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BioC 3.1: CHECK report for MBCB on morelia

This page was generated on 2015-10-09 09:39:24 -0700 (Fri, 09 Oct 2015).

Package 562/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MBCB 1.22.0
Jeff Allen
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/MBCB
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MBCB
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MBCB_1.22.0.tar.gz
StartedAt: 2015-10-09 03:34:18 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 03:34:50 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 31.5 seconds
RetCode: 0
Status:  OK 
CheckDir: MBCB.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MBCB_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/MBCB.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 ‘MBCB/DESCRIPTION’ ... OK
* this is package ‘MBCB’ version ‘1.22.0’
* 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 ... [2s/3s] 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’
* 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 ... [2s/2s] 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-3.1-bioc/meat/MBCB.Rcheck/00check.log’
for details.

MBCB.Rcheck/00install.out:

* 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)

MBCB.Rcheck/MBCB-Ex.timings:

nameusersystemelapsed
bg.mcmc0.6550.0530.702
bg.rma0.1350.0130.148
mbcb.correct0.0930.0300.121
mbcb.gui0.0510.0080.064
mbcb.main0.0290.0080.037
mbcb.parseFile0.0520.0030.054