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 | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings neaGUI_1.8.0.tar.gz
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* 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.