Hi Duncan,

I think this functionality would be much easier to use and understand if
you split it up the functionality of taking snapshots and comparing them
into separate functions.  In addition, the 'timestamp' functionality seems
both confusing and brittle to me.  I think it would be better to store file
modification times in the snapshot and use those instead of an external
file.  Maybe:

# Take a snapshot of the files.
takeFileSnapshot(directory, file.info = TRUE, md5sum = FALSE, full.names =
FALSE, recursive = TRUE, ...)

# Take a snapshot using the same options as used for snapshot.
retakeFileSnapshot(snapshot, directory = snapshot$directory) {
   takeFileSnapshot)(directory, file.info = snapshot$file.info, md5sum =
snapshot$md5sum, etc)
}

compareFileSnapshots(snapshot1, snapshot2)
- or -
getNewFiles(snapshat1, snapshot2)       # These names are probably too
generic
getDeletedFiles(snapshot1, snapshot2)
getUpdatedFiles(snapshot1, snapshot2)
-or-
setdiff(snapshot1, snapshot2)  # Unclear how this should treat updated files


This approach does have the difficulty that users could attempt to compare
snapshots that were taken with different options and that can't be
compared, but that should be an easy error to detect.

Karl


On Wed, Sep 4, 2013 at 10:53 AM, Duncan Murdoch <murdoch.duncan@gmail.com>wrote:

