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Overhaul readDynLib and writeDynLib
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Instead of the argument "file", there are now two arguments "bname" and
"directory" (see updated documentation in man/utilities.Rd).

However, we still have remainders of the old DLL locations and names in
after writing and reading, see eddelbuettel#13.
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@jranke
jranke committed Nov 25, 2020
1 parent 327f932 commit f8ac225
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Showing 2 changed files with 78 additions and 78 deletions.
77 changes: 31 additions & 46 deletions R/utilities.R
View file
Original file line number Diff line number Diff line change
@@ -1,72 +1,57 @@
## ---------------------------------------------------------------------------
# saving and loading CFunc objects (called write and read as it needs to
# be assigned.
# saving and loading CFunc objects

writeDynLib <- function(x, file) {
writeDynLib <- function(x, bname, directory = ".") {

DLL <- getDynLib(x)

if (is.null(DLL))
stop ("'x' DLL not loaded")
DLLname <- DLL[["path"]]

DLLname <- DLL[["path"]]
if (!file.exists(DLLname))
stop ("'x' does not point to an existing DLL")

# correct extension of filename (dll, so)
dname <- dirname(file)
bname <- unlist(strsplit(basename(file), ".", fixed = TRUE))[1]
# get extension of filename (dll, so)
extension <- unlist(strsplit(basename(DLLname), ".", fixed = TRUE))[2]
file <- paste(dname,bname, extension, sep = ".")
newDLLname <- file.path(directory, paste(bname, extension, sep = "."))

try(dyn.unload(file), silent = TRUE)
try(dyn.unload(newDLLname), silent = TRUE)

file.copy(from = DLLname, to = file, overwrite = TRUE)
file.copy(from = DLLname, to = newDLLname, overwrite = TRUE)

# accessory file with compiled code information (DLL name has changed)
fileCF <- paste(dname,"/",bname, ".Cfunc", sep = "")
attributes(x)$DLL <- file
fileCF <- file.path(directory, paste(bname, "CFunc", sep = "."))
attributes(x)$DLL <- newDLLname

# names of functions in compiled code
if (class(x) == "CFunc")
attributes(x)$fname <- DLL[["name"]]
else
attributes(x)$fname <- names(x)

save(file = fileCF, x)

invisible(fileCF)
}

## ---------------------------------------------------------------------------

readDynLib <- function(file) {

# open all the required files
extension <- unlist(strsplit(basename(file), ".", fixed = TRUE))[2]
readDynLib <- function(bname, directory = ".") {

if (is.na(extension)) {
extension <- "CFunc"
file <- paste(file, extension, sep = ".")
}

if (extension != "CFunc")
stop ("'file' should point to a CFunc object, extension '.CFunc'")
# open all the required files
fileCF <- file.path(directory, paste(bname, "CFunc", sep = "."))

if (!file.exists(file))
stop ("'file' does not exist")
if (!file.exists(fileCF))
stop (fileCF, " does not exist")

CF <- get(load(file = file))
CF <- get(load(file = fileCF))
attrs <- attributes(CF)
DLLname <- attrs$DLL

if (!file.exists(DLLname))
stop ("'file' does not point to valid CFunc object: DLL ", DLLname, " does not exist")

# cleanup <- function(env) {
# unlink(DLLname)
# }
# reg.finalizer(environment(), cleanup, onexit = TRUE)


# load routines in DLL

DLL <- dyn.load(DLLname)
Expand All @@ -82,22 +67,22 @@ readDynLib <- function(file) {
code <- CFi@code
body(CFi)[[2]] <- getNativeSymbolInfo(fn[i], DLL)$address
CF[[i]]@.Data <- CFi
}
attributes(CF) <- attrs
return(CF)
}

attributes(CF) <- attrs
return(CF)
}

setGeneric("code", function(x, ...) standardGeneric("code") )
setMethod( "code", signature( x = "character" ),
function( x, linenumbers = TRUE ){
lines <- strsplit(x, "\n")
if (linenumbers)
for (i in 1:length(lines[[1]])) cat(format(i, width = 3),
for (i in 1:length(lines[[1]])) cat(format(i, width = 3),
": ", lines[[1]][i], "\n", sep = "")
else
for (i in 1:length(lines[[1]])) cat(lines[[1]][i], "\n", sep = "")

} )
setMethod( "code", signature( x = "CFunc" ), function( x, linenumbers = TRUE ) code (x@code, linenumbers))
setMethod( "code", signature( x = "CFuncList" ), function(x, linenumbers = TRUE ) code( x[[1L]], linenumbers ) )
Expand All @@ -107,16 +92,16 @@ setMethod( "code", signature( x = "CFuncList" ), function(x, linenumbers = TRUE
setMethod( "print", signature( x = "CFunc" ),
function( x ){
cat("An object of class 'CFunc'\n")
Dat <- x@.Data
print(Dat)
Dat <- x@.Data
print(Dat)
cat("code:\n")
code(x)
} )

setMethod( "print", signature( x = "CFuncList" ), function(x) {
cat("An object of class 'CFuncList'\n")
for (i in 1:length(x)) {
print(names(x)[i])
print(names(x)[i])
print(x[[i]]@.Data )
cat("\n")
}
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79 changes: 47 additions & 32 deletions man/utilities.Rd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,38 +15,38 @@

\description{
\code{writeDynLib} saves the DLL and the CFunc or CFuncList object as
generated by \link{cfunction}; \code{readDynLib} loads it.
The \code{print} and \code{code} methods respectively print the entire
generated by \link{cfunction}; \code{readDynLib} loads it.

