func (this *NumericVector) CopyFrom(src []float64) {
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
for i := 0; i < this.length; i++ {
C.SetNumericVectorElt(this.expr, C.int(i), C.double(src[i]))
}
}
func SetSymbol(name string, val Expression) {
nameC := C.CString(name)
defer C.free(unsafe.Pointer(nameC))
C.Rf_protect(val.ToSexp())
defer C.Rf_unprotect(1)
C.defineVar(C.install(nameC), val.ToSexp(), C.R_GlobalEnv)
}
func (this *ComplexVector) Get(i int) complex128 {
this.boundsCheck(i)
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
c := C.ComplexVectorElt(this.expr, C.int(i))
return complex(float64(c.r), float64(c.i))
}
func (this *NumericVector) ToArray() []float64 {
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
array := make([]float64, this.length)
for i := 0; i < this.length; i++ {
array[i] = float64(C.NumericVectorElt(this.expr, C.int(i)))
}
return array
}
func (this *ComplexVector) Set(i int, val complex128) {
this.boundsCheck(i)
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
var c C.Rcomplex
c.r = C.double(real(val))
c.i = C.double(imag(val))
C.SetComplexVectorElt(this.expr, C.int(i), c)
}
func (this *ComplexVector) ToArray() []complex128 {
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
array := make([]complex128, this.length)
for i := 0; i < this.length; i++ {
c := C.ComplexVectorElt(this.expr, C.int(i))
array[i] = complex(float64(c.r), float64(c.i))
}
return array
}
func (this *ComplexVector) CopyFrom(src []complex128) {
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
for i := 0; i < this.length; i++ {
var c C.Rcomplex
c.r = C.double(real(src[i]))
c.i = C.double(imag(src[i]))
C.SetComplexVectorElt(this.expr, C.int(i), c)
}
}
//export ToMsgpack
func ToMsgpack(s C.SEXP) C.SEXP {
byteSlice := encodeRIntoMsgpack(s)
if len(byteSlice) == 0 {
return C.R_NilValue
}
rawmsg := C.allocVector(C.RAWSXP, C.R_xlen_t(len(byteSlice)))
C.Rf_protect(rawmsg)
C.memcpy(unsafe.Pointer(C.RAW(rawmsg)), unsafe.Pointer(&byteSlice[0]), C.size_t(len(byteSlice)))
C.Rf_unprotect(1)
return rawmsg
}
func main() {
// We always need a main() function to make possible
// CGO compiler to compile the package as C shared library
// The 'import "C"' at the top of the file is also required
// in order to export functions marked with //export
// Note that main() is not run when the .so library is loaded.
// However, since this is main, it is also the natural place
// to give an example also of how to
// embed R in a Go program, should you wish to do that as
// well.
// Note that the following go code is an optional demonstration,
// and not a part of the R package rmq functionality at its core.
// Introduction to embedding R:
//
// While RMQ is mainly designed to embed Go under R, it
// defines functions that make embedding R in Go
// quite easy too. We use SexpToIface() to generate
// a go inteface{} value. For simple uses, this may be
// more than enough.
//
// If you wish to turn results into
// a pre-defined Go structure, the interface{} value could
// transformed into msgpack (as in encodeRIntoMsgpack())
// and from there automatically parsed into Go structures
// if you define the Go structures and use
// https://github.com/tinylib/msgp to generate the
// go struct <-> msgpack encoding/decoding boilerplate.
// The tinylib/msgp library uses go generate and is
// blazing fast. This also avoids maintaining a separate
// IDL file. Your Go source code is always the defining document.
