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code-checking.R
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code-checking.R
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if (getRversion() >= "3.1.0") {
utils::globalVariables(".")
}
# These are known functions that will definitely cause conflicts unless they are
# prefixed by their packages.
conflictingFns <- c("\\<raster::levels\\>", "\\<raster::scale\\>", "\\<raster::which.max\\>")
clashingFns <- c("\\<quickPlot::Plot\\>")
mustBeReturnSim <- c("doEvent\\..*") # module functions that must end with return(sim) or the like
mustAssignToSim <- c("scheduleEvent", "saveFiles") # module functions that must assign to sim <-
ignoreObjectsGet <- c(".userSuppliedObjNames") # objects that shouldn't return an error if "used"
ignoreObjectsAssign <- c("") # objects that shouldn't return an error if "assigned"
conflictingFnsClean <- gsub(pattern = "\\\\<", conflictingFns, replacement = "")
conflictingFnsClean <- gsub(pattern = "\\\\>", conflictingFnsClean, replacement = "")
conflictingFnsSimple <- gsub(conflictingFns, pattern = "^.*::", replacement = "\\\\<")
conflictingFnsSimple <- gsub(pattern = "\\\\<", conflictingFnsSimple, replacement = "")
conflictingFnsSimple <- gsub(pattern = "\\\\>", conflictingFnsSimple, replacement = "")
clashingFnsClean <- gsub(pattern = "\\\\<", clashingFns, replacement = "")
clashingFnsClean <- gsub(pattern = "\\\\>", clashingFnsClean, replacement = "")
clashingFnsSimple <- gsub(clashingFns, pattern = "^.*::", replacement = "\\\\<")
clashingFnsSimple <- gsub(pattern = "\\\\<", clashingFnsSimple, replacement = "")
clashingFnsSimple <- gsub(pattern = "\\\\>", clashingFnsSimple, replacement = "")
allCleanMessage <- "module code appears clean"
cantCodeCheckMessage <- ": line could not be checked "
#' Find all references to sim$
#'
#' @param envToFindSim An environment where sim is defined. This is used when
#' the element accessing the simList is actually a call, e.g.,
#' \code{sim[[P(sim)$stackName]]}
#' @param moduleEnv The environment where the module functions are
#' @param type Either "get", "assign", or "globals". See details.
#'
#'
#' @details
#' \code{.findElementsInEnv} is a wrapper around \code{.findElements}. It will convert
#' function code to a call, and then pass it to \code{.findElements}. It also does
#' some cleaning for duplications, \code{NA} values, and cases where the element
#' inside a \code{sim[["xxx"]]} is a variable that should be evaluated, rather than
#' simply taken verbatim (e.g., \code{sim[[P(sim)$stackName]])}.
#'
#' When \bold{\code{type = "get"}}, the function scans for sim$xxx or sim[["xxx"]]] on
#' the RHS of an assignment operator or when there is no assignment. When
#' \bold{\code{type = "assign"}}, the function scans for sim$xxx or sim[['xxx']] on the
#' LHS of an assignment operator. When \bold{\code{type = "globals"}}, the function
#' scans for all functions (i.e., "globals") being used. This is similar to
#' \code{\link[codetools]{findGlobals}}, but faster.
