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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:flowStats.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings flowStats_4.12.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/flowStats.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '4.12.0'
* package encoding: UTF-8
* 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:
  Warning: replacing previous import 'flowViz::contour' by 'graphics::contour' when loading 'flowStats'
See 'F:/biocbuild/bbs-3.17-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 ... OK
* 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 dependencies in R code ... WARNING
Missing or unexported object: 'flowWorkspace::plotGate'
Missing object imported by a ':::' call: 'flowWorkspace:::.isBooleanGate.graphNEL'
Unexported objects imported by ':::' calls:
  'flowCore:::checkClass' 'flowCore:::copyFlowSet'
  'flowCore:::findTimeChannel' 'flowCore:::inPolygon'
  'flowViz:::evalError' 'flowViz:::plotType'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.combinePriorsForChildNodes: no visible global function definition for
  'adj'
.combinePriorsForChildNodes: no visible global function definition for
  'nodeData'
.graph_parent: no visible global function definition for 'ugraph'
.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'
SimulateMixture: no visible global function definition for 'rbox'
density1d_simple: no visible binding for global variable 'y'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
Undefined global functions or variables:
  adj bogus cluster group hasPeak nodeData params rbox ugraph whichS y
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'SimulateMixture.Rd':
  'flowClust'

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'ellipse'
  'cov' 'centre' 'level'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'flowStats-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: warpSet
> ### Title: Normalization based on landmark registration
> ### Aliases: warpSet warpSetNCDF warpSetGS warpSetNCDFLowMem
> ###   warpSet.cytoset
> 
> ### ** Examples
> 
> library(flowCore)
> data(ITN)
> dat <- transform(ITN, "CD4"=asinh(CD4), "CD3"=asinh(CD3), "CD8"=asinh(CD8))
> lg <- lymphGate(dat, channels=c("CD3", "SSC"), preselection="CD4",scale=1.5)
> dat <- Subset(dat, lg)
> datr <- warpSet(dat, "CD8", grouping="GroupID")

Estimating landmarks for channel CD8 ...
Registering curves for parameter CD8 ...
Warning in warpSet.flowSet(dat, "CD8", grouping = "GroupID") :
  The following landmark is only present in a single group --
stain: CD8
mean value: 1.6936944517483
Warning in warpSet.flowSet(dat, "CD8", grouping = "GroupID") :
  The following landmark is only present in a single group --
stain: CD8
mean value: 6.10788805652371
Error in lnsrch_morph(bvecold, fold, grad, pvec, fngrad_morph, morphList,  : 
  Initial slope not negative.
Calls: warpSet ... withVisible -> landmarkreg -> smooth.morph -> lnsrch_morph
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* 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 ERROR, 4 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/flowStats.Rcheck/00check.log'
for details.