var iface interface{}
C.callInitEmbeddedR()
myRScript := "rnorm(100)" // generate 100 Gaussian(0,1) samples
var evalErrorOccurred C.int
r := C.callParseEval(C.CString(myRScript), &evalErrorOccurred)
if evalErrorOccurred == 0 && r != C.R_NilValue {
C.Rf_protect(r)
iface = SexpToIface(r)
fmt.Printf("\n Embedding R in Golang example: I got back from evaluating myRScript:\n")
goon.Dump(iface)
C.Rf_unprotect(1) // unprotect r
}
C.callEndEmbeddedR()
}
func decodeMsgpackToR(reply []byte) C.SEXP {
h.init()
var r interface{}
decoder := codec.NewDecoderBytes(reply, &h.mh)
err := decoder.Decode(&r)
panicOn(err)
VPrintf("decoded type : %T\n", r)
VPrintf("decoded value: %#v\n", r)
s := decodeHelper(r, 0)
if s != C.R_NilValue {
C.Rf_unprotect(1) // unprotect s before returning it
}
return s
}
//export ListenAndServe
func ListenAndServe(addr_ C.SEXP, handler_ C.SEXP, rho_ C.SEXP) C.SEXP {
if C.TYPEOF(addr_) != C.STRSXP {
fmt.Printf("addr is not a string (STRXSP; instead it is: %d)! addr argument to ListenAndServe() must be a string of form 'ip:port'\n", C.TYPEOF(addr_))
return C.R_NilValue
}
//msglen := 0
if 0 == int(C.isFunction(handler_)) { // 0 is false
C.ReportErrorToR_NoReturn(C.CString("‘handler’ must be a function"))
return C.R_NilValue
}
if rho_ != nil && rho_ != C.R_NilValue {
if 0 == int(C.isEnvironment(rho_)) { // 0 is false
C.ReportErrorToR_NoReturn(C.CString("‘rho’ should be an environment"))
return C.R_NilValue
}
}
caddr := C.R_CHAR(C.STRING_ELT(addr_, 0))
addr := C.GoString(caddr)
fmt.Printf("ListenAndServe listening on address '%s'...\n", addr)
webSockHandler := func(w http.ResponseWriter, r *http.Request) {
if r.URL.Path != "/" {
http.Error(w, "Not found", 404)
return
}
if r.Method != "GET" {
http.Error(w, "Method not allowed, only GET allowed.", 405)
return
}
c, err := upgrader.Upgrade(w, r, nil)
if err != nil {
fmt.Print("websocket handler upgrade error:", err)
return
}
defer c.Close()
mt, message, err := c.ReadMessage()
if err != nil {
fmt.Println("read error: ", err)
return
}
// make the call, and get a response
msglen := len(message)
rawmsg := C.allocVector(C.RAWSXP, C.R_xlen_t(msglen))
C.Rf_protect(rawmsg)
C.memcpy(unsafe.Pointer(C.RAW(rawmsg)), unsafe.Pointer(&message[0]), C.size_t(msglen))
// put msg into env that handler_ is called with.
C.defineVar(C.install(C.CString("msg")), rawmsg, rho_)
R_serialize_fun = C.findVar(C.install(C.CString("serialize")), C.R_GlobalEnv)
// todo: callbacks to R functions here not working. don't really need them if R always acts as a client instead.
// evaluate
C.PrintToR(C.CString("listenAndServe: stuffed msg into env rho_.\n"))
//R_fcall := C.lang3(handler_, rawmsg, C.R_NilValue)
R_fcall := C.lang3(R_serialize_fun, rawmsg, C.R_NilValue)
C.Rf_protect(R_fcall)
C.PrintToR(C.CString("listenAndServe: got msg, just prior to eval.\n"))
evalres := C.eval(R_fcall, rho_)
C.Rf_protect(evalres)
C.PrintToR(C.CString("listenAndServe: after eval.\n"))
/*
var s, t C.SEXP
s = C.allocList(3)
t = s
C.Rf_protect(t)
C.SetTypeToLANGSXP(&s)
//C.SETCAR(t, R_fcall)
C.SETCAR(t, handler_)
t = C.CDR(t)
C.SETCAR(t, rawmsg)
evalres := C.eval(s, rho_)
C.Rf_protect(evalres)
*/
C.PrintToR(C.CString("nnListenAndServe: done with eval.\n"))
if C.TYPEOF(evalres) != C.RAWSXP {
fmt.Printf("rats! handler result was not RAWSXP raw bytes!\n")
} else {
//fmt.Printf("recv: %s\n", message)
err = c.WriteMessage(mt, message)
if err != nil {
fmt.Println("write error: ", err)
}
}
C.Rf_unprotect(3)
} // end handler func
http.HandleFunc("/", webSockHandler)
err := http.ListenAndServe(addr, nil)
if err != nil {
fmt.Println("ListenAndServe: ", err)
}
return C.R_NilValue
}
