BioC 3.3: CHECK report for flowUtils on linux2.bioconductor.org

Package: flowUtils

Version: 1.35.1

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowUtils_1.35.1.tar.gz

StartedAt: 2015-10-27 03:55:27 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:56:16 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 49.1 seconds

RetCode: 0

Status:  OK

CheckDir: flowUtils.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowUtils_1.35.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/flowUtils.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.35.1’
* 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 ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 ... 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 ‘gatingMLData’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
fasinhTr: no visible global function definition for ‘asinhtGml2’
flinTr: no visible global function definition for ‘lintGml2’
flogTr: no visible global function definition for ‘logtGml2’
fratioTr: no visible global function definition for ‘ratiotGml2’
hyperlogTr: no visible global function definition for ‘hyperlogtGml2’
logicleTr: no visible global function definition for ‘logicletGml2’
xmlEllipsoidGateNode: no visible global function definition for
  ‘xmlFociNode’
xmlEllipsoidGateNode: no visible global function definition for
  ‘xmlEdgeNode’
Undefined global functions or variables:
  asinhtGml2 hyperlogtGml2 lintGml2 logicletGml2 logtGml2 ratiotGml2
  xmlEdgeNode xmlFociNode
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/flowUtils.Rcheck/00check.log’
for details.

* installing *source* package ‘flowUtils’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowUtils)

name	user	system	elapsed
read.gatingML	0.833	0.004	0.843
testGatingMLCompliance	0.001	0.000	0.001
write.gatingML	1.604	0.158	1.765