#'
#' @return
#' A character string with all sim objects found
#'
#' @author Eliot McIntire
#' @keywords internal
#' @rdname findElements
.findElementsInEnv <- function(envToFindSim = parent.frame(), moduleEnv = parent.frame(),
type) {
out <- unlist(unique(lapply(names(moduleEnv), function(x) {
if (is.function(moduleEnv[[x]])) {
xAsString <- deparse(body(moduleEnv[[x]]))#, backtick = TRUE, control = "all")
if (identical(type, "returnSim")) {
# returnSim case doesn't need to parse whole function, only last Number
xAsCall <- .isLastLineSim(x = x, xAsString = xAsString)
y <- .findElement(xAsCall, type = type)
} else {
parsedXAsString <- tryCatch(parse(text = xAsString), error = function(yy) NULL)
# In some cases, e.g., Jean Marchal's
if (is.null(parsedXAsString) > 0) {
deparseBody <- deparse(body(moduleEnv[[x]]))
bb <- deparseBody[-c(1, length(deparseBody))]
funStarts <- grep("^ [[:alpha:]]", bb)
bb[funStarts] <- gsub("^ ", "", bb[funStarts])
funEnds <- funStarts - 1
y <- lapply(seq(funStarts)[-length(funStarts)], function(yy) {
parsedXAsString <- tryCatch(parse(text = bb[seq(funStarts[yy], funEnds[yy + 1])]),
error = function(yy) NULL)
if (!is.null(parsedXAsString)) {
xAsCall <- as.call(parsedXAsString)
if (identical(type, "returnSim")) {
xAsCall <- .isLastLineSim(x = x, xAsString = bb[seq(funStarts[yy], funEnds[yy + 1])])
}
y <- .findElement(xAsCall, type = type)
} else {
#y = strsplit(bb[funStarts[yy]], split = "\\s+")[[1]][1]
y <- paste0(cantCodeCheckMessage, "'",bb[funStarts[yy]], "'")
}
})
} else {
xAsCall <- as.call(parsedXAsString)
if (identical(type, "returnSim")) {
xAsCall <- .isLastLineSim(x = x, xAsString = xAsString)
}
y <- .findElement(xAsCall, type = type)
}
}
if (length(y)) {
y <- na.omit(y)
if (all(is.na(y))) y <- character()
hasSim <- grepl(y, pattern = "sim")
isSim <- grepl(y, pattern = "^sim$")
if (length(y[hasSim & !isSim])) {
y[hasSim] <- lapply(y[hasSim], function(yParts) {
tryCatch(eval(parse(text = yParts), envir = envToFindSim),
error = function(x) yParts)
})
}
names(y) <- rep(x, length(y))
isNull <- unlist(lapply(y, is.null))
if (any(isNull))
y <- y[!unlist(isNull)]
isNA <- unlist(lapply(y, is.na))
if (any(isNA))
y <- y[!isNA]
y <- y[unlist(lapply(y, is.character))]
}
y
}
})))
if (is.null(out)) out <- character()
return(out)
}
#' @keywords internal
#' @param x A call in which to search for sim
#' @inheritParams .findElementsInEnv
#' @details
#' \code{.findElement} will omit whatever it finds inside a \code{is.null}, when
#' \code{type = "assign"}. Usually this is a test of existence of that object, in
#' order to assign to that object. It is only reading it to determine whether or
#' not it should write to it.
#'
#' @rdname findElements
.findElement <- function(x, type) {
if (is.atomic(x)) {
character()
} else if (is.name(x)) {
if (identical(type, "returnSim")) { # This is intended for only the last line of a function
out <- as.character(x)
} else {
character()
}
} else if (is.call(x)) {
if (identical(type, "assign")) {
if (identical(x[[1]], quote(`<-`))) {
# if it is an assign, only keep left hand side
x <- x[[2]]
out <- .parsingSim(x, type = type)
} else {
out <- character()
}
unique(c(out, unlist(lapply(x, .findElement, type = type))))
} else if (identical(type, "assignToSim")) {
if (identical(x[[1]], quote(`<-`)) &&
(any(grepl(x, pattern = paste(mustAssignToSim, collapse = "|"))))) {
if (identical(x[[2]], quote(sim))) {
out <- character()
x <- "" # clear x so it doesn't go any further in these cases
} else {
out <- character()
}
} else if (is.name(x[[1]]) &
(any(grepl(x[[1]], pattern = paste(mustAssignToSim, collapse = "|"))))) {
out <- as.character(x[[1]])
x <- "" # clear x so it doesn't go any further in these cases
} else {
out <- character()
}
unique(c(out, unlist(lapply(x, .findElement, type = type))))
} else if (identical(type, "get")) {
if (identical(x[[1]], quote(is.null))) {
# This is case where module may check for absense of a sim object with is.null
# This shouldn't make a message
return(character())
} else if (identical(x[[1]], quote(`<-`)) ) {
if (length(x[[2]]) > 1) {
if (is.call(x[[2]][[2]])) {
