BioC 3.3: CHECK report for neaGUI on zin2

Package: neaGUI

Version: 1.10.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings neaGUI_1.10.0.tar.gz

StartedAt: 2016-10-13 04:43:27 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:43:45 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 18.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: neaGUI.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings neaGUI_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/neaGUI.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘neaGUI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘neaGUI’ version ‘1.10.0’
* 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 ‘neaGUI’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'neaGUI' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.3-bioc/meat/neaGUI.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘hwriter’
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘AnnotationDbi’ ‘GO.db’ ‘GOstats’ ‘KEGG.db’ ‘RUnit’ ‘hwriter’
  ‘org.Hs.eg.db’ ‘reactome.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  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
countcon: warning in sort(table(c(unet)), decr = TRUE): partial
  argument match of 'decr' to 'decreasing'
.test: no visible global function definition for ‘defineTestSuite’
.test: no visible global function definition for ‘runTestSuite’
.test: no visible global function definition for ‘printTextProtocol’
LoadRdata: no visible global function definition for ‘tktoplevel’
LoadRdata: no visible global function definition for ‘tkframe’
LoadRdata: no visible global function definition for ‘tkwm.deiconify’
LoadRdata: no visible global function definition for ‘tkwm.title’
LoadRdata: no visible global function definition for ‘tkgrab.set’
LoadRdata: no visible global function definition for ‘tkfocus’
LoadRdata: no visible global function definition for ‘tkgrid’
LoadRdata: no visible global function definition for ‘tklabel’
LoadRdata: no visible global function definition for ‘tkscrollbar’
LoadRdata : <anonymous>: no visible global function definition for
  ‘tkyview’
LoadRdata: no visible global function definition for ‘tklistbox’
LoadRdata : <anonymous>: no visible global function definition for
  ‘tkset’
LoadRdata: no visible global function definition for ‘tkinsert’
LoadRdata: no visible global function definition for ‘tkselection.set’
LoadRdata: no visible global function definition for ‘tkgrid.configure’
LoadRdata : OnOK: no visible global function definition for
  ‘tkconfigure’
LoadRdata : OnOK: no visible binding for global variable ‘tt’
LoadRdata : OnOK: no visible global function definition for
  ‘tkcurselection’
LoadRdata : OnOK: no visible global function definition for ‘tkdestroy’
LoadRdata : OnOK: no visible global function definition for ‘tkfocus’
LoadRdata : onCancel: no visible global function definition for
  ‘tkgrab.release’
LoadRdata : onCancel: no visible global function definition for
  ‘tkdestroy’
LoadRdata : onCancel: no visible global function definition for
  ‘tkfocus’
LoadRdata : onCancel: no visible binding for global variable ‘tt’
LoadRdata: no visible global function definition for ‘tkbutton’
LoadRdata: no visible global function definition for ‘tkwait.window’
LoadRdata: no visible global function definition for ‘tkconfigure’
LoadRdata: no visible binding for global variable ‘tt’
checkFgs : is.installed: no visible global function definition for
  ‘installed.packages’
checkFgs: no visible global function definition for ‘tkmessageBox’
checkFgs: no visible global function definition for ‘biocLite’
gea: no visible global function definition for ‘phyper’
getAgs: no visible global function definition for ‘tclvalue’
getAgs: no visible global function definition for ‘tkgetOpenFile’
getAgs: no visible global function definition for ‘tkconfigure’
getAgs: no visible binding for global variable ‘tt’
