Merge pull request #5 from snoweye/master

0.2-0

.gitignore

@@ -1,2 +1,5 @@
 *~
 *.swp
+
+config.status
+src/Makevars

.travis.yml

@@ -7,15 +7,15 @@ env:
   global:
     - CRAN: https://cran.rstudio.com
 
-# os:
-  # - linux
+os:
+  - linux
 
-# dist: trusty
+dist: trusty
 
-# r_check_args: --no-build-vignettes --no-manual
+r_check_args: --no-build-vignettes --no-manual
 
-os:
-  - osx
+# os:
+#   - osx
 
 before_install:
   - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh

ChangeLog

@@ -1,3 +1,20 @@
+2018-02-01: Ver. 0.2-0
+  *
+
+2017-01-15: Ver. 0.2-0
+  * Fix rpc_ps() and tunnel().
+  * Modify port forwarding example in vignettes via tunnel().
+
+2017-01-14: Ver. 0.2-0
+  * Rename original rpc() to srpc().
+  * Add tunnel().
+  * Print pid when intern and wait are both FALSE.
+  * Add machine information section in vignettes.
+
+2017-01-12: Ver. 0.2-0
+  * Change API to operate on machine configurations, generated by machine().
+  * Add some type checks/safety.
+
 ======================= Log Before Release =====================================
 2016-12-31: Ver. 0.1-1
   * Add one more advance application with pbdMPI to vignettes.

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: pbdRPC
-Version: 0.1-1
-Date: 2017-01-01
+Version: 0.2-0
+Date: 2018-02-01
 Title: Programming with Big Data -- Remote Procedure Call
 Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
-        "[email protected]"))
-Depends: R (>= 3.2.0)
-Enhances: pbdZMQ, remoter, pbdMPI, pbdCS
+        "[email protected]"), person("Drew", "Schmidt", role="aut"))
+Depends: R (>= 3.2.0), tools
+Enhances: pbdZMQ, remoter, pbdMPI
 LazyLoad: yes
 LazyData: yes
 Copyright: See pbdRPC/inst/putty_LICENCE for files in src/putty/.
@@ -18,6 +18,6 @@ URL: http://r-pbd.org/
 BugReports: http://group.r-pbd.org/
 MailingList: Please send questions and comments regarding pbdR to
         [email protected]
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
 NeedsCompilation: yes
 Maintainer: Wei-Chen Chen <[email protected]>

NAMESPACE

@@ -1,20 +1,30 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,machine)
 export(.rpcopt_init)
 export(RPC.CT)
 export(RPC.LI)
 export(RPC.RR)
 export(check_cs)
 export(check_exec)
 export(check_rr)
+export(checkx_rr)
 export(find_plink)
 export(kill_cs)
 export(kill_rr)
+export(killx_rr)
+export(machine)
 export(plink)
 export(rpc)
+export(rpc_kill)
+export(rpc_ps)
 export(rpcopt_get)
 export(rpcopt_set)
 export(run_args)
+export(srpc)
 export(ssh)
 export(start_cs)
 export(start_rr)
+export(startx_rr)
+export(tunnel)
+importFrom(tools,pskill)

R/111_control.r

@@ -8,14 +8,16 @@
 #' e.g. continuously port forwarding without sending commands to background.
 #'
 #' @param exec.type,args,pport,user,hostname,priv.key,priv.key.ppk
-#' RPC login information used by \code{\link{rpc}()}, \code{\link{ssh}()}, or
+#' RPC login information used by \code{\link{srpc}()}, \code{\link{ssh}()}, or
 #' \code{\link{plink}()}.
 #' 
 # #' @param unix,macos,windows
 #'
-#' @param check,kill,start,preload
+#' @param check,kill,start,preload,checkx,killx,startx
 #' RPC remoter commands used by \code{\link{check_rr}()},
-#' \code{\link{kill_rr}()}, or \code{\link{start_rr}()}.
+#' \code{\link{kill_rr}()}, or \code{\link{start_rr}()} and
+#' virtual X11 related versions \code{\link{checkx_rr}()},
+#' \code{\link{killx_rr}()}, or \code{\link{startx_rr}()}..
 #' RPC pbdCS commands used by \code{\link{check_cs}()},
 #' \code{\link{kill_cs}()}, or \code{\link{start_cs}()}.
 #' 
@@ -58,7 +60,7 @@ RPC.CT <- function(
 RPC.LI <- function(
   exec.type = "ssh",
   args = "",
-  pport = "22",
+  pport = 22,
   user = "snoweye",
   hostname = "192.168.56.101",
   priv.key = "~/.ssh/id_rsa",
@@ -103,16 +105,22 @@ RPC.LI <- function(
 #' @export
 #' @rdname zz_rpc_control
 RPC.RR <- function(
-  check = "ps ax|grep '[r]emoter::server'",
-  kill = "kill -9 $(ps ax|grep '[r]emoter::server'|awk '{print $1}')",
+  check = "ps axww|grep '[r]emoter::server'",
+  kill = "kill -9 $(ps axww|grep '[r]emoter::server'|awk '{print $1}')",
   start = "nohup Rscript -e 'remoter::server()' > .rrlog 2>&1 < /dev/null &",
-  preload = "source ~/work-my/00_set_devel_R; "
+  preload = "source ~/work-my/00_set_devel_R; ",
+  checkx = "ps axww|grep '[r]emoter::server\\|[x]vfb-run'",
+  killx = "kill -9 $(ps axww|grep '[r]emoter::server\\|[x]vfb-run'|awk '{print $1}')",
+  startx = "nohup xvfb-run Rscript -e 'remoter::server()' > .rrlog 2>&1 < /dev/null &"
 ){
   list(
     check = check,
     kill = kill,
     start = start,
-    preload = preload
+    preload = preload,
+    checkx = checkx,
+    killx = killx,
+    startx = startx
   )
 }
 