if (any(grepl(x[[2]][[2]], pattern = ".envir"))) {# i.e., sim@.envir
assigner <- FALSE
} else {
assigner <- TRUE # accessor on LHS like P(sim$a) <- "hi"
}
} else {
if (identical(as.character(x[[2]])[1], "[") |
identical(as.character(x[[2]])[1], "[[")) {
assigner <- TRUE
} else {
assigner <- FALSE
}
}
} else {
assigner <- FALSE
}
if (!assigner) {
x <- x[-(1:2)]
}
out <- character()
#if (is.call(x[[2]][[2]]))
# if on the left side of a function, deleted those from x, we don't care here
} else {
out <- .parsingSim(x, type = type)
}
unique(c(out, unlist(lapply(x, .findElement, type = type))))
} else if (identical(type, "globals")) {
if (identical(x[[1]], quote(`<-`)) && is.call(x[[2]])) {
# left side function assign
# This labels it with an assignment arrow -- e.g., levels<-
out <- paste0(as.character(x[[2]][[1]]), as.character(x)[[1]])
if (length(x[[2]]) > 2) {
x[[2]] <- x[[2]][-(1:2)]
} else {
x[[2]] <- x[[2]][[2]]
}
} else if (is.name(x[[1]])) {
out <- as.character(x[[1]])
} else if (any(as.character(x[[1]]) %in% conflictingFnsSimple)) {
tmp <- deparse(x[[1]])
if (tmp %in% conflictingFnsClean) {
out <- tmp
x <- ""
} else {
out <- character()
}
} else {
out <- character()
}
unique(c(out, unlist(lapply(x, .findElement, type = type))))
} else {
# all other cases, just return empty
out <- character()
unique(c(out, unlist(lapply(x, .findElement, type = type))))
}
} else if (is.pairlist(x)) {
unique(unlist(lapply(x, .findElement, type = type)))
} else {
stop("Don't know how to handle type ", typeof(x),
call. = FALSE)
}
}
#' Runs a series of code checks during simInit
#'
#' This uses codetools::codeCheck for function consistency, and
#' codetools::findGlobals to check for function collisions with known,
#' common function collisions (raster::stack, raster::scale)
#'
#' @param sim simList
#' @param m module name
#' @param message rest of message
#' @param hadPrevMessage
#'
#' @return
#' A message with that starts with paste0(m, ":", message)
#'
#' @keywords internal
#' @rdname runCodeChecks
.runCodeChecks <- function(sim, m, k, hadPrevMessage = FALSE) {
inputObjNames <- na.omit(sim@depends@dependencies[[k]]@inputObjects$objectName)
outputObjNames <- na.omit(sim@depends@dependencies[[k]]@outputObjects$objectName)
# search for all sim$xx <- or sim[[xxx]] <- in module code
simAssigns <- .findElementsInEnv(environment(), sim@.envir[[m]], type = "assign")
simAssigns <- simAssigns[!(simAssigns %in% ignoreObjectsAssign)]
# search for all '<- sim$' or '<- sim[[xxx]]' in module code
simGets <- .findElementsInEnv(environment(), sim@.envir[[m]], type = "get")
simGets <- simGets[!(simGets %in% ignoreObjectsGet)]
returnsSim <- .findElementsInEnv(environment(), sim@.envir[[m]], type = "returnSim")
returnsSim <- tapply(returnsSim, names(returnsSim), function(xx) any(xx == "sim"))
assignToSim <- .findElementsInEnv(environment(), sim@.envir[[m]], type = "assignToSim")
fg <- .findElementsInEnv(environment(), sim@.envir[[m]], type = "globals")
hasConflicts <- fg[fg %in% conflictingFnsSimple]
# Can't code check:
allChecks <- list(simAssigns = simAssigns, simGets = simGets,
returnsSim = returnsSim, assignToSim = assignToSim, fg = fg)
cantCodeCheck <- lapply(allChecks, function(xx) grepl(cantCodeCheckMessage, xx))
anyCantCodeCheck <- unlist(lapply(cantCodeCheck, any))
if (any(anyCantCodeCheck)) {
cant <- lapply(names(cantCodeCheck[anyCantCodeCheck]), function(objName) {
localObj <- allChecks[[objName]]
localObj[cantCodeCheck[[objName]]]
})
textCantCheck <- gsub(paste0(cantCodeCheckMessage, "'"), "", cant[[1]])
textCantCheck <- gsub("'$", "", textCantCheck)
lineNumbers <- .lineNumbersInSrcFile(sim, m, textCantCheck)
dfCant <- data.frame(names = names(unlist(cant)), cant = unlist(cant), stringsAsFactors = FALSE)
dfCant <- unique(dfCant)
cant <- dfCant$cant
names(cant) <- dfCant$names
if (length(cant)) {
verb <- .verb(cant)
hadPrevMessage <- lapply(seq(cant), function(cantNamesIndex) {
cantUnique <- cant[names(cant) == cant[cantNamesIndex]]
.parseMessage(m, "module code",
paste(paste0(names(cant)[cantNamesIndex], " ",
cant[cantNamesIndex],
if (length(lineNumbers[[cantNamesIndex]]))
