BioC 3.1: CHECK report for flowStats on moscato2

Package: flowStats

Version: 3.26.1

Command: rm -rf flowStats.buildbin-libdir flowStats.Rcheck && mkdir flowStats.buildbin-libdir flowStats.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowStats.buildbin-libdir flowStats_3.26.1.tar.gz >flowStats.Rcheck\00install.out 2>&1 && cp flowStats.Rcheck\00install.out flowStats-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=flowStats.buildbin-libdir --install="check:flowStats-install.out" --force-multiarch --no-vignettes --timings flowStats_3.26.1.tar.gz

StartedAt: 2015-10-09 01:48:57 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:53:41 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 283.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: flowStats.Rcheck

Warnings: NA

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### Running command:
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###   rm -rf flowStats.buildbin-libdir flowStats.Rcheck && mkdir flowStats.buildbin-libdir flowStats.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=flowStats.buildbin-libdir flowStats_3.26.1.tar.gz >flowStats.Rcheck\00install.out 2>&1 && cp flowStats.Rcheck\00install.out flowStats-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=flowStats.buildbin-libdir --install="check:flowStats-install.out" --force-multiarch --no-vignettes --timings flowStats_3.26.1.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/flowStats.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '3.26.1'
* 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 'flowStats' 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' 'fda'
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
Package in Depends field not imported from: 'cluster'
  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'
.normalizeGatingSet: no visible global function definition for
  'getNodes'
.normalizeGatingSet: no visible global function definition for 'clone'
.normalizeGatingSet: no visible global function definition for
  'getGate'
.normalizeGatingSet: no visible global function definition for
  'getParent'
.normalizeGatingSet: no visible global function definition for
  'flowData<-'
.normalizeGatingSet: no visible global function definition for
  'flowData'
.normalizeGatingSet: no visible global function definition for
  'recompute'
.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'
density1d_simple: no visible binding for global variable 'y'
fdPar: no visible global function definition for 'fd'
fdPar: no visible global function definition for 'vec2Lfd'
fdPar: no visible global function definition for 'norder.bspline'
fdPar: no visible global function definition for 'int2Lfd'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
singletGate: no visible global function definition for 'polygonGate'
warpSetNCDF: no visible global function definition for
  'clone.ncdfFlowSet'
addName,curv1Filter-character : .local: no visible global function
  definition for 'identifier'
addName,curv1Filter-character : .local: no visible global function
  definition for 'checkParameterMatch'
addName,curv1Filter-character : .local: no visible global function
  definition for 'addName'
addName,curv1Filter-logical : .local: no visible global function
  definition for 'addName'
addName,curv2Filter-character : .local: no visible global function
  definition for 'identifier'
addName,curv2Filter-character : .local: no visible global function
  definition for 'checkParameterMatch'
addName,curv2Filter-character : .local: no visible global function
  definition for 'addName'
addName,curv2Filter-character : .local: no visible global function
  definition for 'polygonGate'
addName,curv2Filter-logical : .local: no visible global function
  definition for 'addName'
densityplot,view-missing : .local: no visible global function
  definition for 'Data'
glines,curv1Filter-ANY : .local: no visible global function definition
  for 'evalError'
glines,curv1Filter-flowFrame : .local: no visible global function
  definition for 'glines'
glines,curv1Filter-missing : .local: no visible global function
  definition for 'evalError'
glines,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for 'identifier'
glines,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for 'brewer.pal'
glines,curv1Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for 'glines'
glines,curv2Filter-ANY : .local: no visible global function definition
  for 'evalError'
glines,curv2Filter-flowFrame : .local: no visible global function
  definition for 'glines'
glines,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for 'identifier'
glines,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for 'brewer.pal'
glines,curv2Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for 'glines'
glines,curv2Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for 'polygonGate'
glpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for 'flowViz.par.get'
glpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for 'multFiltPoints'
glpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for 'addName'
glpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for 'flowViz.par.get'
glpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for 'multFiltPoints'
glpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for 'addName'
glpolygon,curv1Filter-ANY: no visible global function definition for
  'evalError'
glpolygon,curv1Filter-flowFrame : .local: no visible global function
  definition for 'flowViz.par.get'
glpolygon,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for 'flowViz.par.get'
glpolygon,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for 'identifier'
glpolygon,curv2Filter-ANY: no visible global function definition for
  'evalError'
glpolygon,curv2Filter-flowFrame : .local: no visible global function
  definition for 'flowViz.par.get'
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for 'flowViz.par.get'
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for 'identifier'
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for 'polygonGate'
gpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for 'checkParameterMatch'
gpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for 'identifier'
gpoints,curv1Filter-flowFrame-character : .local: no visible global
  function definition for 'brewer.pal'
gpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for 'checkParameterMatch'
gpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for 'identifier'
gpoints,curv2Filter-flowFrame-character : .local: no visible global
  function definition for 'brewer.pal'
gpolygon,curv1Filter-ANY : .local: no visible global function
  definition for 'evalError'
gpolygon,curv1Filter-flowFrame : .local: no visible global function
  definition for 'gpolygon'
gpolygon,curv1Filter-missing : .local: no visible global function
  definition for 'evalError'
gpolygon,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for 'identifier'
gpolygon,curv1Filter-multipleFilterResult : .local: no visible global
  function definition for 'brewer.pal'
gpolygon,curv1Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for 'gpolygon'
gpolygon,curv2Filter-ANY : .local: no visible global function
  definition for 'evalError'
gpolygon,curv2Filter-flowFrame : .local: no visible global function
  definition for 'gpolygon'
gpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for 'identifier'
gpolygon,curv2Filter-multipleFilterResult : .local: no visible global
  function definition for 'brewer.pal'
gpolygon,curv2Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for 'gpolygon'
gpolygon,curv2Filter-multipleFilterResult : .local : <anonymous>: no
  visible global function definition for 'polygonGate'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'flowStats-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lymphFilter-class
> ### Title: Automated gating of elliptical cell populations in 2D.
> ### Aliases: lymphFilter-class %in%,flowFrame,lymphFilter-method lymphGate
> ###   lymphFilter
> ### Keywords: misc classes
> 
> ### ** Examples
> 
> 
> data(GvHD)
> dat <- GvHD[pData(GvHD)$Patient==10]
> dat <- transform(dat, "FL4-H"=asinh(`FL4-H`))
> lg <- lymphGate(dat, channels=c("FSC-H", "SSC-H"), preselection="FL4-H",scale=1.5)
> 
> if(require(flowViz))
+ xyplot(`SSC-H`˜`FSC-H`, dat, filter=lg$n2gate)
> 
> ## This is using the abstract lymphFilter class instead
> lf <- lymphFilter(channels=c("FSC-H", "SSC-H"), preselection="FL4-H")
Error: 'lymphFilter' is defunct.
See help("Defunct")
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'flowStats-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lymphFilter-class
> ### Title: Automated gating of elliptical cell populations in 2D.
> ### Aliases: lymphFilter-class %in%,flowFrame,lymphFilter-method lymphGate
> ###   lymphFilter
> ### Keywords: misc classes
> 
> ### ** Examples
> 
> 
> data(GvHD)
> dat <- GvHD[pData(GvHD)$Patient==10]
> dat <- transform(dat, "FL4-H"=asinh(`FL4-H`))
> lg <- lymphGate(dat, channels=c("FSC-H", "SSC-H"), preselection="FL4-H",scale=1.5)
> 
> if(require(flowViz))
+ xyplot(`SSC-H`˜`FSC-H`, dat, filter=lg$n2gate)
> 
> ## This is using the abstract lymphFilter class instead
> lf <- lymphFilter(channels=c("FSC-H", "SSC-H"), preselection="FL4-H")
Error: 'lymphFilter' is defunct.
See help("Defunct")
Execution halted
* 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: 2 ERRORs, 3 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/flowStats.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'flowStats' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'flowStats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowStats' as flowStats_3.26.1.zip
* DONE (flowStats)

