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Use names= rather than .Names= in structure() #257

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2 changes: 1 addition & 1 deletion R/BiocCheck-class.R
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Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,7 @@ NULL
"<Internal> 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)
Expand Down
6 changes: 3 additions & 3 deletions R/checkRcoding.R
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Expand Up @@ -414,7 +414,7 @@ checkCatInRCode <-
{
rfiles <- .BiocPackage$RSources
parsedCodes <- lapply(
structure(rfiles, .Names = rfiles), parseFile,
structure(rfiles, names = rfiles), parseFile,
.BiocPackage = .BiocPackage
)
parsedCodes <- lapply(parsedCodes, .filtersetMethodRanges)
Expand All @@ -432,7 +432,7 @@ checkEqInAssignment <-
{
rfiles <- .BiocPackage$RSources
parsedCodes <- lapply(
structure(rfiles, .Names = rfiles), parseFile,
structure(rfiles, names = rfiles), parseFile,
.BiocPackage = .BiocPackage
)
msg_res <- findSymbolsInParsedCode(
Expand Down Expand Up @@ -541,7 +541,7 @@ checkExternalData <- function(.BiocPackage) {
checkOnAttachLoadCalls <- function(.BiocPackage) {
rfiles <- .BiocPackage$RSources
parsedCodes <- lapply(
structure(rfiles, .Names = rfiles), parseFile,
structure(rfiles, names = rfiles), parseFile,
.BiocPackage = .BiocPackage
)
parsedCodes <- lapply(parsedCodes, function(tokens) {
Expand Down
12 changes: 6 additions & 6 deletions R/checkVignettes.R
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Expand Up @@ -429,7 +429,7 @@ checkVigEvalAllFalse <- function(.BiocPackage) {
vigfiles <- .BiocPackage$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]
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -624,7 +624,7 @@ try_purl_or_tangle <- function(input, output, quiet, ...) {
checkVigClassUsage <- function(.BiocPackage) {
vigfiles <- .BiocPackage$VigSources
viglist <- structure(
vector("list", length(vigfiles)), .Names = basename(vigfiles)
vector("list", length(vigfiles)), names = basename(vigfiles)
)
for (vfile in vigfiles) {
tempR <- tempfile(fileext=".R")
Expand All @@ -648,11 +648,11 @@ checkVigClassUsage <- function(.BiocPackage) {
checkVigSessionInfo <- function(.BiocPackage) {
vigfiles <- .BiocPackage$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(
Expand Down
6 changes: 3 additions & 3 deletions R/findSymbols.R
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Expand Up @@ -77,7 +77,7 @@ findSymbolsInParsedCode <-
)
{
matches <- structure(vector("list", length(parsedCodeList)),
.Names = names(parsedCodeList))
names = names(parsedCodeList))
allcombos <- expand.grid(
tokenTypes = tokenTypes,
symbolNames = symbolNames,
Expand Down Expand Up @@ -129,7 +129,7 @@ findSymbolsInRFiles <-
{
rfiles <- .BiocPackage$RSources
parsedCodes <- lapply(
structure(rfiles, .Names = rfiles), parseFile,
structure(rfiles, names = rfiles), parseFile,
.BiocPackage = .BiocPackage
)
msg_res <- findSymbolsInParsedCode(
Expand Down Expand Up @@ -161,7 +161,7 @@ findSymbolsInVignettes <-
{
vigfiles <- .BiocPackage$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")
Expand Down
2 changes: 1 addition & 1 deletion R/parseFiles.R
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Expand Up @@ -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)
Expand Down
2 changes: 1 addition & 1 deletion R/util.R
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Expand Up @@ -31,7 +31,7 @@ handleCondition <-
"<Internal> 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,
Expand Down
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