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BioC 3.0: CHECK report for plateCore on zin1

This page was generated on 2015-04-10 09:38:39 -0700 (Fri, 10 Apr 2015).

Package 666/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plateCore 1.24.0
Errol Strain
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/plateCore
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 [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: plateCore
Version: 1.24.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.24.0.tar.gz
StartedAt: 2015-04-10 03:03:10 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:07:07 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 237.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: plateCore.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings plateCore_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/plateCore.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 ‘plateCore/DESCRIPTION’ ... OK
* this is package ‘plateCore’ version ‘1.24.0’
* 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 ... [15s/17s] 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'
* 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 ... [74s/75s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
summaryStats-methods      8.333  0.004   8.451
applyControlGates-methods 8.261  0.008   8.458
mfiPlot-methods           7.608  0.016   7.640
on-methods                6.217  0.076   6.388
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-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-methods2.6080.0122.622
applyControlGates-methods8.2610.0088.458
compensate-methods3.2600.0003.352
compensationSet0.3760.0040.380
densityplot-methods1.3000.0081.311
fixAutoFl-methods3.5960.0003.612
flowPlate-class2.0160.0122.038
flowPlate-method1.8520.0081.935
fpbind-methods3.9850.0044.127
getGroups-methods1.0120.0001.291
gutterPlot-methods1.1640.0041.188
mfiPlot-methods7.6080.0167.640
on-methods6.2170.0766.388
panel.densityplot.flowPlate1.4360.0081.448
panel.xyplot.flowPlate1.2600.0121.361
plateCore-package1.8160.0001.842
plateSet-methods1.7960.0081.816
plotPlate-methods2.3960.0042.515
prepanel.densityplot.flowPlate1.2840.0041.297
prepanel.xyplot.flowPlate0.9240.0040.927
setControlGates-methods1.8920.0041.902
summaryStats-methods8.3330.0048.451
wellAnnotation-methods0.8480.0040.855
xyplot-methods0.9600.0001.004