The \code{print} and \code{code} methods respectively print the entire
object or the code parts.
}

\usage{
writeDynLib(x, file)
readDynLib(file)
writeDynLib(x, bname, directory = ".")
readDynLib(bname, directory = ".")
}

\section{Methods}{

\itemize{
\item Method \code{print(x, ...)} prints the entire object \code{x}
\item Method \code{print(x, ...)} prints the entire object \code{x}

\describe{

\item{\code{signature(x = "CFunc")}}{Prints the CFunc object
generated by \code{\link{cfunction}}, including the code that generated it. }
\item{\code{signature(x = "CFunc")}}{Prints the CFunc object
generated by \code{\link{cfunction}}, including the code that generated it. }

\item{\code{signature(x = "CFuncList")}}{Print all CFunc objects
generated by \code{\link{cfunction}}, including the code that generated them. }
generated by \code{\link{cfunction}}, including the code that generated them. }

}

\item Method \code{code(x, linenumbers = TRUE, ...)} prints the code only
\item Method \code{code(x, linenumbers = TRUE, ...)} prints the code only

\describe{

\item{\code{signature(x)}}{The \code{CFunc} or \code{CFuncList} object as generated by
\code{\link{cfunction}}. }
\item{\code{signature(x)}}{The \code{CFunc} or \code{CFuncList} object as generated by
\code{\link{cfunction}}. }

\item{\code{linenumbers}}{If \code{TRUE} all code lines will be numbered. }

Expand All @@ -57,37 +57,46 @@ generated by \code{\link{cfunction}}, including the code that generated them. }
\arguments{

\item{x}{A \code{CFunc} or \code{CFuncList} object as created by \code{\link{cfunction}} to be saved.}

\item{file}{base name of the file to write the object to or to read from.

\item{bname}{base name of the file to write the object to or to read from.
Two files will be saved, one for the shared object or DLL (extension \code{so}
or \code{dll}) and one that holds the \code{CFunc} or \code{CFuncList} specification, without
the function address (extension \code{CFunc}).}

\item{directory}{name of the directory to write to.
Two files will be saved, one for the shared object or DLL (extension \code{so}
or \code{DLL}) and one that holds the \code{CFunc} or \code{CFuncList} specification, without
or \code{dll}) and one that holds the \code{CFunc} or \code{CFuncList} specification, without
the function address (extension \code{CFunc}).}

}

\value{

Function \code{readDynLib} returns a \code{CFunc} or \code{CFuncList} object.

Function \code{writeDynLib} returns the name of the \code{.CFunc} file that
was created.
}

\details{

Both the CFunc or CFuncList object and the shared object or DLL are saved,
in two files; the first has extension \code{CFunc}; the second \code{so} or
\code{DLL}, depending on the operating system used.
When reading, both files are loaded, and the compiled function address
\code{dll}, depending on the operating system used.

When reading, both files are loaded, and the compiled function address(es)
added to the object.

}

\note{

\itemize{
\item The code of a \code{CFunc} or \code{CFuncList} object \code{x} can be extracted
(rather than printed), using:
\item The code of a \code{CFunc} or \code{CFuncList} object \code{x} can be extracted
(rather than printed), using:

\code{x@code}.
\item To write the code to a file (here called \code{"fn"}),
\code{x@code}.
\item To write the code to a file (here called \code{"fn"}),
without the new-line character \code{"\n"}:

\code{write (strsplit(x, "\n")[[1]], file = "fn")}
Expand All @@ -96,7 +105,7 @@ without the new-line character \code{"\n"}:
}

\seealso{ \code{
\link{getDynLib}
\link{getDynLib}
}}

\examples{
Expand All @@ -109,18 +118,24 @@ code <- "
do 1 i=1, n(1)
1 x(i) = x(i)**3
"
cubefn <- cfunction(signature(n="integer", x="numeric"), code, convention=".Fortran")
cubefn <- cfunction(signature(n="integer", x="numeric"), code,
convention=".Fortran")
code(cubefn)

cubefn(n, x)$x

\dontrun{
fname <- tempfile()
writeDynLib(cubefn, file = fname)
# load and assign different name to object
cfn <- readDynLib(fname)
print(cfn)
cfn(2, 1:2)
writeDynLib(cubefn, bname = "testname", directory = tempdir())
dir(tempdir())
# load and assign different name to object
cfn <- readDynLib("testname", directory = tempdir())

# We still have remainders of the original locations and names:
getDynLib(cfn)
environment(cfn@.Data)$f
environment(cfn@.Data)$libLFile
# although the DLL attribute points to the new DLL
attributes(cfn)
}

}
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