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This page was generated on 2021-06-22 12:05:56 -0400 (Tue, 22 Jun 2021).

BUILD results for flowUtils on riesling1

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raw results

Package 645/1993HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowUtils 1.57.0  (landing page)
Josef Spidlen
Snapshot Date: 2021-06-21 14:50:06 -0400 (Mon, 21 Jun 2021)
URL: https://git.bioconductor.org/packages/flowUtils
Branch: master
Last Commit: fb3adc4
Last Changed Date: 2021-05-19 11:38:23 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: flowUtils
Version: 1.57.0
Command: chmod a+r flowUtils -R && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data flowUtils
StartedAt: 2021-06-21 19:53:37 -0400 (Mon, 21 Jun 2021)
EndedAt: 2021-06-21 19:56:52 -0400 (Mon, 21 Jun 2021)
EllapsedTime: 194.9 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r flowUtils -R && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data flowUtils
###
##############################################################################
##############################################################################


* checking for file 'flowUtils/DESCRIPTION' ... OK
* preparing 'flowUtils':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'HowTo-flowUtils.Rnw' using Sweave
No methods found in package 'flowCore' for requests: 'action', 'assign', 'Data', 'gate', 'tree' when loading 'flowUtils'
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
flowCore
 --- call from context --- 
getSpilloverFromFlowFrame(x, parameter)
 --- call from argument --- 
if (class(mySpill) != "matrix") mySpill <- parseMatrixFromString(mySpill, 
    requiredParameter)
 --- R stacktrace ---
where 1: getSpilloverFromFlowFrame(x, parameter)
where 2: eval(trans)(x)
where 3: resolveTransformReference(parameters[[len]], x)
where 4: resolveTransforms(x, filter)
where 5: FUN(X[[i]], ...)
where 6: FUN(X[[i]], ...)
where 7: lapply(X = X, FUN = FUN, ...)
where 8: sapply(table@filters, filter, x = x)
where 9: x %in% filter
where 10: x %in% filter
where 11: .class1(object)
where 12: as(x %in% filter, "filterResult")
where 13: filter(myFrame, flowEnv[[x]])
where 14: filter(myFrame, flowEnv[[x]])
where 15: eval(expr, .GlobalEnv)
where 16: eval(expr, .GlobalEnv)
where 17: withVisible(eval(expr, .GlobalEnv))
where 18: doTryCatch(return(expr), name, parentenv, handler)
where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 20: tryCatchList(expr, classes, parentenv, handlers)
where 21: tryCatch(expr, error = function(e) {
    call <- conditionCall(e)
    if (!is.null(call)) {
        if (identical(call[[1L]], quote(doTryCatch))) 
            call <- sys.call(-4L)
        dcall <- deparse(call)[1L]
        prefix <- paste("Error in", dcall, ": ")
        LONG <- 75L
        sm <- strsplit(conditionMessage(e), "\n")[[1L]]
        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
        if (is.na(w)) 
            w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], 
                type = "b")
        if (w > LONG) 
            prefix <- paste0(prefix, "\n  ")
    }
    else prefix <- "Error : "
    msg <- paste0(prefix, conditionMessage(e), "\n")
    .Internal(seterrmessage(msg[1L]))
    if (!silent && isTRUE(getOption("show.error.messages"))) {
        cat(msg, file = outFile)
        .Internal(printDeferredWarnings())
    }
    invisible(structure(msg, class = "try-error", condition = e))
})
where 22: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
where 23: evalFunc(ce, options)
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch(evalFunc(ce, options), finally = {
    cat("\n")
    sink()
})
where 26: driver$runcode(drobj, chunk, chunkopts)
where 27: utils::Sweave(...)
where 28: engine$weave(file, quiet = quiet, encoding = enc)
where 29: doTryCatch(return(expr), name, parentenv, handler)
where 30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 31: tryCatchList(expr, classes, parentenv, handlers)
where 32: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
    outputs <- c(outputs, output)
}, error = function(e) {
    thisOK <<- FALSE
    fails <<- c(fails, file)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 33: tools::buildVignettes(dir = ".", tangle = TRUE)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (myFrame, requiredParameter) 
{
    mySpill <- myFrame@description[["SPILL"]]
    if (is.null(mySpill)) 
        mySpill <- myFrame@description[["$SPILLOVER"]]
    if (is.null(mySpill)) 
        mySpill <- myFrame@description[["SPILLOVER"]]
    if (is.null(mySpill)) 
        mySpill <- myFrame@description[["$SPILL"]]
    if (is.null(mySpill)) 
        mySpill <- getIdentityMatrixForParameter(requiredParameter)
    if (class(mySpill) != "matrix") 
        mySpill <- parseMatrixFromString(mySpill, requiredParameter)
    if (!(requiredParameter %in% colnames(mySpill))) 
        mySpill <- getIdentityMatrixForParameter(requiredParameter)
    mySpill
}
<bytecode: 0x000000001ef20ba0>
<environment: namespace:flowCore>
 --- function search by body ---
Function getSpilloverFromFlowFrame in namespace flowCore has this body.
 ----------- END OF FAILURE REPORT -------------- 

Error: processing vignette 'HowTo-flowUtils.Rnw' failed with diagnostics:
 chunk 9 (label = ApplyGatingML1) 
Error in if (class(mySpill) != "matrix") mySpill <- parseMatrixFromString(mySpill,  : 
  the condition has length > 1

--- failed re-building 'HowTo-flowUtils.Rnw'

SUMMARY: processing the following file failed:
  'HowTo-flowUtils.Rnw'

Error: Vignette re-building failed.
Execution halted