paste0(" (possibly at ", lineNumbers[[cantNamesIndex]]), ")"),
collapse = "\n")
)
})
}
allChecks[anyCantCodeCheck] <- lapply(names(cantCodeCheck[anyCantCodeCheck]), function(objName) {
localObj <- allChecks[[objName]]
localObj[!cantCodeCheck[[objName]]]
})
list2env(allChecks, envir = environment())
}
simAssignsInDotInputObjects <- simAssigns[names(simAssigns) == ".inputObjects"]
simAssignsNotInDotInputObjects <- simAssigns[names(simAssigns) != ".inputObjects"]
simGetsInDotInputObjects <- simGets[names(simGets) == ".inputObjects"]
simGetsNotInDotInputObjects <- simGets[names(simGets) != ".inputObjects"]
#############################################################
###### Key fns return sim ###################################
#############################################################
if (!all(returnsSim)) {
verb <- .verb(returnsSim)
hadPrevMessage <- .parseMessage(
m, "module code",
paste0(paste(names(returnsSim), collapse = ", "),
" must return the sim, e.g., return(invisible(sim))")
)
}
#############################################################
###### Key fns outputs get assigned to sim ##################
#############################################################
if (length(assignToSim)) {
verb <- .verb(assignToSim)
hadPrevMessage <- .parseMessage(
m, "module code",
paste0(paste(assignToSim, collapse = ", "),
" inside ", paste(names(assignToSim), collapse = ", "),
" must assign to the sim, e.g., sim <- scheduleEvent(sim, ...)")
)
}
#############################################################
###### Sim Assignments ######################################
#############################################################
# 1
if (length(outputObjNames)) {
missingFrmMod <- outputObjNames[!(outputObjNames) %in% simAssignsNotInDotInputObjects]
missingFrmMod <- unique(missingFrmMod)
if (length(missingFrmMod)) {
verb <- .verb(missingFrmMod)
hadPrevMessage <- .parseMessage(m, "module code",
paste0(paste(missingFrmMod, collapse = ", "),
" ",verb," declared in outputObjects, ",
"but ", verb, " not assigned in the module"
))
}
}
# 2
if (length(inputObjNames)) {
# inputObjects -- Assign in .inputObjects
missingFrmMod <- inputObjNames[!(inputObjNames %in% simAssignsInDotInputObjects)]
missingFrmMod <- unique(missingFrmMod)
if (length(missingFrmMod)) {
verb <- .verb(missingFrmMod)
hadPrevMessage <- .parseMessage(
m, "module code",
paste0(paste(missingFrmMod, collapse = ", "),
" ",verb," declared in inputObjects, ",
"but no default(s) ", verb, " provided in .inputObjects")
)
}
# inputObjects -- Gets
missingFrmMod <- inputObjNames[!(inputObjNames %in% simGets)]
missingFrmMod <- unique(na.omit(missingFrmMod))
if (length(missingFrmMod)) {
verb <- .verb(missingFrmMod)
hadPrevMessage <- .parseMessage(m, "module code",
paste0(paste(missingFrmMod, collapse = ", "), " ",verb,
" declared in inputObjects, ", "but ", verb,
" not used in the module"
))
}
}
#############################################################
##### checkUsage -- From codetools ##########################
#############################################################
checks <- if (isTRUE(getOption("spades.moduleCodeChecks"))) {
list(suppressParamUnused = FALSE, suppressUndefined = TRUE,
suppressPartialMatchArgs = FALSE, suppressNoLocalFun = TRUE,
skipWith = TRUE)
} else {
getOption("spades.moduleCodeChecks")
}
checkUsageMsg <- capture.output(
do.call(checkUsageEnv, args = append(list(env = sim@.envir[[m]]), checks))
)
checkUsageMsg <- grep(checkUsageMsg, pattern = "doEvent.*: parameter",
invert = TRUE, value = TRUE)
if (length(checkUsageMsg)) {
hadPrevMessage <- unique(unlist(lapply(checkUsageMsg, function(x)
.parseMessage(m, "module code", message = x))))
}
#############################################################
####### Conflicting Functions ##############################
#############################################################
# search for conflicts in function names with common problems like raster::levels
if (length(hasConflicts)) {
theFns <- names(hasConflicts)
names(theFns) <- theFns
whichFnsWithPackage <- conflictingFnsClean[conflictingFnsSimple %in% hasConflicts]
