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CHECK report for plateCore on tokay2

This page was generated on 2019-03-11 11:23:03 -0400 (Mon, 11 Mar 2019).

Package 1181/1676HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plateCore 1.41.1
Errol Strain
Snapshot Date: 2019-03-10 17:02:02 -0400 (Sun, 10 Mar 2019)
URL: https://git.bioconductor.org/packages/plateCore
Branch: master
Last Commit: c3480a3
Last Changed Date: 2019-01-04 13:44:09 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: plateCore
Version: 1.41.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plateCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plateCore_1.41.1.tar.gz
StartedAt: 2019-03-11 05:16:56 -0400 (Mon, 11 Mar 2019)
EndedAt: 2019-03-11 05:21:01 -0400 (Mon, 11 Mar 2019)
EllapsedTime: 245.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: plateCore.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plateCore.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings plateCore_1.41.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/plateCore.Rcheck'
* using R Under development (unstable) (2019-01-10 r75962)
* 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 '1.41.1'
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
mfiPlot-methods           6.83   0.04    6.87
applyControlGates-methods 6.41   0.08    6.48
summaryStats-methods      6.07   0.00    6.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
summaryStats-methods 5.94   0.00    5.94
mfiPlot-methods      5.13   0.02    5.14
* 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-3.9-bioc/meat/plateCore.Rcheck/00check.log'
for details.



Installation output

plateCore.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/plateCore_1.41.1.tar.gz && rm -rf plateCore.buildbin-libdir && mkdir plateCore.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plateCore.buildbin-libdir plateCore_1.41.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL plateCore_1.41.1.zip && rm plateCore_1.41.1.tar.gz plateCore_1.41.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2301k  100 2301k    0     0  14.8M      0 --:--:-- --:--:-- --:--:-- 15.6M

install for i386

* installing *source* package 'plateCore' ...
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package 'flowStats' for request: '%on%' when loading 'plateCore'
** help
*** installing help indices
  converting help for package 'plateCore'
    finding HTML links ... done
    Subset-methods                          html  
    applyControlGates-methods               html  
    compensate-methods                      html  
    compensationSet                         html  
    densityplot-methods                     html  
    fixAutoFl-methods                       html  
    flowPlate-class                         html  
    finding level-2 HTML links ... done

    flowPlate-method                        html  
    fpbind-methods                          html  
    getGroups-methods                       html  
    gutterPlot-methods                      html  
    mfiPlot-methods                         html  
    on-methods                              html  
    panel.densityplot.flowPlate             html  
    panel.xyplot.flowPlate                  html  
    pbmcPlate                               html  
    plateCore-package                       html  
    plateSet-methods                        html  
    plotPlate-methods                       html  
    prepanel.densityplot.flowPlate          html  
    prepanel.xyplot.flowPlate               html  
    setControlGates-methods                 html  
    summaryStats-methods                    html  
    wellAnnotation-methods                  html  
    xyplot-methods                          html  
** 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_1.41.1.zip
* DONE (plateCore)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'plateCore' successfully unpacked and MD5 sums checked

Tests output


Example timings

plateCore.Rcheck/examples_i386/plateCore-Ex.timings

nameusersystemelapsed
Subset-methods1.740.101.83
applyControlGates-methods6.410.086.48
compensate-methods2.200.072.28
compensationSet0.170.020.19
densityplot-methods1.230.081.31
fixAutoFl-methods2.690.032.72
flowPlate-class1.670.031.70
flowPlate-method1.580.141.72
fpbind-methods2.560.062.63
getGroups-methods0.940.111.04
gutterPlot-methods0.720.020.74
mfiPlot-methods6.830.046.87
on-methods4.310.004.32
panel.densityplot.flowPlate1.140.021.15
panel.xyplot.flowPlate0.890.020.91
plateCore-package0.970.010.98
plateSet-methods1.300.031.33
plotPlate-methods1.230.031.27
prepanel.densityplot.flowPlate0.610.000.61
prepanel.xyplot.flowPlate0.630.020.64
setControlGates-methods1.150.001.15
summaryStats-methods6.070.006.06
wellAnnotation-methods0.810.000.82
xyplot-methods0.980.000.98

plateCore.Rcheck/examples_x64/plateCore-Ex.timings

nameusersystemelapsed
Subset-methods1.650.001.65
applyControlGates-methods4.950.034.98
compensate-methods1.980.001.98
compensationSet0.110.020.13
densityplot-methods0.660.010.67
fixAutoFl-methods2.050.032.08
flowPlate-class1.060.021.08
flowPlate-method1.530.011.54
fpbind-methods2.200.072.27
getGroups-methods0.710.000.70
gutterPlot-methods0.710.010.74
mfiPlot-methods5.130.025.14
on-methods3.840.013.86
panel.densityplot.flowPlate0.720.030.75
panel.xyplot.flowPlate0.610.020.62
plateCore-package0.910.030.94
plateSet-methods1.000.051.05
plotPlate-methods1.610.031.64
prepanel.densityplot.flowPlate0.560.010.57
prepanel.xyplot.flowPlate0.550.000.55
setControlGates-methods1.030.001.03
summaryStats-methods5.940.005.94
wellAnnotation-methods0.600.000.61
xyplot-methods0.580.020.59