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Duncan Murdoch

2013-Sep-04 17:53 UTC

[Rd] Comments requested on "changedFiles" function

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}

Karl Millar

2013-Sep-05 00:02 UTC

head link

[Rd] Comments requested on "changedFiles" function

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>
>
	[[alternative HTML version deleted]]

Scott Kostyshak

2013-Sep-05 03:36 UTC

head link

[Rd] Comments requested on "changedFiles" function

On Wed, Sep 4, 2013 at 1:53 PM, Duncan Murdoch <murdoch.duncan at
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.
This looks like a useful function. Thanks for writing it. I have only
one (picky) comment 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)
Should a different name than 'dir' be used since 'dir' is a base
function?

Further, if someone is not very familiar with R (or just not in "R
mode" at the time of reading), they might think that 'dir.create'
is
calling the create member of the object named 'dir' that you just
made.

Scott
> 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

--
Scott Kostyshak
Economics PhD Candidate
Princeton University

Dr Gregory Jefferis

2013-Sep-05 16:32 UTC

head link

[Rd] Comments requested on "changedFiles" function

Dear Duncan,

This certainly looks useful. Might you consider adding the ability to 
supply an alternative digest function? Details below.

I often use a homemade "make" type function which starts by looking at
modification times e.g. in a private package

https://github.com/jefferis/nat.utils/blob/master/R/make.r

For some of my work, I use hash functions. However because I typically 
work with many large files I often use a special digest process e.g. 
using the crc checksum embedded in a gzip file directly or hashing only 
the part of a large file that is (almost) certain to change.

Perhaps (code unchecked) along the lines of:

changedFiles <- function(snapshot, timestamp =
tempfile("timestamp"),
file.info = NULL,
	digest = FALSE, digestfun=NULL, full.names = FALSE, ...)

if(digest){
	if(is.null(digestfun)) digestfun=tools::md5sum
	else digestfun=match.fun(digestfun)
	info <- data.frame(info, digest = digestfun(fullnames))
}

etc

OR alternatively using only one argument:

changedFiles <- function(snapshot, timestamp =
tempfile("timestamp"),
file.info = NULL,
	digest = FALSE, full.names = FALSE, ...)

if(is.logical(digest)){
	if(digest) digestfun=tools::md5sum
} else {
	# Assume that digest specifies a function that we want to use
	digestfun=match.fun(digest)
	digest=TRUE
}

if(digest)
	info <- data.frame(info, digest = digestfun(fullnames))

etc

Many thanks,

Greg.

On 4 Sep 2013, at 18:53, Duncan Murdoch 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)

--
Gregory Jefferis, PhD                   Tel: 01223 267048
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://flybrain.stanford.edu

Duncan Murdoch

2013-Sep-09 17:21 UTC

head link

[Rd] Comments requested on "changedFiles" function

Thanks for everyone's comments on this.  I have now committed a version 
to R-devel.  I don't plan to backport it to 3.0.2 (coming out in a 
couple of weeks), but it should appear in 3.1.0 in the spring, and it's 
conceivable it could make it into 3.0.3 (not yet scheduled).

Duncan Murdoch

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