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This page was generated on 2021-07-31 12:05:36 -0400 (Sat, 31 Jul 2021).

BUILD results for epiNEM on nebbiolo2

To the developers/maintainers of the epiNEM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/epiNEM.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 574/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epiNEM 1.17.1  (landing page)
Martin Pirkl
Snapshot Date: 2021-07-30 14:50:06 -0400 (Fri, 30 Jul 2021)
URL: https://git.bioconductor.org/packages/epiNEM
Branch: master
Last Commit: f322aa3
Last Changed Date: 2021-07-28 05:07:09 -0400 (Wed, 28 Jul 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: epiNEM
Version: 1.17.1
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data epiNEM
StartedAt: 2021-07-30 17:09:25 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 17:10:01 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 36.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data epiNEM
###
##############################################################################
##############################################################################


* checking for file ‘epiNEM/DESCRIPTION’ ... OK
* preparing ‘epiNEM’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epiNEM.Rmd’ using rmarkdown
Registered S3 methods overwritten by 'RcppEigen':
  method               from         
  predict.fastLm       RcppArmadillo
  print.fastLm         RcppArmadillo
  summary.fastLm       RcppArmadillo
  print.summary.fastLm RcppArmadillo
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
lattice
 --- call from context --- 
construct.legend(foo$legend, colorkey, fun = "draw.colorkey")
 --- call from argument --- 
space != "inside" && space %in% names(legend)
 --- R stacktrace ---
where 1: construct.legend(foo$legend, colorkey, fun = "draw.colorkey")
where 2: levelplot.formula(form, data, aspect = aspect, xlim = xlim, ylim = ylim, 
    ...)
where 3: levelplot(form, data, aspect = aspect, xlim = xlim, ylim = ylim, 
    ...)
where 4: levelplot.matrix(d, main = list(label = main, cex = cexMain), 
    sub = list(label = sub, cex = cexSub), aspect = aspect, xlab = xlab, 
    ylab = ylab, scales = list(x = xtck, y = ytck, tck = c(1, 
        0)), par.settings = myTheme, border = bordercol, border.lwd = borderwidth, 
    shrink = shrink, legend = legend, at = at, colorkey = colorkey, 
    contour = contour, panel = if (useRaster) {
        function(...) {
            panel.fill(col = colNA)
            panel.levelplot.raster(...)
        }
    } else {
        function(...) {
            panel.fill(col = colNA)
            panel.levelplot(...)
        }
    })
where 5: levelplot(d, main = list(label = main, cex = cexMain), sub = list(label = sub, 
    cex = cexSub), aspect = aspect, xlab = xlab, ylab = ylab, 
    scales = list(x = xtck, y = ytck, tck = c(1, 0)), par.settings = myTheme, 
    border = bordercol, border.lwd = borderwidth, shrink = shrink, 
    legend = legend, at = at, colorkey = colorkey, contour = contour, 
    panel = if (useRaster) {
        function(...) {
            panel.fill(col = colNA)
            panel.levelplot.raster(...)
        }
    } else {
        function(...) {
            panel.fill(col = colNA)
            panel.levelplot(...)
        }
    })
where 6: HeatmapOP(distmat, Colv = FALSE, Rowv = FALSE, main = "logic gate distribution", 
    sub = "", col = "Paired", breaks = seq(0.5, 7.5, length.out = 8), 
    colorkey = colorkey, xlab = "double knock-outs", ylab = "modulators\n(different order for each pair)", 
    ...)
where 7: plot.epiScreen(res)
where 8: plot(res)
where 9: eval(expr, envir, enclos)
where 10: eval(expr, envir, enclos)
where 11: withVisible(eval(expr, envir, enclos))
where 12: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, 
    error = eHandler, message = mHandler)
where 13: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, 
    enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, 
    envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 15: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 16: evaluate::evaluate(...)
where 17: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options))
where 18: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options)))
where 19: eng_r(options)
where 20: block_exec(params)
where 21: call_block(x)
where 22: process_group.block(group)
where 23: process_group(group)
where 24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 25: process_file(text, output)
where 26: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 27: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 28: vweave_rmarkdown(...)
where 29: engine$weave(file, quiet = quiet, encoding = enc)
where 30: doTryCatch(return(expr), name, parentenv, handler)
where 31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 32: tryCatchList(expr, classes, parentenv, handlers)
where 33: tryCatch({
    engine$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 34: tools::buildVignettes(dir = ".", tangle = TRUE)

 --- value of length: 4 type: logical ---
 space labels  width     at 
  TRUE   TRUE   TRUE   TRUE 
 --- function from context --- 
function (legend = NULL, key = NULL, fun = "draw.key") 
{
    if (is.null(legend) && is.null(key)) 
        return(NULL)
    if (is.null(legend)) 
        legend <- list()
    if (!is.null(key)) {
        space <- key$space
        x <- y <- corner <- NULL
        if (is.null(space)) {
            if (any(c("x", "y", "corner") %in% names(key))) {
                stopifnot(is.null(x) || (length(x) == 1 && x >= 
                  0 && x <= 1))
                stopifnot(is.null(y) || (length(y) == 1 && y >= 
                  0 && y <= 1))
                stopifnot(is.null(corner) || (length(corner) == 
                  2 && all(corner %in% c(0, 1))))
                space <- "inside"
                x <- key$x
                y <- key$y
                corner <- key$corner
            }
            else space <- "top"
        }
        if (space != "inside" && space %in% names(legend)) 
            stop(gettextf("component '%s' duplicated in key and legend", 
                space))
        key.legend <- list(fun = fun, args = list(key = key, 
            draw = FALSE))
        key.legend$x <- x
        key.legend$y <- y
        key.legend$corner <- corner
        legend <- c(list(key.legend), legend)
        names(legend)[1] <- space
    }
    legend
}
<bytecode: 0x558c2c3191e0>
<environment: namespace:lattice>
 --- function search by body ---
Function construct.legend in namespace lattice has this body.
 ----------- END OF FAILURE REPORT -------------- 
Quitting from lines 113-114 (epiNEM.Rmd) 
Error: processing vignette 'epiNEM.Rmd' failed with diagnostics:
'length(x) = 4 > 1' in coercion to 'logical(1)'
--- failed re-building ‘epiNEM.Rmd’

SUMMARY: processing the following file failed:
  ‘epiNEM.Rmd’

Error: Vignette re-building failed.
Execution halted