> In a number of places internal to R, we need to know which files have
> changed (e.g. after building a vignette).  I've just written a general
> purpose function "changedFiles" that I'll probably commit to R-devel.
>  Comments on the design (or bug reports) would be appreciated.
>
> The source for the function and the Rd page for it are inline below.
>
> ----- changedFiles.R:
> changedFiles <- function(snapshot, timestamp = tempfile("timestamp"),
> file.info = NULL,
>              md5sum = FALSE, full.names = FALSE, ...) {
>     dosnapshot <- function(args) {
>         fullnames <- do.call(list.files, c(full.names = TRUE, args))
>         names <- do.call(list.files, c(full.names = full.names, args))
>         if (isTRUE(file.info) || (is.character(file.info) && length(
> file.info))) {
>             info <- file.info(fullnames)
>         rownames(info) <- names
>             if (isTRUE(file.info))
>                 file.info <- c("size", "isdir", "mode", "mtime")
>         } else
>             info <- data.frame(row.names=names)
>     if (md5sum)
>         info <- data.frame(info, md5sum = tools::md5sum(fullnames))
>     list(info = info, timestamp = timestamp, file.info = file.info,
>          md5sum = md5sum, full.names = full.names, args = args)
>     }
>     if (missing(snapshot) || !inherits(snapshot, "changedFilesSnapshot")) {
>         if (length(timestamp) == 1)
>             file.create(timestamp)
>         if (missing(snapshot)) snapshot <- "."
>         pre <- dosnapshot(list(path = snapshot, ...))
>         pre$pre <- pre$info
>         pre$info <- NULL
>         pre$wd <- getwd()
>         class(pre) <- "changedFilesSnapshot"
>         return(pre)
>     }
>
>     if (missing(timestamp)) timestamp <- snapshot$timestamp
>     if (missing(file.info) || isTRUE(file.info)) file.info <- snapshot$
> file.info
>     if (identical(file.info, FALSE)) file.info <- NULL
>     if (missing(md5sum))    md5sum <- snapshot$md5sum
>     if (missing(full.names)) full.names <- snapshot$full.names
>
>     pre <- snapshot$pre
>     savewd <- getwd()
>     on.exit(setwd(savewd))
>     setwd(snapshot$wd)
>
>     args <- snapshot$args
>     newargs <- list(...)
>     args[names(newargs)] <- newargs
>     post <- dosnapshot(args)$info
>     prenames <- rownames(pre)
>     postnames <- rownames(post)
>
>     added <- setdiff(postnames, prenames)
>     deleted <- setdiff(prenames, postnames)
>     common <- intersect(prenames, postnames)
>
>     if (length(file.info)) {
>         preinfo <- pre[common, file.info]
>         postinfo <- post[common, file.info]
>         changes <- preinfo != postinfo
>     }
>     else changes <- matrix(logical(0), nrow = length(common), ncol = 0,
>                            dimnames = list(common, character(0)))
>     if (length(timestamp))
>         changes <- cbind(changes, Newer = file_test("-nt", common,
> timestamp))
>     if (md5sum) {
>         premd5 <- pre[common, "md5sum"]
>         postmd5 <- post[common, "md5sum"]
>     changes <- cbind(changes, md5sum = premd5 != postmd5)
>     }
>     changes1 <- changes[rowSums(changes, na.rm = TRUE) > 0, , drop = FALSE]
>     changed <- rownames(changes1)
>     structure(list(added = added, deleted = deleted, changed = changed,
>         unchanged = setdiff(common, changed), changes = changes), class =
> "changedFiles")
> }
>
> print.changedFilesSnapshot <- function(x, ...) {
>     cat("changedFiles snapshot:\n timestamp = \"", x$timestamp, "\"\n
> file.info = ",
>         if (length(x$file.info)) paste(paste0('"', x$file.info, '"'),
> collapse=","),
>         "\n md5sum = ", x$md5sum, "\n args = ", deparse(x$args, control =
> NULL), "\n", sep="")
>     x
> }
>
> print.changedFiles <- function(x, ...) {
>     if (length(x$added)) cat("Files added:\n",  paste0("  ", x$added,
> collapse="\n"), "\n", sep="")
>     if (length(x$deleted)) cat("Files deleted:\n",  paste0("  ",
> x$deleted, collapse="\n"), "\n", sep="")
>     changes <- x$changes
>     changes <- changes[rowSums(changes, na.rm = TRUE) > 0, , drop=FALSE]
>     changes <- changes[, colSums(changes, na.rm = TRUE) > 0, drop=FALSE]
>     if (nrow(changes)) {
>         cat("Files changed:\n")
>         print(changes)
>     }
>     x
> }
> ----------------------
>
> --- changedFiles.Rd:
> \name{changedFiles}
> \alias{changedFiles}
> \alias{print.changedFiles}
> \alias{print.**changedFilesSnapshot}
> \title{
> Detect which files have changed
> }
> \description{
> On the first call, \code{changedFiles} takes a snapshot of a selection of
> files.  In subsequent
> calls, it takes another snapshot, and returns an object containing data on
> the
> differences between the two snapshots.  The snapshots need not be the same
> directory;
> this could be used to compare two directories.
> }
> \usage{
> changedFiles(snapshot, timestamp = tempfile("timestamp"), file.info =
> NULL,
>              md5sum = FALSE, full.names = FALSE, ...)
> }
> \arguments{
>   \item{snapshot}{
> The path to record, or a previous snapshot.  See the Details.
> }
>   \item{timestamp}{
> The name of a file to write at the time the initial snapshot
> is taken.  In subsequent calls, modification times of files will be
> compared to
> this file, and newer files will be reported as changed.  Set to \code{NULL}
> to skip this test.
> }
>   \item{file.info}{
> A vector of columns from the result of the \code{file.info} function, or
> a logical value.  If
> \code{TRUE}, columns \code{c("size", "isdir", "mode", "mtime")} will be
> used.  Set to
> \code{FALSE} or \code{NULL} to skip this test.  See the Details.
> }
>   \item{md5sum}{
> A logical value indicating whether MD5 summaries should be taken as part
> of the snapshot.
> }
>   \item{full.names}{
> A logical value indicating whether full names (as in
> \code{\link{list.files}}) should be
> recorded.
> }
>   \item{\dots}{
> Additional parameters to pass to \code{\link{list.files}} to control the
> set of files
> in the snapshots.
> }
> }
> \details{
> This function works in two modes.  If the \code{snapshot} argument is
> missing or is
> not of S3 class \code{"changedFilesSnapshot"}, it is used as the
> \code{path} argument
> to \code{\link{list.files}} to obtain a list of files.  If it is of class
> \code{"changedFilesSnapshot"}, then it is taken to be the baseline file
> and a new snapshot is taken and compared with it.  In the latter case,
> missing
> arguments default to match those from the initial snapshot.
>
> If the \code{timestamp} argument is length 1, a file with that name is
> created
> in the current directory during the initial snapshot, and
> \code{\link{file_test}}
> is used to compare the age of all files to it during subsequent calls.
>
> If the \code{file.info} argument is \code{TRUE} or it contains a non-empty
> character vector, the indicated columns from the result of a call to
> \code{\link{file.info}} will be recorded and compared.
>
> If \code{md5sum} is \code{TRUE}, the \code{tools::\link{md5sum}} function
> will be called to record the 32 byte MD5 checksum for each file, and these
> values
> will be compared.
> }
> \value{
> In the initial snapshot phase, an object of class
> \code{"changedFilesSnapshot"} is returned.  This
> is a list containing the fields
> \item{pre}{a dataframe whose rownames are the filenames, and whose columns
> contain the
> requested snapshot data}
> \item{timestamp, file.info, md5sum, full.names}{a record of the arguments
> in the initial call}
> \item{args}{other arguments passed via \code{...} to
> \code{\link{list.files}}.}
>
> In the comparison phase, an object of class \code{"changedFiles"}. This is
> a list containing
> \item{added, deleted, changed, unchanged}{character vectors of filenames
> from the before
> and after snapshots, with obvious meanings}
> \item{changes}{a logical matrix with a row for each common file, and a
> column for each
> comparison test.  \code{TRUE} indicates a change in that test.}
>
> \code{\link{print}} methods are defined for each of these types. The
> \code{\link{print}} method for \code{"changedFilesSnapshot"} objects
> displays the arguments used to produce it, while the one for
> \code{"changedFiles"} displays the \code{added}, \code{deleted}
> and \code{changed} fields if non-empty, and a submatrix of the
> \code{changes}
> matrix containing all of the \code{TRUE} values.
> }
> \author{
> Duncan Murdoch
> }
> \seealso{
> \code{\link{file.info}}, \code{\link{file_test}}, \code{\link{md5sum}}.
> }
> \examples{
> # Create some files in a temporary directory
> dir <- tempfile()
> dir.create(dir)
> writeBin(1, file.path(dir, "file1"))
> writeBin(2, file.path(dir, "file2"))
> dir.create(file.path(dir, "dir"))
>
> # Take a snapshot
> snapshot <- changedFiles(dir, file.info=TRUE, md5sum=TRUE)
>
> # Change one of the files
> writeBin(3, file.path(dir, "file2"))
>
> # Display the detected changes
> changedFiles(snapshot)
> changedFiles(snapshot)$changes
> }
> \keyword{utilities}
> \keyword{file}
>
> ______________________________**________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/**listinfo/r-devel<https://stat.ethz.ch/mailman/listinfo/r-devel>
>

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