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BioC 3.2: CHECK report for neaGUI on perceval

This page was generated on 2015-10-27 17:35:52 -0400 (Tue, 27 Oct 2015).

Package 699/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
neaGUI 1.8.0
Setia Pramana
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/neaGUI
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: neaGUI
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings neaGUI_1.8.0.tar.gz
StartedAt: 2015-10-27 10:27:05 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 10:27:32 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 27.2 seconds
RetCode: 0
Status:  OK 
CheckDir: neaGUI.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings neaGUI_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/neaGUI.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* 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 ... [1s/1s] OK
* 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 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’ ‘hwriter’ ‘KEGG.db’ ‘org.Hs.eg.db’
  ‘reactome.db’ ‘RUnit’
  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’
checkFgs: no visible global function definition for ‘tkmessageBox’
checkFgs: no visible global function definition for ‘biocLite’
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 binding for global variable ‘inptObjt’
getDb: no visible global function definition for ‘tkconfigure’
getDb: no visible binding for global variable ‘tt’
getDb: no visible global function definition for ‘tkmessageBox’
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 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’
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’
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 ‘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 : instbioc: no visible global function definition for ‘biocLite’
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 : 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: 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 ‘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’
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’
* 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘neagui_unit_tests.R’ [1s/1s]
 [1s/1s] 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/neaGUI.Rcheck/00check.log’
for details.


neaGUI.Rcheck/00install.out:

* 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
* DONE (neaGUI)

neaGUI.Rcheck/neaGUI-Ex.timings:

nameusersystemelapsed
nea0.0010.0010.001
neaGUI-package0.0010.0000.000
neaGUI0.0010.0000.001