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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MaxContrastProjection.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MaxContrastProjection_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MaxContrastProjection.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 ‘MaxContrastProjection/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MaxContrastProjection’ version ‘1.12.0’
* 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 ‘MaxContrastProjection’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'MaxContrastProjection' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.11-bioc/meat/MaxContrastProjection.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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’ ... OK
* checking examples ... ERROR
Running examples in ‘MaxContrastProjection-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MaxContrastProjection
> ### Title: MaxContrastProjection: A package for performing z-projections of
> ###   image stacks
> ### Aliases: MaxContrastProjection MaxContrastProjection-package
> 
> ### ** Examples
> 
> data(cells)
> proj = contrastProjection(imageStack = cells, w_x = 15, smoothing = 5)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
MaxContrastProjection
 --- call from context --- 
FUN(X[[i]], ...)
 --- call from argument --- 
if (class(image) == "Image") image = imageData(image)
 --- R stacktrace ---
where 1: FUN(X[[i]], ...)
where 2: lapply(img_frames, calcContrast, w_x, w_y, brushShape)
where 3: getContrastStack(imageStack = imageStack, w_x = w_x, w_y = w_y, 
    brushShape = brushShape, validate = FALSE)
where 4: contrastProjection(imageStack = cells, w_x = 15, smoothing = 5)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (image, w_x, w_y, brushShape = "disc", validate = TRUE) 
{
    if (missing(image)) 
        stop("'image' is missing")
    if (missing(w_x)) 
        stop("'w_x' is missing")
    if (missing(w_y)) 
        stop("'w_y' is missing")
    if (class(image) == "Image") 
        image = imageData(image)
    if (validate) 
        valid = validateVariables(image = image, w_x = w_x, w_y = w_y, 
            brushShape = brushShape)
    f = NULL
    if (brushShape == "box") 
        f = matrix(1/((2 * w_x + 1) * (2 * w_y + 1)), nrow = (2 * 
            w_y + 1), ncol = (2 * w_x + 1))
    if (brushShape == "disc") {
        f = makeBrush(size = 2 * w_x + 1, shape = "disc", step = TRUE)
        f = f/sum(f)
    }
    imgSquared = image^2
    contrast = filter2(x = Image(imgSquared), filter = f, boundary = "replicate") - 
        filter2(x = Image(image), filter = f, boundary = "replicate")^2
    return(contrast)
}
<bytecode: 0x5562d65a0a00>
<environment: namespace:MaxContrastProjection>
 --- function search by body ---
Function calcContrast in namespace MaxContrastProjection 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, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/MaxContrastProjection.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MaxContrastProjection
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘MaxContrastProjection’ ...
** using staged installation
** 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 'MaxContrastProjection' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'MaxContrastProjection' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (MaxContrastProjection)