func decodeHelper(r interface{}, depth int) (s C.SEXP) {
VPrintf("decodeHelper() at depth %d, decoded type is %T\n", depth, r)
switch val := r.(type) {
case string:
VPrintf("depth %d found string case: val = %#v\n", depth, val)
return C.Rf_mkString(C.CString(val))
case int:
VPrintf("depth %d found int case: val = %#v\n", depth, val)
return C.Rf_ScalarReal(C.double(float64(val)))
case int32:
VPrintf("depth %d found int32 case: val = %#v\n", depth, val)
return C.Rf_ScalarReal(C.double(float64(val)))
case int64:
VPrintf("depth %d found int64 case: val = %#v\n", depth, val)
return C.Rf_ScalarReal(C.double(float64(val)))
case []interface{}:
VPrintf("depth %d found []interface{} case: val = %#v\n", depth, val)
var sxpTy C.SEXPTYPE = C.VECSXP
lenval := len(val)
if lenval == 0 {
emptyvec := C.allocVector(C.NILSXP, C.R_xlen_t(0))
if depth == 0 {
C.Rf_protect(emptyvec)
}
return emptyvec
}
if lenval > 0 {
first := val[0]
VPrintf(" ... also at depth %d, ---> first has type '%T' and value '%v'\n", depth, first, first)
switch first.(type) {
case string:
sxpTy = C.STRSXP
stringSlice := C.allocVector(sxpTy, C.R_xlen_t(lenval))
C.Rf_protect(stringSlice)
for i := range val {
C.SET_STRING_ELT(stringSlice, C.R_xlen_t(i), C.mkChar(C.CString(val[i].(string))))
}
if depth != 0 {
C.Rf_unprotect(1) // unprotect for stringSlice, now that we are returning it
}
return stringSlice
case int64:
// we can only realistically hope to preserve 53 bits worth here.
// todo? unless... can we require bit64 package be available somehow?
sxpTy = C.REALSXP
numSlice := C.allocVector(sxpTy, C.R_xlen_t(lenval))
C.Rf_protect(numSlice)
size := unsafe.Sizeof(C.double(0))
naflag := false
rmax := int64(C.pow(FLT_RADIX, DBL_MANT_DIG) - 1)
//VPrintf("rmax = %v\n", rmax) // rmax = 9007199254740991
rmin := -rmax
ptrNumSlice := unsafe.Pointer(C.REAL(numSlice))
var ui uintptr
var rhs C.double
for i := range val {
n := val[i].(int64)
fmt.Printf("n = %d, rmax = %d, n > rmax = %v\n", n, rmax, n > rmax)
if n < rmin || n > rmax {
naflag = true
}
ui = uintptr(i)
rhs = C.double(float64(n))
// Try to avoid any gc activity by avoiding conversions
// and hence do pointer arithmetic all at once in one expression. See
// https://github.com/golang/go/issues/8994 for discussion.
*((*C.double)(unsafe.Pointer(uintptr(ptrNumSlice) + size*ui))) = rhs
}
if naflag {
C.WarnAndContinue(C.CString("integer precision lost while converting to double"))
}
if depth != 0 {
C.Rf_unprotect(1) // unprotect for numSlice, now that we are returning it
}
return numSlice
case float64:
sxpTy = C.REALSXP
numSlice := C.allocVector(sxpTy, C.R_xlen_t(lenval))
C.Rf_protect(numSlice)
size := unsafe.Sizeof(C.double(0))
// unfortunately C.memmove() doesn't work here (I tried). I speculate this is because val[i] is
// really wrapped in an interface{} rather than being a actual float64. val *is* an
// []interface{} after all.
var rhs C.double
ptrNumSlice := unsafe.Pointer(C.REAL(numSlice))
for i := range val {
rhs = C.double(val[i].(float64))
*((*C.double)(unsafe.Pointer(uintptr(ptrNumSlice) + size*uintptr(i)))) = rhs
}
if depth != 0 {
C.Rf_unprotect(1) // unprotect for numSlice, now that we are returning it
}
return numSlice
}
}
intslice := C.allocVector(sxpTy, C.R_xlen_t(lenval))
C.Rf_protect(intslice)
for i := range val {
C.SET_VECTOR_ELT(intslice, C.R_xlen_t(i), decodeHelper(val[i], depth+1))
}
if depth != 0 {
C.Rf_unprotect(1) // unprotect for intslice, now that we are returning it
}
return intslice
case map[string]interface{}:
s = C.allocVector(C.VECSXP, C.R_xlen_t(len(val)))
if depth == 0 {
// only protect the top parent of the returned value, recursively
// geneated are transitively protected by their parent.
