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CHECK report for MBCB on merida2

This page was generated on 2019-04-09 13:25:19 -0400 (Tue, 09 Apr 2019).

Package 916/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBCB 1.37.0
Jeff Allen
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MBCB
Branch: master
Last Commit: a363447
Last Changed Date: 2018-10-30 11:54:29 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: MBCB
Version: 1.37.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MBCB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MBCB_1.37.0.tar.gz
StartedAt: 2019-04-09 01:59:31 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:00:05 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 33.8 seconds
RetCode: 0
Status:  OK 
CheckDir: MBCB.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MBCB.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MBCB_1.37.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MBCB.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MBCB/DESCRIPTION’ ... OK
* this is package ‘MBCB’ version ‘1.37.0’
* 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 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 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-3.9-bioc/meat/MBCB.Rcheck/00check.log’
for details.

Installation output

MBCB.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MBCB
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MBCB’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MBCB)

Tests output

Example timings

MBCB.Rcheck/MBCB-Ex.timings

nameusersystemelapsed
bg.mcmc0.6150.0680.693
bg.rma0.0680.0230.090
mbcb.correct0.1190.0320.151
mbcb.gui0.0850.0100.100
mbcb.main0.0300.0040.033
mbcb.parseFile0.0390.0040.042