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BioC 3.5: CHECK report for plateCore on malbec2

This page was generated on 2017-08-16 13:13:24 -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: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.34.0.tar.gz
StartedAt: 2017-08-16 01:18:27 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:20:49 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 142.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: plateCore.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/plateCore.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 1 WARNING, 3 NOTEs
See
  ‘/home/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
No methods found in "flowStats" for requests: %on%
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "flowStats" for requests: %on%
* DONE (plateCore)

plateCore.Rcheck/plateCore-Ex.timings:

nameusersystemelapsed
Subset-methods1.6600.0241.687
applyControlGates-methods4.6120.0124.629
compensate-methods1.9200.0001.922
compensationSet0.3800.0000.378
densityplot-methods0.5640.0000.564
fixAutoFl-methods2.0360.0042.044
flowPlate-class0.9800.0040.986
flowPlate-method1.0160.0001.020
fpbind-methods2.2320.0042.242
getGroups-methods0.5320.0000.532
gutterPlot-methods0.8080.0000.808
mfiPlot-methods4.5680.0004.575
on-methods3.6040.0123.619
panel.densityplot.flowPlate0.7640.0000.765
panel.xyplot.flowPlate0.9360.0040.941
plateCore-package1.3600.0001.361
plateSet-methods0.9840.0040.987
plotPlate-methods1.2040.0001.206
prepanel.densityplot.flowPlate0.6080.0040.611
prepanel.xyplot.flowPlate0.5920.0040.595
setControlGates-methods1.0560.0001.059
summaryStats-methods4.8840.0004.892
wellAnnotation-methods0.4960.0000.496
xyplot-methods0.5680.0040.570