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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:flowVS.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings flowVS_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/flowVS.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowVS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowVS’ version ‘1.20.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘flowVS’ can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bartlettTestMicro: no visible binding for global variable ‘var’
curvPeaks: no visible global function definition for ‘density’
curvPeaks: no visible global function definition for ‘quantile’
curvPeaks: no visible global function definition for ‘approxfun’
curvPeaks: no visible global function definition for ‘optimize’
densityPeaks: no visible global function definition for ‘quantile’
densityPeaks: no visible global function definition for ‘density’
densityPeaks: no visible global function definition for ‘median’
densityPeaks: no visible global function definition for ‘var’
densityPeaks: no visible global function definition for ‘colorRamp’
densityPeaks: no visible global function definition for ‘rgb’
densityPeaks: no visible global function definition for ‘polygon’
densityPeaks: no visible global function definition for ‘lines’
densityPeaks: no visible global function definition for ‘abline’
densityPeaks: no visible global function definition for ‘dev.copy2pdf’
flowVS1D: no visible global function definition for ‘median’
lymphs: no visible global function definition for ‘as.formula’
lymphs: no visible global function definition for ‘colorRampPalette’
microVS: no visible global function definition for ‘quantile’
microVS: no visible global function definition for ‘points’
optimStat: no visible global function definition for ‘optimize’
optimStat: no visible global function definition for ‘points’
peakStats1D: no visible global function definition for ‘median’
plotMeanSd : mediwind: no visible global function definition for
  ‘median’
plotMeanSd: no visible global function definition for ‘quantile’
plotMeanSd: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline approxfun as.formula colorRamp colorRampPalette density
  dev.copy2pdf lines median optimize points polygon quantile rgb var
Consider adding
  importFrom("grDevices", "colorRamp", "colorRampPalette",
             "dev.copy2pdf", "rgb")
  importFrom("graphics", "abline", "lines", "points", "polygon")
  importFrom("stats", "approxfun", "as.formula", "density", "median",
             "optimize", "quantile", "var")
to your NAMESPACE file.
* 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’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... ERROR
Running examples in ‘flowVS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: microVS
> ### Title: Variance stabilization for microarray data.
> ### Aliases: microVS
> ### Keywords: transformation variance stabilization
> 
> ### ** Examples
> 
> 
> # stabilize variance of the Kidney microarray data from the vsn package
> library(vsn)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:flowStats’:

    normalize

The following object is masked from ‘package:flowCore’:

    normalize

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> data(kidney)
> kidney.t = microVS(exprs(kidney))
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
flowVS
 --- call from context --- 
microVS(exprs(kidney))
 --- call from argument --- 
if (class(data) != "matrix") stop(" The microarray data must be a Matrix.")
 --- R stacktrace ---
where 1: microVS(exprs(kidney))

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (data, cfLow = 0, cfHigh = 10, frac = 1) 
{
    if (class(data) != "matrix") 
        stop(" The microarray data must be a Matrix.")
    if (frac > 1 || frac <= 0) 
        stop(" 0< frac<=1 ")
    if (cfLow >= cfHigh) {
        print("Warning: cfLow>=cfHigh, using default values")
        cfLow = 0
        cfHigh = 10
    }
    cat("====================================================================\n")
    cat("Finding optimum cofactor for asinh transformation\n")
    cat("====================================================================\n")
    cat(sprintf("%15s     %15s \n", "cofactor(log scale)", "Bartlett's stat"))
    cat("====================================================================\n")
    cofactors = seq(cfLow, cfHigh, 1)
    bartlett = NULL
    for (cf in cofactors) {
        data.t = asinh(data/exp(cf))
        if (frac < 1) {
            diff = quantile(abs(data.t[, 1] - data.t[, 2]), frac)
            keep.idx = which(abs(data.t[, 1] - data.t[, 2]) <= 
                diff)
            data.t = data.t[keep.idx, ]
        }
        bt = bartlettTestMicro(data.t)
        bartlett = c(bartlett, bt)
        cat(sprintf("%10d %25.2f \n", cf, bt))
    }
    minIdx = which.min(bartlett)
    cat("\n Optimum cofactor :", sprintf("exp(%d)", cofactors[minIdx]), 
        "\n")
    cat("====================================================================\n\n")
    plot(cofactors, bartlett, type = "o", pch = 16, xlab = "Cofactors (log scale)", 
        ylab = "Bartlett's statistics", main = paste("Optimum cofactor: ", 
            sprintf("exp(%d)", cofactors[minIdx]), sep = ""))
    points(cofactors[minIdx], bartlett[minIdx], pch = 16, col = "red")
    data.t = asinh(data/exp(cofactors[minIdx]))
    return(data.t)
}
<bytecode: 0x55f5d6c37878>
<environment: namespace:flowVS>
 --- function search by body ---
Function microVS in namespace flowVS has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/flowVS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL flowVS
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘flowVS’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowVS)