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BioC 3.5: CHECK report for plateCore on veracruz2

This page was generated on 2017-08-16 13:28:38 -0400 (Wed, 16 Aug 2017).

Package 988/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plateCore 1.34.0
Errol Strain
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/plateCore
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: plateCore
Version: 1.34.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings plateCore_1.34.0.tar.gz
StartedAt: 2017-08-16 06:33:39 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 06:36:33 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 173.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: plateCore.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings plateCore_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/plateCore.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plateCore/DESCRIPTION’ ... OK
* this is package ‘plateCore’ version ‘1.34.0’
* 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 ‘plateCore’ can be installed ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/plateCore.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘flowCore’ ‘lattice’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘flowViz’ ‘latticeExtra’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
panel.xyplot.flowPlate: warning in filterBoundary(filter =
  filter[[nm]], parameters = c(channel.x.name, channel.y.name), frame =
  frames[[nm]]): partial argument match of 'filter' to 'filter.object'
fixAutoFl,flowPlate: no visible binding for global variable
  ‘Sample.Type’
fpbind,flowPlate-flowPlate : <anonymous>: no visible binding for global
  variable ‘name’
gutterPlot,flowPlate: no visible global function definition for ‘plot’
mfiPlot,flowPlate: no visible global function definition for ‘plot’
plotPlate,flowPlate: no visible global function definition for ‘plot’
setControlGates,flowPlate: no visible binding for global variable
  ‘Sample.Type’
setControlGates,flowPlate: no visible binding for global variable
  ‘Channel’
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable ‘Well.Id’
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable ‘plateName’
setControlGates,flowPlate : <anonymous>: no visible binding for global
  variable ‘name’
Undefined global functions or variables:
  Channel Sample.Type Well.Id name plateName plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'flowPlate,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mfiPlot-methods      5.656  0.032   5.853
summaryStats-methods 5.469  0.025   5.614
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/plateCore.Rcheck/00check.log’
for details.


plateCore.Rcheck/00install.out:

* installing *source* package ‘plateCore’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
No methods found in "flowStats" for requests: %on%
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
No methods found in "flowStats" for requests: %on%
* DONE (plateCore)

plateCore.Rcheck/plateCore-Ex.timings:

nameusersystemelapsed
Subset-methods1.7030.0651.800
applyControlGates-methods4.7070.0404.817
compensate-methods2.1670.0372.256
compensationSet0.1450.0110.157
densityplot-methods0.9480.0150.983
fixAutoFl-methods2.4640.0222.531
flowPlate-class0.9750.0191.007
flowPlate-method1.3040.0231.357
fpbind-methods2.2250.0172.281
getGroups-methods0.5870.0210.622
gutterPlot-methods0.8400.0160.877
mfiPlot-methods5.6560.0325.853
on-methods4.5420.0414.718
panel.densityplot.flowPlate0.9280.0220.974
panel.xyplot.flowPlate1.0550.0181.116
plateCore-package1.2720.0151.320
plateSet-methods1.2740.0181.321
plotPlate-methods1.7870.0191.876
prepanel.densityplot.flowPlate0.8090.0120.849
prepanel.xyplot.flowPlate0.7360.0190.779
setControlGates-methods1.4870.0191.554
summaryStats-methods5.4690.0255.614
wellAnnotation-methods0.6380.0140.671
xyplot-methods0.7950.0160.824