Package: flowStats

Version: 3.38.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowStats_3.38.0.tar.gz

StartedAt: 2018-10-17 02:02:39 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 02:07:13 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 273.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowStats.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowStats.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings flowStats_3.38.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowStats.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '3.38.0'
* 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 'flowStats' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAtzPKK/R.INSTALL1b50b447930/flowStats/man/normalize.Rd:58: file link 'ncdfFlowSet' in package 'ncdfFlow' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/flowStats.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' 'fda' 'ncdfFlow'
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:
  'cluster' 'ncdfFlow'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: 'flowWorkspace::getDimensions'
Missing object imported by a ':::' call: 'flowWorkspace:::.isBooleanGate.graphNEL'
Unexported objects imported by ':::' calls:
  'flowCore:::checkClass' 'flowCore:::copyFlowSet'
  'flowCore:::findTimeChannel' 'flowCore:::inPolygon'
  'flowViz:::plotType' 'flowWorkspace:::.isBoolGate'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'backGating' 'curvPeaks' 'getPeakRegions' 'idFeaturesByBackgating'
  'landmarkMatrixWithoutFilterResult'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
%in%,flowFrame-lymphFilter: warning in lymphGate(x, channels =
  parameters(table), preselection = pre, scale = table@scale, bwFac =
  table@bwFac, filterId = table@filterId, eval = TRUE, plot = FALSE):
  partial argument match of 'eval' to 'evaluate'
.plotGPAprocess: no visible binding for global variable 'whichS'
.plotGPAprocess: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'bogus'
.usingSVD: no visible binding for global variable 'params'
SignifFeatureRegion: no visible global function definition for 'pchisq'
density1d_simple: no visible binding for global variable 'y'
dfltBWrange: no visible binding for global variable 'IQR'
fdPar: no visible global function definition for 'norder.bspline'
gate_singlet: no visible global function definition for 'predict'
hubers1: no visible global function definition for 'pnorm'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
pcout: no visible global function definition for 'qchisq'
singletGate: no visible global function definition for 'predict'
symconv.ks: no visible global function definition for 'fft'
symconv2D.ks: no visible global function definition for 'fft'
symconv3D.ks: no visible global function definition for 'fft'
symconv4D.ks: no visible global function definition for 'fft'
warpSetNCDF: no visible global function definition for
  'clone.ncdfFlowSet'
warpSetNCDFLowMem: no visible global function definition for
  'clone.ncdfFlowSet'
addName,curv1Filter-character: no visible global function definition
  for 'checkParameterMatch'
addName,curv2Filter-character: no visible global function definition
  for 'checkParameterMatch'
glines,curv1Filter-ANY: no visible global function definition for
  'evalError'
glines,curv1Filter-missing: no visible global function definition for
  'evalError'
glines,curv1Filter-multipleFilterResult: no visible global function
  definition for 'colorRampPalette'
glines,curv1Filter-multipleFilterResult: no visible global function
  definition for 'brewer.pal'
glines,curv2Filter-ANY: no visible global function definition for
  'evalError'
glines,curv2Filter-multipleFilterResult: no visible global function
  definition for 'colorRampPalette'
glines,curv2Filter-multipleFilterResult: no visible global function
  definition for 'brewer.pal'
glpoints,curv1Filter-flowFrame-character: no visible global function
  definition for 'multFiltPoints'
glpoints,curv2Filter-flowFrame-character: no visible global function
  definition for 'multFiltPoints'
glpolygon,curv1Filter-ANY: no visible global function definition for
  'evalError'
glpolygon,curv2Filter-ANY: no visible global function definition for
  'evalError'
gpoints,curv1Filter-flowFrame-character: no visible global function
  definition for 'checkParameterMatch'
gpoints,curv1Filter-flowFrame-character: no visible global function
  definition for 'colorRampPalette'
gpoints,curv1Filter-flowFrame-character: no visible global function
  definition for 'brewer.pal'
gpoints,curv2Filter-flowFrame-character: no visible global function
  definition for 'checkParameterMatch'
gpoints,curv2Filter-flowFrame-character: no visible global function
  definition for 'colorRampPalette'
gpoints,curv2Filter-flowFrame-character: no visible global function
  definition for 'brewer.pal'
gpolygon,curv1Filter-ANY: no visible global function definition for
  'evalError'
gpolygon,curv1Filter-missing: no visible global function definition for
  'evalError'
gpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for 'colorRampPalette'
gpolygon,curv1Filter-multipleFilterResult: no visible global function
  definition for 'brewer.pal'
gpolygon,curv2Filter-ANY: no visible global function definition for
  'evalError'
gpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for 'colorRampPalette'
gpolygon,curv2Filter-multipleFilterResult: no visible global function
  definition for 'brewer.pal'
summarizeFilter,multipleFilterResult-curv1Filter: no visible global
  function definition for 'callNextMethod'
summarizeFilter,multipleFilterResult-curv2Filter: no visible global
  function definition for 'callNextMethod'
Undefined global functions or variables:
  IQR bogus brewer.pal callNextMethod checkParameterMatch
  clone.ncdfFlowSet cluster colorRampPalette evalError fft group
  hasPeak multFiltPoints norder.bspline params pchisq pnorm predict
  qchisq whichS y
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("methods", "callNextMethod")
  importFrom("stats", "IQR", "fft", "pchisq", "pnorm", "predict",
             "qchisq")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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
warpSet   20.77   0.60   21.39
gaussNorm 11.06   0.29   11.40
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
warpSet   16.17   1.06   17.23
gaussNorm  6.81   0.25    7.06
* 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-3.7-bioc/meat/flowStats.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/flowStats_3.38.0.tar.gz && rm -rf flowStats.buildbin-libdir && mkdir flowStats.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowStats.buildbin-libdir flowStats_3.38.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL flowStats_3.38.0.zip && rm flowStats_3.38.0.tar.gz flowStats_3.38.0.zip
###
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install for i386

* installing *source* package 'flowStats' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'flowStats'
    finding HTML links ... done
    BackGating                              html  
    ITN                                     html  
    autoGate                                html  
    binByRef                                html  
    calcPBChiSquare                         html  
    calcPearsonChi                          html  
    curv1Filter-class                       html  
    finding level-2 HTML links ... done

    curv2Filter-class                       html  
    curvPeaks                               html  
    density1d                               html  
    flowStats-package                       html  
    gaussNorm                               html  
    gpaSet                                  html  
    iProcrustes                             html  
    idFeaturesByBackgating                  html  
    landmarkMatrix                          html  
    lymphGate                               html  
    normQA                                  html  
    normalize                               html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAtzPKK/R.INSTALL1b50b447930/flowStats/man/normalize.Rd:58: file link 'ncdfFlowSet' in package 'ncdfFlow' does not exist and so has been treated as a topic
    plotBins                                html  
    proBin                                  html  
    quadrantGate                            html  
    rangeGate                               html  
    singletGate                             html  
    warpSet                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'flowStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowStats' as flowStats_3.38.0.zip
* DONE (flowStats)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'flowStats' successfully unpacked and MD5 sums checked
In R CMD INSTALL