getAgs: no visible global function definition for ‘tkmessageBox’
getAgs: no visible binding for '<<-' assignment to ‘filetype’
getAgs: no visible binding for global variable ‘filetype’
getAgs: no visible binding for '<<-' assignment to ‘fileAgs’
getAgs: no visible binding for global variable ‘fileAgs’
getAgs: no visible global function definition for ‘tclvalue<-’
getAgs: no visible global function definition for ‘read.csv’
getAgs: no visible binding for global variable ‘inptObjt’
getDb: no visible global function definition for ‘tkconfigure’
getDb: no visible binding for global variable ‘tt’
getDb : is.installed: no visible global function definition for
  ‘installed.packages’
getDb: no visible global function definition for ‘tkmessageBox’
getDb: no visible global function definition for ‘setRepositories’
getDb: no visible global function definition for ‘install.packages’
getFGS: no visible global function definition for ‘tclvalue’
getFGS: no visible global function definition for ‘tkgetOpenFile’
getFGS: no visible global function definition for ‘tkconfigure’
getFGS: no visible binding for global variable ‘tt’
getNtw: no visible global function definition for ‘tclvalue’
getNtw: no visible global function definition for ‘tkgetOpenFile’
getNtw: no visible global function definition for ‘tkconfigure’
getNtw: no visible binding for global variable ‘tt’
getNtw: no visible global function definition for ‘tkmessageBox’
getNtw: no visible binding for '<<-' assignment to ‘filetype’
getNtw: no visible binding for global variable ‘filetype’
getNtw: no visible binding for '<<-' assignment to ‘Ntwk’
getNtw: no visible binding for global variable ‘Ntwk’
getNtw: no visible global function definition for ‘tclvalue<-’
getNtw: no visible global function definition for ‘read.csv’
getNtw: no visible binding for global variable ‘inptObjt’
getPnet: no visible global function definition for ‘tclvalue’
getPnet: no visible global function definition for ‘tkgetOpenFile’
getPnet: no visible global function definition for ‘tkconfigure’
getPnet: no visible binding for global variable ‘tt’
getPnet: no visible binding for '<<-' assignment to ‘filepnet’
getPnet: no visible binding for global variable ‘filepnet’
getPnet: no visible global function definition for ‘tclvalue<-’
getPnet: no visible binding for global variable ‘inptObjt’
nea: no visible binding for global variable ‘KEGGPATHID2EXTID’
nea: no visible binding for global variable ‘org.Hs.egSYMBOL’
nea: no visible binding for global variable ‘reactomePATHID2EXTID’
nea: no visible binding for global variable ‘org.Hs.egGO2ALLEGS’
nea: no visible global function definition for ‘Ontology’
nea: no visible binding for global variable ‘reactomeGO2REACTOMEID’
nea: no visible binding for global variable ‘sd’
nea: no visible binding for global variable ‘KEGGPATHID2NAME’
nea : GoTerm: no visible binding for global variable ‘GOTERM’
nea : GoTerm: no visible global function definition for ‘GOID’
nea : GoTerm: no visible global function definition for ‘Term’
nea : GoTerm: no visible global function definition for ‘Definition’
nea : GoTerm: no visible global function definition for ‘Ontology’
nea: no visible binding for global variable ‘reactomePATHID2NAME’
neaGUI : is.installed: no visible global function definition for
  ‘installed.packages’
neaGUI : instbioc: no visible global function definition for ‘biocLite’
neaGUI : instcran: no visible global function definition for
  ‘install.packages’
neaGUI: no visible global function definition for ‘tkmessageBox’
neaGUI: no visible global function definition for ‘tclvalue’
neaGUI: no visible global function definition for ‘tclRequire’
neaGUI: no visible binding for '<<-' assignment to ‘tt’
neaGUI: no visible global function definition for ‘tktoplevel’
neaGUI: no visible global function definition for ‘tkwm.title’
neaGUI: no visible binding for global variable ‘tt’
