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BioC 3.0: CHECK report for flowUtils on zin1

This page was generated on 2015-04-10 09:37:33 -0700 (Fri, 10 Apr 2015).

Package 322/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowUtils 1.30.0
Josef Spidlen
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flowUtils
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: flowUtils
Version: 1.30.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings flowUtils_1.30.0.tar.gz
StartedAt: 2015-04-09 23:58:18 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:59:26 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 67.7 seconds
RetCode: 0
Status:  OK 
CheckDir: flowUtils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings flowUtils_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/flowUtils.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.30.0’
* 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 ... [6s/6s] 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’
* 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 ... [5s/6s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/flowUtils.Rcheck/00check.log’
for details.

flowUtils.Rcheck/00install.out:

* 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)

flowUtils.Rcheck/flowUtils-Ex.timings:

nameusersystemelapsed
read.gatingML0.8400.0081.030
testGatingMLCompliance0.0000.0000.001
write.gatingML1.7800.1161.978