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CHECK report for prada on tokay2

This page was generated on 2020-10-17 11:57:26 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE prada PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1341/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
prada 1.64.0
Florian Hahne
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/prada
Branch: RELEASE_3_11
Last Commit: a3977ac
Last Changed Date: 2020-04-27 14:09:49 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: prada
Version: 1.64.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:prada.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings prada_1.64.0.tar.gz
StartedAt: 2020-10-17 07:01:43 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:03:11 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 88.4 seconds
RetCode: 1
Status:  ERROR  
CheckDir: prada.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:prada.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings prada_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/prada.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.64.0'
* 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-3.11-bioc/tmpdir/Rtmpmu1Z7D/R.INSTALL18b05876350e/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-3.11-bioc/tmpdir/Rtmpmu1Z7D/R.INSTALL18b05876350e/prada/man/readCytoSet.Rd:11: file link 'dir' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/R/library/prada/libs/i386/prada.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-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: 0x083b6068>
<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: 0x000000000c898b30>
<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-3.11-bioc/meat/prada.Rcheck/00check.log'
for details.

Installation output

prada.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/prada_1.64.0.tar.gz && rm -rf prada.buildbin-libdir && mkdir prada.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=prada.buildbin-libdir prada_1.64.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL prada_1.64.0.zip && rm prada_1.64.0.tar.gz prada_1.64.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  280k  100  280k    0     0  4351k      0 --:--:-- --:--:-- --:--:-- 4833k

install for i386

* installing *source* package 'prada' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inPolygon.c -o inPolygon.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o prada.dll tmp.def inPolygon.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/prada.buildbin-libdir/00LOCK-prada/00new/prada/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'prada'
    finding HTML links ... done
    analysePlate                            html  
    as.all                                  html  
    barploterrbar                           html  
    combineFrames                           html  
    csApply                                 html  
    cytoFrame-class                         html  
    cytoSet-class                           html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpmu1Z7D/R.INSTALL18b05876350e/prada/man/cytoSet-class.Rd:88: file link 'phenoData-class' in package 'Biobase' does not exist and so has been treated as a topic
    data-cytoFrame                          html  
    data-cytoSet                            html  
    devDims                                 html  
    devRes                                  html  
    fitNorm2                                html  
    gate-class                              html  
    gateSet-class                           html  
    getAlphaNumeric                         html  
    getPradaPar                             html  
    new-internal                            html  
    plotNorm2                               html  
    plotPlate                               html  
    readCytoSet                             html  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/Rtmpmu1Z7D/R.INSTALL18b05876350e/prada/man/readCytoSet.Rd:11: file link 'dir' in package 'base' does not exist and so has been treated as a topic
    readFCS                                 html  
    readFCSaux                              html  
    removeCensored                          html  
    tcltkProgress                           html  
    threePanelPlot                          html  
    thresholds                              html  
    touchFCS                                html  
    vpLocation                              html  
** 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

install for x64

* installing *source* package 'prada' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c inPolygon.c -o inPolygon.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o prada.dll tmp.def inPolygon.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/prada.buildbin-libdir/prada/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'prada' as prada_1.64.0.zip
* DONE (prada)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'prada' successfully unpacked and MD5 sums checked

Tests output

Example timings

prada.Rcheck/examples_i386/prada-Ex.timings

nameusersystemelapsed
analysePlate000
as.all000
barploterrbar0.020.000.02
combineFrames0.120.000.48
csApply0.030.000.04
cytoFrame-class0.080.000.08
cytoSet-class0.040.020.06
data-cytoFrame0.030.020.05
data-cytoSet000
devDims000
devRes0.020.000.01

prada.Rcheck/examples_x64/prada-Ex.timings

nameusersystemelapsed
analysePlate000
as.all000
barploterrbar000
combineFrames0.080.000.08
csApply0.010.000.01
cytoFrame-class0.040.020.05
cytoSet-class0.030.000.03
data-cytoFrame0.030.000.03
data-cytoSet000
devDims000
devRes000