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neaGUI log file (check_x86_64_linux)

Wed Aug 21 00:23:49 2013: Checking package neaGUI (SVN revision 50) ...
* using log directory ‘/mnt/building/build_2013-08-21-00-07/RF_PKG_CHECK/PKGS/neaGUI.Rcheck’
* using R version 3.0.1 Patched (2013-08-19 r63623)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘neaGUI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘neaGUI’ version ‘0.99.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘setia pramana ’
New submission
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... WARNING
Found the following files with non-portable file names:
  inst/doc/neaGUI vignette.R
  inst/doc/neaGUI vignette.Rnw
  inst/doc/neaGUI vignette.pdf
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘neaGUI’ can be installed ... [2s/3s] OK
* checking installed package size ... OK
* checking package 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 ... WARNING
Subdirectory ‘inst/doc’ contains invalid file names:
  ‘neaGUI vignette.Rnw’ ‘neaGUI vignette.pdf’
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.
* 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 ... WARNING
‘library’ or ‘require’ calls not declared from:
  ‘GOstats’ ‘hwriter’
‘library’ or ‘require’ call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'
LoadRdata : OnOK: no visible binding for global variable ‘tt’
LoadRdata : onCancel: no visible binding for global variable ‘tt’
LoadRdata: no visible binding for global variable ‘tt’
checkFgs: no visible global function definition for ‘biocLite’
getAgs: no visible binding for global variable ‘tt’
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 binding for global variable ‘inptObjt’
getDb: no visible binding for global variable ‘tt’
getFGS: no visible binding for global variable ‘tt’
getNtw: no visible binding for global variable ‘tt’
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 binding for global variable ‘inptObjt’
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 binding for global variable ‘inptObjt’
neaGUI : instbioc: no visible global function definition for ‘biocLite’
neaGUI: no visible binding for '<<-' assignment to ‘tt’
neaGUI: no visible binding for global variable ‘tt’
neaGUI: no visible binding for '<<-' assignment to ‘fileAgs’
neaGUI: no visible binding for global variable ‘fileAgs’
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 : 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 binding for '<<-' assignment to ‘stat’
neaGUI : OnOK: no visible binding for global variable ‘stat’
neaGUI : onCancel: no visible binding for '<<-' assignment to
  ‘ReturnVal’
neaGUI : onCancel: no visible binding for global variable ‘tt’
saveHtml: no visible binding for global variable ‘FGS’
saveHtml: no visible binding for global variable ‘AnnotationDB’
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 binding for '<<-' assignment to ‘SavefileName’
savingRwd: no visible binding for global variable ‘SavefileName’

Found the following assignments to the global environment:
File ‘neaGUI/R/LoadRdata.R’:
  assign(paste(objt), inpt, envir = .GlobalEnv)
  assign("inptObjt", name, envir = .GlobalEnv)
File ‘neaGUI/R/getAgs.R’:
  assign("initdir", initdir, envir = .GlobalEnv)
  assign("AGS", ags, envir = .GlobalEnv)
  assign("AGS", ags, envir = .GlobalEnv)
File ‘neaGUI/R/getNtw.R’:
  assign("NETWORK", network, envir = .GlobalEnv)
  assign("NETWORK", network, envir = .GlobalEnv)
File ‘neaGUI/R/savingRwd.R’:
  assign("fileRwd", fileRwd, envir = .GlobalEnv)
  assign("filecsv", filecsv, envir = .GlobalEnv)
* checking Rd files ... NOTE
prepare_Rd: nea.Rd:58-60: Dropping empty section \details
prepare_Rd: nea.Rd:77-79: Dropping empty section \note
prepare_Rd: nea.Rd:71-73: Dropping empty section \references
prepare_Rd: nea.Rd:83-85: Dropping empty section \seealso
prepare_Rd: neaGUI-package.Rd:21-23: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file ‘/mnt/building/build_2013-08-21-00-07/RF_PKG_CHECK/PKGS/neaGUI.Rcheck/00_pkg_src/neaGUI/man/nea.Rd’:
  \examples lines wider than 100 characters:
     res<-nea(ags=AGS, fgs = FGS, fgslib = NULL, network=NETWORK, pnet = NULL, nperm = 50, stat="F", seed = 1234)
     NETWORK<-c("DNAJC6 RGL1","C1ORF156 NCBP2","AHCYL1 RTN3","PLK4 SKIV2L2","C22ORF28 MESDC2","TINP1 UTP23",    
     res<-nea(ags=AGS, fgs = "KEGG", fgslib = "KEGG.db", network=NETWORK, pnet = NULL, nperm = 5, stat="F", seed = 1234)

These lines will be truncated in the PDF manual.
* 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’ ... NOTE
The following directories should probably not be installed:
  ‘images’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘neagui_unit_tests.R’
 [1s/2s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
   ‘neaGUI vignette.Rnw’ ... [69s/132s] OK
 [69s/132s] OK
* checking re-building of vignette outputs ... [67s/130s] OK
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 5 notes.
See
  ‘/mnt/building/build_2013-08-21-00-07/RF_PKG_CHECK/PKGS/neaGUI.Rcheck/00check.log’
for details.

Run time: 355.44 seconds.
Additional Logs:   00install.out
Thanks to:
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