verb <- .verb(length(whichFnsWithPackage))
hadPrevMessage <- .parseMessage(
m, "module code",
paste0("the following function(s) ", verb, " used that conflict(s)",
"\n with base functions: ", crayon::bold(paste(hasConflicts, collapse = ", ")),
"\n It is a good idea to be explicit about the package sources",
", e.g., ", paste(whichFnsWithPackage, collapse = ", "),
" but only for the 'get' functions, not the 'set' function ","
(e.g., don't change when on the left hand side of an assignment operator)")
)
}
if (length(simAssigns)) {
# does module name occur as a sim$ assign
if (m %in% simAssigns) {
stop(m, ": You have created an object with the same name as the module. ",
"Currently, this is not allowed.", call. = FALSE)
}
# First do all but .inputObjects, i.e,. outputObjects
missingInMetadata <- simAssignsNotInDotInputObjects[!(simAssignsNotInDotInputObjects %in% outputObjNames)]
if (length(missingInMetadata)) {
missingInMetadataByFn <- tapply(missingInMetadata, names(missingInMetadata), unique)
verbs <- lapply(missingInMetadataByFn, .verb)
hadPrevMessage <- any(unlist(
lapply(names(missingInMetadataByFn), function(fn)
.parseMessage(
m, "outputObjects",
paste0(paste(missingInMetadataByFn[[fn]], collapse = ", "),
" ",verbs[[fn]]," assigned to sim inside ",
fn, ", but ",verbs[[fn]]," not declared in outputObjects")
)
)
))
}
# Now do .inputObjects, i.e., inputObjects
missingInMetadata <- simAssignsInDotInputObjects[!(simAssignsInDotInputObjects %in% inputObjNames)]
if (length(missingInMetadata)) {
missingInMetadataByFn <- tapply(missingInMetadata, names(missingInMetadata), unique)
verbs <- lapply(missingInMetadataByFn, .verb)
hadPrevMessage <- any(unlist(
lapply(names(missingInMetadataByFn), function(fn)
.parseMessage(
m, "inputObjects",
paste0(paste(missingInMetadataByFn[[fn]], collapse = ", "),
" ",verbs[[fn]]," assigned to sim inside ",
fn, ", but ",verbs[[fn]]," not declared in inputObjects")
)
)
))
}
}
#############################################################
###### Sim Gets #############################################
#############################################################
# compare to inputObjNames -- this is about inputs
if (length(simGets)) {
missingInMetadata <- simGetsNotInDotInputObjects[!(simGetsNotInDotInputObjects %in%
c(inputObjNames, outputObjNames))]
if (length(missingInMetadata)) {
missingInMetadataByFn <- tapply(missingInMetadata, names(missingInMetadata), unique)
verbs <- lapply(missingInMetadataByFn, .verb)
hadPrevMessage <- any(unlist(
lapply(names(missingInMetadataByFn), function(fn)
.parseMessage(
m, "inputObjects",
paste0(paste(missingInMetadataByFn[[fn]], collapse = ", "),
" ",verbs[[fn]]," used from sim inside ",
fn, ", but ",verbs[[fn]]," not declared in inputObjects")
)
)
))
}
# Now do .inputObjects, i.e., inputObjects
missingInMetadata <- simGetsInDotInputObjects[!(simGetsInDotInputObjects %in% inputObjNames)]
if (length(missingInMetadata)) {
verb <- .verb(missingInMetadata)
hadPrevMessage <-
.parseMessage(m, "inputObjects", paste0(paste(missingInMetadata, collapse = ", "),
" ",verb," used from sim inside ",
paste(unique(names(missingInMetadata)), collapse = ", "),
", but ",verb," not declared in inputObjects"
))
}
}
# search for conflicts in module function names with common problems, like quickPlot::Plot
clashingFuns <- names(sim@.envir[[m]])[names(sim@.envir[[m]]) %in% clashingFnsSimple]
if (length(clashingFuns)) {
fnNames <- clashingFnsClean[clashingFnsSimple %in% names(sim@.envir[[m]])]
verb <- .verb(clashingFuns)
hadPrevMessage <- .parseMessage(m, "module functions", paste0(
paste(clashingFuns, collapse = ", "), " ", verb,
" defined, which ", verb, " in conflict with ",
paste(fnNames, collapse = ", "), ". It is recommended to ",
" use non-conflicting function names"))
}
#############################################################
###### Message if all clean #################################
#############################################################
if (!hadPrevMessage) .parseMessage(m, "", allCleanMessage)
return(invisible())
}
#' Prepend module name to a message
#'
#' Also makes it blue.
