BioC 2.13: CHECK report for flowUtils on moscato1

Package: flowUtils

Version: 1.22.0

Command: rm -rf flowUtils.buildbin-libdir && mkdir flowUtils.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowUtils.buildbin-libdir flowUtils_1.22.0.tar.gz >flowUtils-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=flowUtils.buildbin-libdir --install="check:flowUtils-install.out" --force-multiarch --no-vignettes --timings flowUtils_1.22.0.tar.gz && mv flowUtils.buildbin-libdir/* flowUtils.Rcheck/ && rmdir flowUtils.buildbin-libdir

StartedAt: 2014-04-05 03:55:04 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:57:13 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 129.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowUtils.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/flowUtils.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'flowUtils' can be installed ... 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
* 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
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 ...
** running examples for arch 'i386' ... [6s] OK
** running examples for arch 'x64' ... [6s] OK
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/flowUtils.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flowUtils' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowUtils' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowUtils' as flowUtils_1.22.0.zip
* DONE (flowUtils)

name	user	system	elapsed
read.gatingML	0.52	0.00	1.05
testGatingCompliance	0	0	0

name	user	system	elapsed
read.gatingML	0.55	0.02	0.56
testGatingCompliance	0	0	0