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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:prada.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings prada_1.66.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/prada.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'prada' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpcJCuiM/R.INSTALLbcc66d921e3/prada/man/cytoSet-class.Rd:88: file link 'phenoData-class' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpcJCuiM/R.INSTALLbcc66d921e3/prada/man/readCytoSet.Rd:11: file link 'dir' in package 'base' does not exist and so has been treated as a topic
Warning: Package 'prada' is deprecated and will be removed from Bioconductor
See 'C:/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
* 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
'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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/prada/libs/i386/prada.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/prada/libs/x64/prada.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... 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: 0x024fb6b0>
<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
** running examples for arch 'x64' ... 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: 0x00000000058351c0>
<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: 2 ERRORs, 1 WARNING, 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/prada.Rcheck/00check.log'
for details.