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Merged
TroyHernandez merged 1 commit into from
May 19, 2026
Merged

Split title/description/details and use base-R macros for package Rd #11

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181 changes: 95 additions & 86 deletions R/cran.R
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14 changes: 6 additions & 8 deletions R/document.R
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Original file line number Diff line number Diff line change
Expand Up @@ -39,14 +39,15 @@
#' # Clean up
#' unlink(pkg, recursive = TRUE)
#' }
document <- function (path = ".", namespace = c("overwrite", "append", "none"),
cran_check = TRUE) {
document <- function(path = ".",
namespace = c("overwrite", "append", "none"),
cran_check = TRUE) {
namespace <- match.arg(namespace)

# Validate path
if (!file.exists(file.path(path, "DESCRIPTION"))) {
stop("No DESCRIPTION file found in ", path,
". Is this an R package?", call. = FALSE)
". Is this an R package?", call. = FALSE)
}

# Check CRAN compliance
Expand Down Expand Up @@ -79,10 +80,7 @@ document <- function (path = ".", namespace = c("overwrite", "append", "none"),
message("Updated NAMESPACE.")
}

invisible(list(
rd_files = rd_files,
namespace = ns_file
))
invisible(list(rd_files = rd_files, namespace = ns_file))
}

#' Clean Generated Files
Expand Down Expand Up @@ -110,7 +108,7 @@ document <- function (path = ".", namespace = c("overwrite", "append", "none"),
#' # Clean up
#' unlink(pkg, recursive = TRUE)
#' }
clean <- function (path = ".", namespace = FALSE) {
clean <- function(path = ".", namespace = FALSE) {
man_dir <- file.path(path, "man")

if (dir.exists(man_dir)) {
Expand Down
157 changes: 75 additions & 82 deletions R/namespace.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,54 +3,54 @@
#' List of base R S3 generics for auto-detection when @export is used.
#' @keywords internal
KNOWN_S3_GENERICS <- c(
# Print/display
"print", "format", "summary", "str",
# Coercion
"as.array", "as.character", "as.data.frame", "as.list", "as.matrix",
"as.vector",
"as.numeric", "as.integer", "as.logical", "as.double", "as.complex",
"as.Date", "as.POSIXct", "as.POSIXlt", "as.factor",
# Type checking
"is.na", "is.null", "is.finite", "is.infinite", "is.nan",
# Subsetting
"[", "[[", "$", "[<-", "[[<-", "$<-",
# Arithmetic operators
"+", "-", "*", "/", "^", "%%", "%/%",
# Comparison operators
"==", "!=", "<", "<=", ">=", ">",
# Logical operators
"&", "|", "!",
# Math/ops group generics
"mean", "median", "quantile", "range", "sum", "prod", "min", "max",
"Math", "Ops", "Summary", "Complex",
# Dimensions
"length", "dim", "nrow", "ncol", "names", "dimnames", "row.names",
"length<-", "dim<-", "names<-", "dimnames<-", "row.names<-",
# Model methods
"coef", "fitted", "residuals", "predict", "simulate", "update",
"vcov", "confint", "logLik", "AIC", "BIC", "nobs", "df.residual",
"deviance", "extractAIC", "model.frame", "model.matrix",
"anova", "effects", "weights", "variable.names", "case.names",
# Plot
"plot", "lines", "points", "text", "image", "contour", "persp",
"pairs", "hist", "barplot", "boxplot", "dotchart",
# Other common
"c", "t", "rep", "rev", "sort", "unique", "duplicated", "anyDuplicated",
"merge", "split", "cut", "cbind", "rbind", "stack", "unstack",
"head", "tail", "within", "transform", "subset", "aggregate",
"droplevels", "xtfrm", "labels", "levels", "levels<-",
# Connection/IO
"open", "close", "flush", "read", "write", "seek", "truncate",
# Misc
"all.equal", "Negate"
# Print/display
"print", "format", "summary", "str",
# Coercion
"as.array", "as.character", "as.data.frame", "as.list", "as.matrix",
"as.vector",
"as.numeric", "as.integer", "as.logical", "as.double", "as.complex",
"as.Date", "as.POSIXct", "as.POSIXlt", "as.factor",
# Type checking
"is.na", "is.null", "is.finite", "is.infinite", "is.nan",
# Subsetting
"[", "[[", "$", "[<-", "[[<-", "$<-",
# Arithmetic operators
"+", "-", "*", "/", "^", "%%", "%/%",
# Comparison operators
"==", "!=", "<", "<=", ">=", ">",
# Logical operators
"&", "|", "!",
# Math/ops group generics
"mean", "median", "quantile", "range", "sum", "prod", "min", "max",
"Math", "Ops", "Summary", "Complex",
# Dimensions
"length", "dim", "nrow", "ncol", "names", "dimnames", "row.names",
"length<-", "dim<-", "names<-", "dimnames<-", "row.names<-",
# Model methods
"coef", "fitted", "residuals", "predict", "simulate", "update",
"vcov", "confint", "logLik", "AIC", "BIC", "nobs", "df.residual",
"deviance", "extractAIC", "model.frame", "model.matrix",
"anova", "effects", "weights", "variable.names", "case.names",
# Plot
"plot", "lines", "points", "text", "image", "contour", "persp",
"pairs", "hist", "barplot", "boxplot", "dotchart",
# Other common
"c", "t", "rep", "rev", "sort", "unique", "duplicated", "anyDuplicated",
"merge", "split", "cut", "cbind", "rbind", "stack", "unstack",
"head", "tail", "within", "transform", "subset", "aggregate",
"droplevels", "xtfrm", "labels", "levels", "levels<-",
# Connection/IO
"open", "close", "flush", "read", "write", "seek", "truncate",
# Misc
"all.equal", "Negate"
)

