neaGUI 1.9.0
Setia Pramana
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/neaGUI | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### rm -rf neaGUI.buildbin-libdir neaGUI.Rcheck && mkdir neaGUI.buildbin-libdir neaGUI.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=neaGUI.buildbin-libdir neaGUI_1.9.0.tar.gz >neaGUI.Rcheck\00install.out 2>&1 && cp neaGUI.Rcheck\00install.out neaGUI-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=neaGUI.buildbin-libdir --install="check:neaGUI-install.out" --force-multiarch --no-vignettes --timings neaGUI_1.9.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/neaGUI.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'neaGUI/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'neaGUI' version '1.9.0'
* 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 whether package 'neaGUI' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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' '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: 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'
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'
Undefined global functions or variables:
AGS AnnotationDB Definition GOID GOTERM KEGGPATHID2EXTID
KEGGPATHID2NAME NETWORK Ntwk Ontology SavefileName Term biocLite
closePage dbEntry defineTestSuite fileAgs filepnet filetype inptObjt
nperm openPage org.Hs.egGO2ALLEGS org.Hs.egSYMBOL pb pkgDb
printTextProtocol reactomeGO2REACTOMEID reactomePATHID2EXTID
reactomePATHID2NAME runTestSuite 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
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [0s] OK
** running examples for arch 'x64' ... [0s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'neagui_unit_tests.R' [0s]
[0s] OK
** running tests for arch 'x64' ...
Running 'neagui_unit_tests.R' [0s]
[0s] 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
'c:/biocbld/bbs-3.3-bioc/meat/neaGUI.Rcheck/00check.log'
for details.
install for i386
* 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
install for x64
* installing *source* package 'neaGUI' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'neaGUI' as neaGUI_1.9.0.zip
* DONE (neaGUI)