C.Rf_protect(s)
}
names := C.allocVector(C.VECSXP, C.R_xlen_t(len(val)))
C.Rf_protect(names)
VPrintf("depth %d found map[string]interface case: val = %#v\n", depth, val)
sortedMapKey, sortedMapVal := makeSortedSlicesFromMap(val)
for i := range sortedMapKey {
ele := decodeHelper(sortedMapVal[i], depth+1)
C.Rf_protect(ele)
C.SET_VECTOR_ELT(s, C.R_xlen_t(i), ele)
C.Rf_unprotect(1) // unprotect for ele, now that it is safely inside s.
ksexpString := C.Rf_mkString(C.CString(sortedMapKey[i]))
C.SET_VECTOR_ELT(names, C.R_xlen_t(i), ksexpString)
}
C.setAttrib(s, C.R_NamesSymbol, names)
C.Rf_unprotect(1) // unprotect for names, now that it is attached to s.
case []byte:
VPrintf("depth %d found []byte case: val = %#v\n", depth, val)
rawmsg := C.allocVector(C.RAWSXP, C.R_xlen_t(len(val)))
if depth == 0 {
C.Rf_protect(rawmsg)
}
C.memcpy(unsafe.Pointer(C.RAW(rawmsg)), unsafe.Pointer(&val[0]), C.size_t(len(val)))
return rawmsg
case nil:
return C.R_NilValue
default:
fmt.Printf("unknown type in type switch, val = %#v. type = %T.\n", val, val)
}
return s
}
func (this *NumericVector) Get(i int) float64 {
this.boundsCheck(i)
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
return float64(C.NumericVectorElt(this.expr, C.int(i)))
}
func (this *Vector) Get(i int) *Result {
this.boundsCheck(i)
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
return NewResult(C.GenericVectorElt(this.expr, C.int(i)))
}
//export ListenAndServe
//
// ListenAndServe is the server part that expects calls from client
// in the form of RmqWebsocketCall() invocations.
// The underlying websocket library is the battle tested
// https://github.com/gorilla/websocket library from the
// Gorilla Web toolkit. http://www.gorillatoolkit.org/
//
// addr_ is a string in "ip:port" format. The server
// will bind this address and port on the local host.
//
// handler_ is an R function that takes a single argument.
// It will be called back each time the server receives
// an incoming message. The returned value of handler
// becomes the reply to the client.
//
// rho_ is an R environment in which the handler_ callback
// will occur. The user-level wrapper rmq.server() provides
// a new environment for every call back by default, so
// most users won't need to worry about rho_.
//
// Return value: this is always R_NilValue.
//
// Semantics: ListenAndServe() will start a new
// webserver everytime it is called. If it exits
// due to a call into R_CheckUserInterrupt()
// or Rf_error(), then a background watchdog goroutine
// will notice the lack of heartbeating after 300ms,
// and will immediately shutdown the listening
// websocket server goroutine. Hence cleanup
// is fairly automatic.
//
// Signal handling:
//
// SIGINT (ctrl-c) is noted by R, and since we
// regularly call R_CheckUserInterrupt(), the
// user can stop the server by pressing ctrl-c
// at the R-console. The go-runtime, as embedded
// in the c-shared library, is not accustomed to being
// embedded yet, and so its (system) signal handling
// facilities (e.g. signal.Notify) should *not* be
// used. We go to great pains to actually preserve
// the signal handling that R sets up and expects,
// as allowing the go runtime to see any signals just
// creates heartache and crashes.
//
func ListenAndServe(addr_ C.SEXP, handler_ C.SEXP, rho_ C.SEXP) C.SEXP {
addr, err := getAddr(addr_)
if err != nil {
C.ReportErrorToR_NoReturn(C.CString(err.Error()))
return C.R_NilValue
}
if 0 == int(C.isFunction(handler_)) { // 0 is false
C.ReportErrorToR_NoReturn(C.CString("‘handler’ must be a function"))
return C.R_NilValue
}
if rho_ != nil && rho_ != C.R_NilValue {
if 0 == int(C.isEnvironment(rho_)) { // 0 is false
C.ReportErrorToR_NoReturn(C.CString("‘rho’ should be an environment"))
return C.R_NilValue
}
}
fmt.Printf("ListenAndServe listening on address '%s'...\n", addr)
// Motivation: One problem when acting as a web server is that
// webSockHandler will be run on a separate goroutine and this will surely
// be a separate thread--distinct from the R callback thread. This is a
// problem because if we call back into R from the goroutine thread
// instead of R's thread, R will see the small stack and freak out.
