diff --git a/R/BiocCheck-class.R b/R/BiocCheck-class.R index f0cc59f..8cb0a31 100644 --- a/R/BiocCheck-class.R +++ b/R/BiocCheck-class.R @@ -142,7 +142,7 @@ NULL " Input to '$add' must be a list" = is.list(mlist) ) ins <- Filter(length, list(mlist, help_text, messages)) - nist <- structure(list(ins), .Names = names(mlist)) + nist <- structure(list(ins), names = names(mlist)) .messages$setMessage(nist, condition = condition) .self[[condition]] <- append(.self[[condition]], nist) .self$log[[checkName]] <- append(.self$log[[checkName]], nist) diff --git a/R/checkRcoding.R b/R/checkRcoding.R index 59e3321..8bfd90c 100644 --- a/R/checkRcoding.R +++ b/R/checkRcoding.R @@ -414,7 +414,7 @@ checkCatInRCode <- { rfiles <- .BiocPackage$RSources parsedCodes <- lapply( - structure(rfiles, .Names = rfiles), parseFile, + structure(rfiles, names = rfiles), parseFile, .BiocPackage = .BiocPackage ) parsedCodes <- lapply(parsedCodes, .filtersetMethodRanges) @@ -432,7 +432,7 @@ checkEqInAssignment <- { rfiles <- .BiocPackage$RSources parsedCodes <- lapply( - structure(rfiles, .Names = rfiles), parseFile, + structure(rfiles, names = rfiles), parseFile, .BiocPackage = .BiocPackage ) msg_res <- findSymbolsInParsedCode( @@ -541,7 +541,7 @@ checkExternalData <- function(.BiocPackage) { checkOnAttachLoadCalls <- function(.BiocPackage) { rfiles <- .BiocPackage$RSources parsedCodes <- lapply( - structure(rfiles, .Names = rfiles), parseFile, + structure(rfiles, names = rfiles), parseFile, .BiocPackage = .BiocPackage ) parsedCodes <- lapply(parsedCodes, function(tokens) { diff --git a/R/checkVignettes.R b/R/checkVignettes.R index c620ded..0183137 100644 --- a/R/checkVignettes.R +++ b/R/checkVignettes.R @@ -429,7 +429,7 @@ checkVigEvalAllFalse <- function(.BiocPackage) { vigfiles <- .BiocPackage$VigSources shortnames <- .getDirFiles(vigfiles) viglist <- structure( - vector("logical", length(vigfiles)), .Names = shortnames + vector("logical", length(vigfiles)), names = shortnames ) for (i in seq_along(vigfiles)) { shortName <- shortnames[i] @@ -462,7 +462,7 @@ checkVigEvalAllFalse <- function(.BiocPackage) { checkDupChunkLabels <- function(vigfiles) { viglist <- structure( vector("logical", length(vigfiles)), - .Names = vigfiles + names = vigfiles ) for (vfile in vigfiles) { tempR <- tempfile(fileext=".R") @@ -519,7 +519,7 @@ checkDupChunkLabels <- function(vigfiles) { checkChunkLabels <- function(vigfiles) { viglist <- structure( vector("logical", length(vigfiles)), - .Names = vigfiles + names = vigfiles ) for (vfile in vigfiles) { viglines <- readLines(vfile, warn = FALSE) @@ -624,7 +624,7 @@ try_purl_or_tangle <- function(input, output, quiet, ...) { checkVigClassUsage <- function(.BiocPackage) { vigfiles <- .BiocPackage$VigSources viglist <- structure( - vector("list", length(vigfiles)), .Names = basename(vigfiles) + vector("list", length(vigfiles)), names = basename(vigfiles) ) for (vfile in vigfiles) { tempR <- tempfile(fileext=".R") @@ -648,11 +648,11 @@ checkVigClassUsage <- function(.BiocPackage) { checkVigSessionInfo <- function(.BiocPackage) { vigfiles <- .BiocPackage$VigSources notFoundVig <- structure( - vector("logical", length(vigfiles)), .Names = vigfiles + vector("logical", length(vigfiles)), names = vigfiles ) for (vfile in vigfiles) { pc <- structure( - list(parseFile(.BiocPackage, vfile)), .Names = vfile + list(parseFile(.BiocPackage, vfile)), names = vfile ) if (nrow(pc[[vfile]])) { res <- findSymbolsInParsedCode( diff --git a/R/findSymbols.R b/R/findSymbols.R index cc2a54b..c3da003 100644 --- a/R/findSymbols.R +++ b/R/findSymbols.R @@ -77,7 +77,7 @@ findSymbolsInParsedCode <- ) { matches <- structure(vector("list", length(parsedCodeList)), - .Names = names(parsedCodeList)) + names = names(parsedCodeList)) allcombos <- expand.grid( tokenTypes = tokenTypes, symbolNames = symbolNames, @@ -129,7 +129,7 @@ findSymbolsInRFiles <- { rfiles <- .BiocPackage$RSources parsedCodes <- lapply( - structure(rfiles, .Names = rfiles), parseFile, + structure(rfiles, names = rfiles), parseFile, .BiocPackage = .BiocPackage ) msg_res <- findSymbolsInParsedCode( @@ -161,7 +161,7 @@ findSymbolsInVignettes <- { vigfiles <- .BiocPackage$VigSources shortnames <- .getDirFiles(vigfiles) - viglist <- structure(vector("list", length(vigfiles)), .Names = shortnames) + viglist <- structure(vector("list", length(vigfiles)), names = shortnames) for (i in seq_along(vigfiles)) { shortName <- shortnames[i] tempR <- tempfile(fileext=".R") diff --git a/R/parseFiles.R b/R/parseFiles.R index 9471aae..734d2a0 100644 --- a/R/parseFiles.R +++ b/R/parseFiles.R @@ -30,7 +30,7 @@ parseFiles <- function(.BiocPackage) manfiles <- .BiocPackage$manSources vigfiles <- .BiocPackage$VigSources files <- c(rfiles, manfiles, vigfiles) - parsedCode <- structure(vector("list", length(files)), .Names = files) + parsedCode <- structure(vector("list", length(files)), names = files) for (file in files) { df <- parseFile(.BiocPackage, file) diff --git a/R/util.R b/R/util.R index 0271a02..07f36e5 100644 --- a/R/util.R +++ b/R/util.R @@ -31,7 +31,7 @@ handleCondition <- " Designate input with 'warning', 'error', or 'note'." ) cl <- sys.call(sys.parent(n = nframe))[[1L]] - ml <- structure(msg, .Names = tail(as.character(cl), 1L)) + ml <- structure(msg, names = tail(as.character(cl), 1L)) .BiocCheck$add( ml, condition = condition,