bg.mcmc	0.602	0.031	0.630
bg.rma	0.144	0.012	0.154
mbcb.correct	0.064	0.015	0.079
mbcb.gui	0.047	0.007	0.057
mbcb.main	0.244	0.020	0.262
mbcb.parseFile	0.041	0.003	0.045