//
// So: we'll use a channel to send the request to the main R thread
// for call back into R. The *[]byte passed on these channels represent
// msgpack serialized R objects.
requestToRCh := make(chan *[]byte)
replyFromRCh := make(chan *[]byte)
reqStopCh := make(chan bool)
doneCh := make(chan bool)
var lastControlHeartbeatTimeNano int64
beatHeart := func() {
now := int64(time.Now().UnixNano())
atomic.StoreInt64(&lastControlHeartbeatTimeNano, now)
}
webSockHandler := func(w http.ResponseWriter, r *http.Request) {
if r.URL.Path != "/" {
http.Error(w, "Not found", 404)
return
}
if r.Method != "GET" {
http.Error(w, "Method not allowed, only GET allowed.", 405)
return
}
c, err := upgrader.Upgrade(w, r, nil)
if err != nil {
msg := fmt.Sprintf("server webSockHandler() handler saw "+
"websocket upgrader.Upgrade() error: '%s'", err)
fmt.Printf("%s\n", msg)
http.Error(w, msg, 500)
return
}
defer c.Close()
_, message, err := c.ReadMessage()
if err != nil {
msg := fmt.Sprintf("server webSockHandler() handler saw "+
"websocket ReadMessage() error: '%s'", err)
fmt.Printf("%s\n", msg)
http.Error(w, msg, 500)
return
}
requestToRCh <- &message
reply := <-replyFromRCh
err = c.WriteMessage(websocket.BinaryMessage, *reply)
if err != nil {
msg := fmt.Sprintf("server webSockHandler() handler saw "+
"websocket WriteMessage() error: '%s'", err)
fmt.Printf("%s\n", msg)
http.Error(w, msg, 500)
return
}
} // end webSockHandler
// start a new server, to avoid registration issues with
// the default http library mux/server which may be in use
// already for other purposes.
mux := http.NewServeMux()
mux.HandleFunc("/", webSockHandler)
server := NewWebServer(addr.String(), mux)
server.Start()
// This watchdog will shut the webserver down
// if lastControlHeartbeatTimeNano goes
// too long without an update. This will
// happen when C.R_CheckUserInterrupt()
// doesn't return below in the main control loop.
beatHeart()
go func() {
for {
select {
case <-time.After(time.Millisecond * 100):
last := atomic.LoadInt64(&lastControlHeartbeatTimeNano)
lastTm := time.Unix(0, last)
deadline := lastTm.Add(300 * time.Millisecond)
now := time.Now()
if now.After(deadline) {
VPrintf("\n web-server watchdog: no heartbeat "+
"after %v, shutting down.\n", now.Sub(lastTm))
server.Stop()
return
}
}
}
}()
// This is the main control routine that lives on the main R thread.
// All callbacks into R must come from this thread, as it is a
// C thread with a big stack. Go routines have tiny stacks and
// R detects this and crashes if you try to call back from one of them.
for {
select {
case <-time.After(time.Millisecond * 100):
//
// Our heartbeat logic:
//
// R_CheckUserInterrupt() will check if Ctrl-C
// was pressed by user and R would like us to stop.
// (R's SIGINT signal handler is installed in our
// package init() routine at the top of this file.)
//
// Note that R_CheckUserInterrupt() may not return!
// So, Q: how will the server know to cancel/cleanup?
// A: we'll have the other goroutines check the following
// timestamp. If it is too out of date, then they'll
// know that they should cleanup.
beatHeart()
C.R_CheckUserInterrupt()
case msgpackRequest := <-requestToRCh:
rRequest := decodeMsgpackToR(*msgpackRequest)
C.Rf_protect(rRequest)
// Call into the R handler_ function, and get its reply.
R_fcall := C.lang2(handler_, rRequest)
C.Rf_protect(R_fcall)
if Verbose {
C.PrintToR(C.CString("listenAndServe: got msg, just prior to eval.\n"))
}
evalres := C.eval(R_fcall, rho_)
C.Rf_protect(evalres)
if Verbose {
C.PrintToR(C.CString("listenAndServe: after eval.\n"))
}
// send back the reply, first converting to msgpack
reply := encodeRIntoMsgpack(evalres)
C.Rf_unprotect(3)
replyFromRCh <- &reply
case <-reqStopCh:
// not sure who should close(reqStopCh). At the moment it isn't used.
close(doneCh)
return C.R_NilValue
}
}
}
func (this *protector) Unprotect() {
C.Rf_unprotect(C.int(this.count))
this.count = 0
}
func (this *NumericVector) Set(i int, val float64) {
this.boundsCheck(i)
C.Rf_protect(this.expr)
defer C.Rf_unprotect(1)
C.SetNumericVectorElt(this.expr, C.int(i), C.double(val))
}