name	user	system	elapsed
autoGate	2.72	0.04	2.77
binByRef	1.09	0.04	1.12
calcPBChiSquare	1.21	0.01	1.23
calcPearsonChi	1.27	0.05	1.31
curv1Filter-class	0.34	0.01	0.39
curv2Filter-class	2.14	0.02	2.15
curvPeaks	1.47	0.03	1.81
density1d	5.75	0.08	5.85
gaussNorm	10.53	0.26	10.80
gpaSet	5.27	0.11	5.38
iProcrustes	0.18	0.00	0.17
idFeaturesByBackgating	1.37	0.00	1.47
landmarkMatrix	1.28	0.08	1.35

name	user	system	elapsed
autoGate	4.29	0.06	4.35
binByRef	1.57	0.06	1.64
calcPBChiSquare	1.15	0.02	1.17
calcPearsonChi	1.16	0.06	1.21
curv1Filter-class	0.29	0.02	0.31
curv2Filter-class	2.45	0.06	2.52
curvPeaks	0.77	0.01	0.78
density1d	5.88	0.22	6.59
gaussNorm	11.02	0.27	11.65
gpaSet	5.38	0.03	5.42
iProcrustes	0.2	0.0	0.2
idFeaturesByBackgating	1.58	0.01	1.59
landmarkMatrix	1.17	0.05	1.21