BioC 2.13: CHECK report for flowUtils on perceval

Package: flowUtils

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowUtils_1.22.0.tar.gz

StartedAt: 2014-04-05 01:19:27 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:21:17 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 109.4 seconds

RetCode: 0

Status:  OK

CheckDir: flowUtils.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/flowUtils.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 ‘flowUtils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowUtils’ version ‘1.22.0’
* 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 ‘flowUtils’ can be installed ... [10s/10s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’
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
Unexported objects imported by ‘:::’ calls:
  ‘flowViz:::ell2Polygon’ ‘flowViz:::norm2Polygon’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.fuEnv’
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
testGatingCompliance: warning in defineTestSuite("GatingTestSuite", dir
  = system.file("RUnitScript_Files", package = "flowUtils"),
  testFileRegexp = "^runit.+\\.[rR]$", testFuncRegexp = "^test.+"):
  partial argument match of 'dir' to 'dirs'
testGatingCompliance: warning in printHTMLProtocol(testResult, file =
  paste(file, ".html", sep = "")): partial argument match of 'file' to
  'fileName'
xmlEllipsoidGateNode: no visible global function definition for
  ‘xmlFociNode’
xmlEllipsoidGateNode: no visible global function definition for
  ‘xmlEdgeNode’
* checking Rd files ... OK
* 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 examples ... [5s/6s] OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/flowUtils.Rcheck/00check.log’
for details.

* installing *source* package ‘flowUtils’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
* DONE (flowUtils)

name	user	system	elapsed
read.gatingML	0.545	0.022	0.626
testGatingCompliance	0.008	0.001	0.011