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BioC 2.13: CHECK report for neaGUI on perceval

This page was generated on 2014-04-05 09:53:14 -0700 (Sat, 05 Apr 2014).

Package 477/750HostnameOS / ArchBUILDCHECKBUILD BIN
neaGUI 1.0.0
Setia Pramana
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/neaGUI
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: neaGUI
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch neaGUI_1.0.0.tar.gz
StartedAt: 2014-04-05 03:00:20 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:01:12 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 51.1 seconds
RetCode: 0
Status:  OK 
CheckDir: neaGUI.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/neaGUI.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.0.0’
* 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 ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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.
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'
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’
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’
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 ‘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 binding for global variable ‘tt’
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’
savingRwd: no visible binding for '<<-' assignment to ‘SavefileName’
savingRwd: no visible binding for global variable ‘SavefileName’
* 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’ ... 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘neaGUI_vignette.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* 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

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
nea0.0070.0010.008
neaGUI-package0.0040.0010.005
neaGUI0.0040.0010.005