#'
#' @param m module name
#' @param message rest of message
#'
#' @return
#' A message with that starts with paste0(m, ":", message)
#'
#' @keywords internal
#' @rdname parseMessage
.parseMessage <- function(m, problem, message) {
sub <- if (nzchar(problem)) {
paste0(": ", problem)
} else {
""
}
message <- if (nzchar(message)) {
paste0(": ", message)
} else {
""
}
message(crayon::magenta(
paste0(m, sub, message)
))
return(TRUE)
}
#' Chose verb conjugation for "to be"
#'
#' @param item The item to accord conjugation with. If length 1, then "is"
#' else "are"
#'
#' @return
#' "is" or "are"
#'
#' @keywords internal
#' @rdname verb
.verb <- function(item) {
c("is", "are")[1 + as.numeric(length(item) > 1)]
}
#' \code{.parsingSim} will pull out the various ways to use sim, e.g.,
#' \code{sim$xxx}, \code{sim[['xxx']]}, \code{sim[[P(sim)$xxx]]}
#' @keywords internal
#' @inheritParams .findElements
#' @rdname findElements
.parsingSim <- function(x, type) {
if (length(x) > 1) {
if (!is.pairlist(x[[2]])) {
grepForSim <- grepl("^sim|^sim@.envir", deparse(x[[2]], backtick = TRUE))
if (as.character(x)[1] %in% c("$", "[[") &&
grepForSim &&
is.name(x[[3]])) {
out <- as.character(x[[3]])
} else if (as.character(x)[1] %in% "[[" &&
grepForSim &&
is.character(x[[3]])) {
out <- x[[3]]
} else if (as.character(x)[1] %in% "[[" &&
grepForSim &&
is.call(x[[3]])) {
out <- deparse(x[[3]])
}
} else {
out <- character()
}
}
if (!exists("out", inherits = FALSE)) {
if (type == "assign") {
if (is.name(x)) {
out <- character()
} else if (identical(as.character(x)[1], "[") |
identical(as.character(x)[1], "[[")) {
out <- character()
} else {
out <- .findElement(x, type = "get")
}
} else {
out <- character()
}
}
return(out)
}
.isLastLineSim <- function(x, xAsString) {
if (grepl(x, pattern = mustBeReturnSim)) {
# only pull out last line
# must end with sim or return(sim) or return(invisible(sim))
xAsString <- xAsString[length(xAsString) - 1]
xAsCall <- as.call(parse(text = xAsString))
} else {
xAsCall <- ""
}
}
.lineNumbersInSrcFile <- function(sim, module, namedTxt,
pd) {
if (!missing(sim)) {
pd <- sim@.envir[[module]][["._parsedData"]]
}
lineNumbers <- lapply(seq(namedTxt), function(patternIndex) {
wh <- which(grepl(pattern = paste0("\\b", namedTxt[patternIndex], "\\b"), pd$text) &
(pd$line1 == pd$line2) & (pd$token == "expr"))
if (length(wh) == 0) {
wh <- which(agrepl(pattern = paste0(namedTxt[patternIndex]), pd$text) &
(pd$line1 == pd$line2) & (pd$token == "expr"))
}
outerWh <- which(grepl(paste0("\\b", names(namedTxt)[patternIndex], "\\b"), pd$text) &
(pd$token == "expr"))
linesWithFail <- unique(pd[wh, "line1"])
#unique(pd[outerWh, "line1"])
# Make sure they are inside the correct function
linesWithFail <- lapply(linesWithFail, function(lwf) {
whInner <- any((pd[outerWh,"line1"] < lwf) & (pd[outerWh,"line2"] > lwf) )
if (isTRUE(whInner)) lwf else numeric()
})
if (length(linesWithFail) == length(namedTxt[patternIndex]))
names(linesWithFail) <- namedTxt[patternIndex]
unlist(linesWithFail)
})
unlist(lineNumbers)
}