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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:prada.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings prada_1.66.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/prada.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘prada/DESCRIPTION’ ... OK
* this is package ‘prada’ version ‘1.66.0’
* 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 ‘prada’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'prada' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/prada.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:
  ‘Biobase’ ‘grid’ ‘methods’ ‘RColorBrewer’ ‘rrcov’
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
* 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
'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
analysePlate: no visible binding for global variable ‘dat’
gatePoints: no visible binding for global variable ‘prev’
killProgress: no visible binding for global variable
  ‘.tkprogress.canceled’
killProgress: no visible global function definition for ‘tkdestroy’
killProgress: no visible binding for global variable
  ‘.tkprogress.window’
progress: no visible global function definition for ‘tktoplevel’
progress: no visible global function definition for ‘tclVar’
progress: no visible global function definition for ‘tkwm.geometry’
progress: no visible binding for global variable ‘.tkprogress.window’
progress: no visible global function definition for ‘tkwm.title’
progress: no visible global function definition for ‘tkconfigure’
progress: no visible global function definition for ‘tkframe’
progress: no visible global function definition for ‘tkfont.create’
progress: no visible binding for '<<-' assignment to
  ‘.tkprogress.labelText’
progress: no visible binding for global variable
  ‘.tkprogress.labelText’
progress: no visible global function definition for ‘tclvalue<-’
progress: no visible global function definition for ‘tklabel’
progress: no visible global function definition for ‘tclvalue’
progress: no visible global function definition for ‘tkgrid’
progress: no visible global function definition for ‘tclRequire’
progress: no visible global function definition for ‘tkwidget’
progress: no visible binding for global variable ‘.tkprogress.iterator’
progress: no visible binding for global variable
  ‘.tkprogress.fallbackIterator’
progress: no visible global function definition for ‘tkbind’
progress : <anonymous>: no visible binding for '<<-' assignment to
  ‘.tkprogress.canceled’
updateProgress: no visible binding for '<<-' assignment to
  ‘.tkprogress.iterator’
updateProgress: no visible binding for global variable
  ‘.tkprogress.iterator’
updateProgress: no visible global function definition for ‘tclvalue<-’
updateProgress: no visible binding for '<<-' assignment to
  ‘.tkprogress.fallbackIterator’
updateProgress: no visible binding for global variable
  ‘.tkprogress.fallbackIterator’
updateProgress: no visible binding for '<<-' assignment to
  ‘.tkprogress.labelText’
updateProgress: no visible binding for global variable
  ‘.tkprogress.labelText’
updateProgress: no visible global function definition for ‘tcl’
Undefined global functions or variables:
  .tkprogress.canceled .tkprogress.fallbackIterator
  .tkprogress.iterator .tkprogress.labelText .tkprogress.window dat
  prev tcl tclRequire tclVar tclvalue tclvalue<- tkbind tkconfigure
  tkdestroy tkfont.create tkframe tkgrid tklabel tktoplevel tkwidget
  tkwm.geometry tkwm.title
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘prada-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fitNorm2
> ### Title: Fit bivariate normal distribution.
> ### Aliases: fitNorm2
> 
> ### ** Examples
> 
>  sampdat <- readFCS(system.file("extdata",
+    "fas-Bcl2-plate323-04-04.A01", package="prada"))
>  nfit    <- fitNorm2(exprs(sampdat[,1:2]), scalefac=2)
>  plotNorm2(nfit, selection=TRUE, ellipse=TRUE) 
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
prada
 --- call from context --- 
stopifnot((is.matrix(S) && dim(S) == c(2, 2)), is.numeric(mu), 
    length(mu) == 2, is.numeric(rad), length(rad) == 1)
 --- call from argument --- 
is.matrix(S) && dim(S) == c(2, 2)
 --- R stacktrace ---
where 1: stopifnot((is.matrix(S) && dim(S) == c(2, 2)), is.numeric(mu), 
    length(mu) == 2, is.numeric(rad), length(rad) == 1)
where 2: .addEllipse(S = fn$S, mu = fn$mu, rad = fn$scalefac)
where 3: plotNorm2(nfit, selection = TRUE, ellipse = TRUE)

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (..., exprs, exprObject, local = TRUE) 
{
    n <- ...length()
    if ((has.e <- !missing(exprs)) || !missing(exprObject)) {
        if (n || (has.e && !missing(exprObject))) 
            stop("Only one of 'exprs', 'exprObject' or expressions, not more")
        envir <- if (isTRUE(local)) 
            parent.frame()
        else if (isFALSE(local)) 
            .GlobalEnv
        else if (is.environment(local)) 
            local
        else stop("'local' must be TRUE, FALSE or an environment")
        E1 <- if (has.e && is.call(exprs <- substitute(exprs))) 
            exprs[[1]]
        cl <- if (is.symbol(E1) && E1 == quote(`{`)) {
            exprs[[1]] <- quote(stopifnot)
            exprs
        }
        else as.call(c(quote(stopifnot), if (!has.e) exprObject else as.expression(exprs)))
        names(cl) <- NULL
        return(eval(cl, envir = envir))
    }
    Dparse <- function(call, cutoff = 60L) {
        ch <- deparse(call, width.cutoff = cutoff)
        if (length(ch) > 1L) 
            paste(ch[1L], "....")
        else ch
    }
    head <- function(x, n = 6L) x[seq_len(if (n < 0L) max(length(x) + 
        n, 0L) else min(n, length(x)))]
    abbrev <- function(ae, n = 3L) paste(c(head(ae, n), if (length(ae) > 
        n) "...."), collapse = "\n  ")
    for (i in seq_len(n)) {
        r <- ...elt(i)
        if (!(is.logical(r) && !anyNA(r) && all(r))) {
            dots <- match.call()[-1L]
            if (is.null(msg <- names(dots)) || !nzchar(msg <- msg[i])) {
                cl.i <- dots[[i]]
                msg <- if (is.call(cl.i) && identical(cl.i[[1]], 
                  quote(all.equal)) && (is.null(ni <- names(cl.i)) || 
                  length(cl.i) == 3L || length(cl.i <- cl.i[!nzchar(ni)]) == 
                  3L)) 
                  sprintf(gettext("%s and %s are not equal:\n  %s"), 
                    Dparse(cl.i[[2]]), Dparse(cl.i[[3]]), abbrev(r))
                else sprintf(ngettext(length(r), "%s is not TRUE", 
                  "%s are not all TRUE"), Dparse(cl.i))
            }
            stop(simpleError(msg, call = if (p <- sys.parent(1L)) 
                sys.call(p)))
        }
    }
    invisible()
}
<bytecode: 0x7fc070245c50>
<environment: namespace:base>
 --- function search by body ---
Function stopifnot in namespace base has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* 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, 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/prada.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL prada
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘prada’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c inPolygon.c -o inPolygon.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o prada.so inPolygon.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-prada/00new/prada/libs
** R
** data
** inst
** 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
Warning: Package 'prada' is deprecated and will be removed from Bioconductor
  version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'prada' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (prada)