neaGUI: no visible global function definition for ‘tkfocus’
neaGUI: no visible global function definition for ‘tkframe’
neaGUI: no visible global function definition for ‘tkfont.create’
neaGUI: no visible binding for '<<-' assignment to ‘fileAgs’
neaGUI: no visible global function definition for ‘tclVar’
neaGUI: no visible global function definition for ‘tkbutton’
neaGUI: no visible global function definition for ‘tkentry’
neaGUI: no visible binding for global variable ‘fileAgs’
neaGUI: no visible global function definition for ‘tklabel’
neaGUI: no visible global function definition for ‘tkgrid’
neaGUI: no visible global function definition for ‘tkgrid.configure’
neaGUI: no visible global function definition for ‘tkradiobutton’
neaGUI: no visible global function definition for ‘tkconfigure’
neaGUI: no visible global function definition for ‘tkwidget’
neaGUI: no visible binding for '<<-' assignment to ‘pkgDb’
neaGUI: no visible binding for '<<-' assignment to ‘dbEntry’
neaGUI: no visible binding for global variable ‘pkgDb’
neaGUI: no visible binding for global variable ‘dbEntry’
neaGUI: no visible binding for '<<-' assignment to ‘Ntwk’
neaGUI: no visible binding for global variable ‘Ntwk’
neaGUI: no visible binding for '<<-' assignment to ‘filepnet’
neaGUI: no visible binding for global variable ‘filepnet’
neaGUI: no visible global function definition for ‘tkcheckbutton’
neaGUI : OnOK: no visible global function definition for ‘tclvalue’
neaGUI : OnOK: no visible global function definition for ‘tcl’
neaGUI : OnOK: no visible global function definition for ‘tkmessageBox’
neaGUI : OnOK: no visible global function definition for ‘tkconfigure’
neaGUI : OnOK: no visible binding for global variable ‘tt’
neaGUI : OnOK: no visible binding for global variable ‘pkgDb’
neaGUI : OnOK: no visible binding for '<<-' assignment to
  ‘AnnotationDB’
neaGUI : OnOK: no visible global function definition for ‘tclvalue<-’
neaGUI : OnOK: no visible global function definition for ‘tkfocus’
neaGUI : OnOK: no visible binding for '<<-' assignment to ‘stat’
neaGUI : OnOK: no visible binding for global variable ‘AnnotationDB’
neaGUI : OnOK: no visible binding for global variable ‘stat’
neaGUI : OnOK: no visible binding for global variable ‘pb’
neaGUI : OnOK: no visible global function definition for ‘write.csv2’
neaGUI : onCancel: no visible binding for '<<-' assignment to
  ‘ReturnVal’
neaGUI : onCancel: no visible global function definition for
  ‘tkgrab.release’
neaGUI : onCancel: no visible binding for global variable ‘tt’
neaGUI : onCancel: no visible global function definition for
  ‘tkdestroy’
neaGUI : onHelp: no visible global function definition for
  ‘tkgrab.release’
neaGUI : onHelp: no visible binding for global variable ‘window’
neaGUI : onHelp: no visible global function definition for ‘browseURL’
neaGUI: no visible global function definition for ‘tkwait.window’
neaMod: no visible global function definition for ‘tkProgressBar’
neaMod: no visible binding for global variable ‘KEGGPATHID2EXTID’
neaMod: no visible binding for global variable ‘org.Hs.egSYMBOL’
neaMod: no visible binding for global variable ‘reactomePATHID2EXTID’
neaMod: no visible binding for global variable ‘org.Hs.egGO2ALLEGS’
neaMod: no visible global function definition for ‘Ontology’
neaMod: no visible binding for global variable ‘reactomeGO2REACTOMEID’
neaMod: no visible global function definition for ‘setTkProgressBar’
neaMod: no visible binding for global variable ‘sd’
neaMod: no visible binding for global variable ‘KEGGPATHID2NAME’
neaMod : GoTerm: no visible binding for global variable ‘GOTERM’
neaMod : GoTerm: no visible global function definition for ‘GOID’
neaMod : GoTerm: no visible global function definition for ‘Term’
neaMod : GoTerm: no visible global function definition for ‘Definition’
neaMod : GoTerm: no visible global function definition for ‘Ontology’
