Added compatibility to Java 17+ #92
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…ion in convertToMAE.Rd
…y data type in buildPredictor.R
…ensive tests for convertToMAE() function
Adding MAE wrapper functions
Easier PSN specification + tests added for predict()
* Updated download links to Pai Lab server at OICR * Updated vignette with convertToMAE()
Added Project Statement + Docker Install instructions
…itioning step and use of built-in similarity functions
Update README.md and ThreeWayClassifier.Rmd
Error description:
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
netDx
--- call from context ---
checkMakeNetFuncSims(makeNetFunc = makeNetFunc, sims = sims,
groupList = groupList)
--- call from argument ---
if (all.equal(sort(names(sims)), sort(names(groupList))) != TRUE) stop("names(sims) must match names(groupList).")
--- R stacktrace ---
where 1: checkMakeNetFuncSims(makeNetFunc = makeNetFunc, sims = sims,
groupList = groupList)
where 2: plotIntegratedPatientNetwork(dataList = dat, groupList = g2,
makeNetFunc = makeNetFunc, sims = sims, aggFun = aggFun,
prune_pctX = prune_pctX, prune_useTop = prune_useTop, numCores = numCores,
calcShortestPath = calcShortestPath, showStats = FALSE, verbose = TRUE,
plotCytoscape = plotCytoscape)
where 3: getPSN(brca, groupList, sims = sims, selectedFeatures = results$selectedFeatures)
where 4: withCallingHandlers(expr, message = function(c) if (inherits(c,
classes)) tryInvokeRestart("muffleMessage"))
where 5: suppressMessages(getPSN(brca, groupList, sims = sims, selectedFeatures = results$selectedFeatures))
where 6: eval(expr, envir, enclos)
where 7: eval(expr, envir, enclos)
where 8: withVisible(eval(expr, envir, enclos))
where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 13: evaluate::evaluate(...)
where 14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 15: 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$render, options)))
where 16: eng_r(options)
where 17: block_exec(params)
where 18: call_block(x)
where 19: process_group.block(group)
where 20: process_group(group)
where 21: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 22: process_file(text, output)
where 23: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 24: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 25: vweave_rmarkdown(...)
where 26: engine$weave(file, quiet = quiet, encoding = enc)
where 27: doTryCatch(return(expr), name, parentenv, handler)
where 28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 29: tryCatchList(expr, classes, parentenv, handlers)
where 30: tryCatch({
engine$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 31: tools::buildVignettes(dir = ".", tangle = TRUE)
--- value of length: 2 type: logical ---
[1] TRUE TRUE
--- function from context ---
function (makeNetFunc, sims, groupList)
{
if (is.null(makeNetFunc) && is.null(sims)) {
stop("Provide either makeNetFunc or sims (preferred).")
}
if (!is.null(makeNetFunc) && !is.null(sims)) {
stop("Provide either makeNetFunc or sims (preferred).")
}
if (!is.null(sims)) {
if (class(sims) != "list")
stop("sims must be a list.")
if (all.equal(sort(names(sims)), sort(names(groupList))) !=
TRUE)
stop("names(sims) must match names(groupList).")
}
return(TRUE)
}
<bytecode: 0x5616e1414570>
<environment: namespace:netDx>
--- function search by body ---
Function checkMakeNetFuncSims in namespace netDx has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 417-419 (ThreeWayClassifier.Rmd)
Error: processing vignette 'ThreeWayClassifier.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'ThreeWayClassifier.Rmd'
ThreeWayClassifier fix
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