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BioC 3.5: CHECK report for plateCore on tokay2

This page was generated on 2017-10-18 14:20:29 -0400 (Wed, 18 Oct 2017).

Package 988/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plateCore 1.34.0
Errol Strain
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/plateCore
Branch: RELEASE_3_5
Last Commit: 09fbef6
Last Changed Date: 2017-04-24 15:45:44 -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: rm -rf plateCore.buildbin-libdir plateCore.Rcheck && mkdir plateCore.buildbin-libdir plateCore.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=plateCore.buildbin-libdir plateCore_1.34.0.tar.gz >plateCore.Rcheck\00install.out 2>&1 && cp plateCore.Rcheck\00install.out plateCore-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=plateCore.buildbin-libdir --install="check:plateCore-install.out" --force-multiarch --no-vignettes --timings plateCore_1.34.0.tar.gz
StartedAt: 2017-10-18 02:03:41 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:08:12 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 271.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: plateCore.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf plateCore.buildbin-libdir plateCore.Rcheck && mkdir plateCore.buildbin-libdir plateCore.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=plateCore.buildbin-libdir plateCore_1.34.0.tar.gz >plateCore.Rcheck\00install.out 2>&1 && cp plateCore.Rcheck\00install.out plateCore-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=plateCore.buildbin-libdir --install="check:plateCore-install.out" --force-multiarch --no-vignettes --timings plateCore_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/plateCore.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
summaryStats-methods 5.03      0    5.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
applyControlGates-methods 6.62      0    6.62
mfiPlot-methods           5.62      0    5.62
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/plateCore.Rcheck/00check.log'
for details.


plateCore.Rcheck/00install.out:

install for i386

* installing *source* package 'plateCore' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'

install for x64

* installing *source* package 'plateCore' ...
** testing if installed package can be loaded
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
* MD5 sums
packaged installation of 'plateCore' as plateCore_1.34.0.zip
* DONE (plateCore)

plateCore.Rcheck/examples_i386/plateCore-Ex.timings:

nameusersystemelapsed
Subset-methods1.450.101.56
applyControlGates-methods4.310.044.34
compensate-methods1.650.031.68
compensationSet0.140.010.16
densityplot-methods0.620.030.65
fixAutoFl-methods2.350.022.38
flowPlate-class1.330.001.33
flowPlate-method1.020.001.02
fpbind-methods2.340.032.37
getGroups-methods0.500.050.55
gutterPlot-methods0.810.010.83
mfiPlot-methods4.320.024.33
on-methods3.540.083.62
panel.densityplot.flowPlate0.830.010.84
panel.xyplot.flowPlate0.920.000.93
plateCore-package1.030.001.03
plateSet-methods1.080.001.08
plotPlate-methods1.270.001.26
prepanel.densityplot.flowPlate0.730.020.75
prepanel.xyplot.flowPlate0.960.010.97
setControlGates-methods1.140.001.14
summaryStats-methods5.030.005.03
wellAnnotation-methods0.530.000.53
xyplot-methods0.580.020.60

plateCore.Rcheck/examples_x64/plateCore-Ex.timings:

nameusersystemelapsed
Subset-methods2.270.022.28
applyControlGates-methods6.620.006.62
compensate-methods2.380.002.38
compensationSet0.120.020.14
densityplot-methods1.240.001.23
fixAutoFl-methods3.700.013.74
flowPlate-class1.340.001.34
flowPlate-method1.500.021.52
fpbind-methods2.360.002.36
getGroups-methods0.530.010.55
gutterPlot-methods1.190.001.19
mfiPlot-methods5.620.005.62
on-methods4.410.054.45
panel.densityplot.flowPlate0.860.030.89
panel.xyplot.flowPlate1.080.001.08
plateCore-package1.550.001.54
plateSet-methods1.190.001.19
plotPlate-methods1.480.051.53
prepanel.densityplot.flowPlate0.740.010.75
prepanel.xyplot.flowPlate0.980.000.99
setControlGates-methods1.370.021.39
summaryStats-methods4.960.004.95
wellAnnotation-methods0.540.000.55
xyplot-methods0.660.000.65