neaMod: no visible binding for global variable ‘reactomePATHID2NAME’
saveHtml: no visible global function definition for ‘openPage’
saveHtml: no visible binding for global variable ‘AGS’
saveHtml: no visible binding for global variable ‘stat’
saveHtml: no visible binding for global variable ‘NETWORK’
saveHtml: no visible binding for global variable ‘nperm’
saveHtml: no visible global function definition for ‘closePage’
saveHtml: no visible global function definition for ‘browseURL’
savingRwd: no visible global function definition for ‘tclvalue’
savingRwd: no visible global function definition for ‘tkgetSaveFile’
savingRwd: no visible binding for '<<-' assignment to ‘SavefileName’
savingRwd: no visible binding for global variable ‘SavefileName’
savingRwd: no visible global function definition for ‘tclvalue<-’
savingRwd: no visible global function definition for ‘tkmessageBox’
zstat: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  AGS AnnotationDB Definition GOID GOTERM KEGGPATHID2EXTID
  KEGGPATHID2NAME NETWORK Ntwk Ontology SavefileName Term biocLite
  browseURL closePage dbEntry defineTestSuite fileAgs filepnet filetype
  inptObjt install.packages installed.packages nperm openPage
  org.Hs.egGO2ALLEGS org.Hs.egSYMBOL pb phyper pkgDb printTextProtocol
  reactomeGO2REACTOMEID reactomePATHID2EXTID reactomePATHID2NAME
  read.csv runTestSuite sd setRepositories setTkProgressBar stat tcl
  tclRequire tclVar tclvalue tclvalue<- tkProgressBar tkbutton
  tkcheckbutton tkconfigure tkcurselection tkdestroy tkentry tkfocus
  tkfont.create tkframe tkgetOpenFile tkgetSaveFile tkgrab.release
  tkgrab.set tkgrid tkgrid.configure tkinsert tklabel tklistbox
  tkmessageBox tkradiobutton tkscrollbar tkselection.set tkset
  tktoplevel tkwait.window tkwidget tkwm.deiconify tkwm.title tkyview
  tt window write.csv2
Consider adding
  importFrom("stats", "phyper", "sd", "window")
  importFrom("utils", "browseURL", "install.packages",
             "installed.packages", "read.csv", "setRepositories",
             "write.csv2")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: nea.Rd:58-60: Dropping empty section \details
prepare_Rd: neaGUI-package.Rd:21-23: Dropping empty section \references
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘neagui_unit_tests.R’
 ERROR
Running the tests in ‘tests/neagui_unit_tests.R’ failed.
Last 13 lines of output:
  Loading required package: neaGUI
  Loading required package: tcltk
  [1] TRUE
  Warning message:
  Package 'neaGUI' is deprecated and will be removed from Bioconductor
    version 3.3 
  > neaGUI:::.test()
  Error in is(testSuite, "RUnitTestSuite") : 
    object 'testsuite.neaGUI' not found
  Error in .testData[[.currentTestSuiteName]] : 
    attempt to select less than one element in get1index
  Calls: <Anonymous> ... runTestSuite -> .sourceTestFile -> <Anonymous> -> .addError
  Execution halted
* 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 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/neaGUI.Rcheck/00check.log’
for details.

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("neaGUI") || stop("unable to load neaGUI package")
Loading required package: neaGUI
Loading required package: tcltk
[1] TRUE
Warning message:
Package 'neaGUI' is deprecated and will be removed from Bioconductor
  version 3.3 
> neaGUI:::.test()
Error in is(testSuite, "RUnitTestSuite") : 
  object 'testsuite.neaGUI' not found
Error in .testData[[.currentTestSuiteName]] : 
  attempt to select less than one element in get1index
Calls: <Anonymous> ... runTestSuite -> .sourceTestFile -> <Anonymous> -> .addError
Execution halted

* installing *source* package ‘neaGUI’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'neaGUI' is deprecated and will be removed from Bioconductor
  version 3.3
* DONE (neaGUI)

name	user	system	elapsed
nea	0.001	0.000	0.001
neaGUI-package	0.001	0.000	0.000
neaGUI	0	0	0