@@ -133,4 +141,3 @@ RPC.CS <- function(
     preload = preload
   )
 }
-

R/machine.r

@@ -0,0 +1,116 @@
+#' machine
+#' 
+#' Remote machine configuration settings. 
+#' 
+#' @param exec.type
+#' either "ssh" or "plink" in character. Windows will force to use "plink".
+#' @param args
+#' further arguments to "ssh" or "plink" for connecting to the server
+#' in addition to port, user id, and host name.
+#' @param pport
+#' ssh port opened on the server.
+#' @param user
+#' user id for logging to the server.  If none is supplied, then the system user
+#' name will be used instead.
+#' @param hostname
+#' the server ip or host name.
+#' @param priv.key,priv.key.ppk
+#' location of the private key for user authentication, the file will be
+#' checked first then \code{-i priv.key} will be added to \code{args}
+#' when the file exists.
+#' \code{priv.key.ppk} is only used when \code{plink} is called.
+#' 
+#' @return
+#' An object of class \code{machine}.
+#' 
+#' @examples
+#' \dontrun{
+#' # note: not my actual aws url
+#' myaws <- machine("ec2-1-2-3-4.compute-1.amazonaws.com", user="my_aws_username")
+#' 
+#' # if you don't specify 'user', we use your host machine's user name
+#' myvm <- machine("192.168.1.10")
+#' }
+#' 
+#' @name machine
+#' @export
+machine <- function(hostname, user, exec.type = .pbd_env$RPC.LI$exec.type,
+  args = .pbd_env$RPC.LI$args, pport = .pbd_env$RPC.LI$pport,
+  priv.key = .pbd_env$RPC.LI$priv.key,
+  priv.key.ppk = .pbd_env$RPC.LI$priv.key.ppk)
+{
+  if (missing(user))
+  {
+    if (.Platform$OS.type == "windows")
+      user <- shell("echo %username%", intern=TRUE)
+    else
+      user <- system("whoami", intern=TRUE)
+    warning("No user name supplied; using system user name...")
+  }
+
+  if (missing(hostname))
+    stop("You must supply a host name or ip in machine() call; i.e. what do you want to connect to?")
+
+  check.is.string(hostname)
+  check.is.string(user)
+  check.is.string(exec.type)
+  check.is.string(args)
+  check.is.posint(pport)
+  check.is.string(priv.key)
+  check.is.string(priv.key.ppk)
+
+  if (.Platform$OS.type == "windows")
+    exec.type <- "plink"
+  if (exec.type != "ssh" && exec.type != "plink")
+    stop(paste0("exec.type (", exec.type, ") is not found."))
+
+  m <- list(hostname=hostname, user=user, exec.type=exec.type, args=args,
+    pport=pport, priv.key=priv.key, priv.key.ppk=priv.key.ppk)
+  class(m) <- "machine"
+
+  return(m)
+}
+
+check.is.machine <- function(machine)
+{
+  # the error message isn't super informative, but the individual argument
+  # checks can only fail if they go meddling with an object after creation
+  # via machine(), and such people get what they deserve
+  errmsg <- "argument 'machine' seemingly not generated via call to machine()"
+
+  if (!inherits(machine, "machine"))
+    stop(errmsg)
+
+  check.is.string(machine$hostname, msg=errmsg)
+  check.is.string(machine$user, msg=errmsg)
+  check.is.string(machine$exec.type, msg=errmsg)
+  check.is.string(machine$args, msg=errmsg)
+  check.is.posint(machine$pport, msg=errmsg)
+  check.is.string(machine$priv.key, msg=errmsg)
+  check.is.string(machine$priv.key.ppk, msg=errmsg)
+
+  if (machine$exec.type != "ssh" && machine$exec.type != "plink")
+    stop(errmsg)
+
+  invisible(TRUE)
+}
+
+
+
+#' @title print-machine
+#' @description Printing for machine class objects.
+#' @param x machine class object
+#' @param ... ignored
+#' @rdname print-machine
+#' @name print-machine
+#' @method print machine
+#' @export
+print.machine <- function(x, ...)
+{
+  cat(paste0("Machine config for ", x$user, "@", x$hostname, "\n"))
+  cat(paste0("    pport = ", x$pport, "\n"))
+  cat(paste0("    type = ", x$exec.type, "\n"))
+  cat(paste0("    args = \"", x$args, "\"\n"))
+  cat(paste0("    priv.key = ", x$priv.key, "\n"))
+  cat(paste0("    priv.key.ppk = ", x$priv.key.ppk, "\n"))
+}

R/pbdRPC-package.r

@@ -3,9 +3,11 @@
 #' A very light yet secure implementation of remote procedure call.
 #'
 #' @references Project URL: \url{https://github.com/RBigData/pbdRPC}
-#' @author Wei-Chen Chen
+#' @author Wei-Chen Chen and Drew Schmidt
 #' 
 #' @name pbdRPC-package
+#'
+#' @importFrom tools pskill
 #' 
 #' @docType package
 #' @keywords package