#' Generate NAMESPACE Content
#'
#' @param blocks List of documentation blocks from parse_package().
#' @return Character string of NAMESPACE content.
#' @keywords internal
generate_namespace <- function (blocks) {
generate_namespace <- function(blocks) {
exports <- character()
export_classes <- character()
s3methods <- list()
Expand All @@ -62,12 +62,7 @@ generate_namespace <- function (blocks) {
pkg_generics <- find_package_generics(blocks)

for (block in blocks) {
tags <- parse_tags(
block$lines,
block$object,
block$file,
block$line
)
tags <- parse_tags(block$lines, block$object, block$file, block$line)

# Check for S3 method pattern in exports
if (tags$export) {
Expand All @@ -85,17 +80,15 @@ generate_namespace <- function (blocks) {
if (!is.null(tags$exportS3Method)) {
s3m <- tags$exportS3Method
if (!is.null(s3m$generic) && !is.null(s3m$class)) {
s3methods <- c(s3methods, list(list(
generic = s3m$generic,
class = s3m$class
)))
s3methods <- c(s3methods, list(list(generic = s3m$generic,
class = s3m$class)))
} else if (!is.null(s3m$explicit)) {
# Try to parse from function name: generic.class
parts <- strsplit(block$object, "\\.") [[1]]
parts <- strsplit(block$object, "\\.")[[1]]
if (length(parts) >= 2) {
s3methods <- c(s3methods, list(list(
generic = parts[1],
class = paste(parts[- 1], collapse = ".")
class = paste(parts[-1], collapse = ".")
)))
}
}
Expand Down Expand Up @@ -143,18 +136,22 @@ generate_namespace <- function (blocks) {
# Export classes (sorted)
export_classes <- sort(unique(export_classes))
if (length(export_classes) > 0) {
if (length(exports) > 0) lines <- c(lines, "")
if (length(exports) > 0) {
lines <- c(lines, "")
}
for (cls in export_classes) {
lines <- c(lines, paste0("exportClasses(", cls, ")"))
}
}

# S3 methods (sorted by generic, then class)
if (length(s3methods) > 0) {
if (length(exports) > 0 || length(export_classes) > 0) lines <- c(lines, "")
if (length(exports) > 0 || length(export_classes) > 0) {
lines <- c(lines, "")
}
s3methods <- s3methods[order(
vapply(s3methods, function (x) paste(x$generic, x$class), character(1))
)]
vapply(s3methods, function(x) paste(x$generic, x$class), character(1))
)]
for (s3m in s3methods) {
gen <- s3m$generic
cls <- s3m$class
Expand Down Expand Up @@ -188,7 +185,9 @@ generate_namespace <- function (blocks) {
by_pkg[[impf$pkg]] <- c(by_pkg[[impf$pkg]], impf$symbols)
}

if (length(imports) == 0) lines <- c(lines, "")
if (length(imports) == 0) {
lines <- c(lines, "")
}
for (pkg in sort(names(by_pkg))) {
syms <- sort(unique(by_pkg[[pkg]]))
for (sym in syms) {
Expand All @@ -215,11 +214,7 @@ generate_namespace <- function (blocks) {
#' @param path Package root path.
#' @param mode Either "overwrite" or "append".
#' @keywords internal
write_namespace <- function(
content,
path = ".",
mode = "overwrite"
) {
write_namespace <- function(content, path = ".", mode = "overwrite") {
filepath <- file.path(path, "NAMESPACE")

if (mode == "overwrite") {
Expand All @@ -244,34 +239,30 @@ write_namespace <- function(
before <- character()
}
if (end_pos[1] < length(existing)) {
after <- existing[(end_pos[1] + 1) :length(existing)]
after <- existing[(end_pos[1] + 1):length(existing)]
} else {
after <- character()
}

new_content <- c(
before,
start_marker,
strsplit(content, "\n") [[1]],
end_marker,
after
)
new_content <- c(before, start_marker,
strsplit(content, "\n")[[1]], end_marker,
after)
} else {
# No markers - append at end
new_content <- c(
existing,
"",
start_marker,
strsplit(content, "\n") [[1]],
end_marker
existing,
"",
start_marker,
strsplit(content, "\n")[[1]],
end_marker
)
}
} else {
# New file
new_content <- c(
start_marker,
strsplit(content, "\n") [[1]],
end_marker
start_marker,
strsplit(content, "\n")[[1]],
end_marker
)
}

Expand Down Expand Up @@ -299,11 +290,11 @@ detect_s3_method <- function(name, pkg_generics = character()) {

# Try progressively longer generic names
# e.g., for "as.data.frame.foo", try "as", "as.data", "as.data.frame"
parts <- strsplit(name, "\\.") [[1]]
parts <- strsplit(name, "\\.")[[1]]

for (i in seq_len(length(parts) - 1)) {
generic <- paste(parts[1:i], collapse = ".")
class <- paste(parts[(i + 1) :length(parts)], collapse = ".")
class <- paste(parts[(i + 1):length(parts)], collapse = ".")

if (generic %in% all_generics) {
return(list(generic = generic, class = class))
Expand All @@ -327,7 +318,9 @@ find_package_generics <- function(blocks) {
generics <- character()

for (f in files) {
if (!file.exists(f)) next
if (!file.exists(f)) {
next
}
lines <- readLines(f, encoding = "UTF-8", warn = FALSE)
# Find lines with UseMethod("name")
m <- regmatches(lines, regexpr('UseMethod\\("([^"]+)"\\)', lines))
Expand Down
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