Add special env to take r shadowing functions

.Rbuildignore

@@ -10,3 +10,4 @@ example-notebooks/.*$
 ^\.travis.yml$
 Dockerfile
 test_ir.py
+cran-comments.md

DESCRIPTION

@@ -1,16 +1,13 @@
 Package: IRkernel
-Title: Native R kernel for the Jupyter notebook
-Description: This package provides a native interface to the R kernel from the
-    Jupyter notebook.
+Title: Native R Kernel for the Jupyter Notebook
+Description: The R kernel for the jupyter environment executes R code which the 
+    frontend (Jupyter Notebook or other frontends) submits to the kernel via the
+    network.
 Version: 0.6
-Authors@R: c(person("Thomas", "Kluyver", role = c("aut", "cre"),
-    email = "thomas@kluyver.me.uk"),
-    person("Philipp", "A.", role = "aut",
-    email = "flying-sheep@web.de"),
-    person("Karthik", "Ram", role = "aut",
-    email = "karthik.ram@gmail.com"))
-Author: Thomas Kluyver <thomas@kluyver.me.uk>
-Maintainer: Thomas Kluyver <thomas@kluyver.me.uk>
+Authors@R: c(person("Thomas", "Kluyver", role = c("aut", "cre"), email = "thomas@kluyver.me.uk"),
+    person("Philipp", "A.", role = "aut", email = "flying-sheep@web.de"),
+    person("Jan", "Schulz", role = "aut", email = "jasc@gmx.net"),
+    person("Karthik", "Ram", role = "aut", email = "karthik.ram@gmail.com"))
 Depends:
     R (>= 3.0.1)
 License: MIT + file LICENSE
@@ -34,4 +31,5 @@ Collate:
     'help.r'
     'installspec.r'
     'kernel.r'
+    'environment.r'
 RoxygenNote: 5.0.1

R/environment.r

@@ -0,0 +1,18 @@
+# Everthing related to the environment which takes functions which shadow base R functions.
+# This is needed to build in our own needs, like properly shutting down the kernel
+# when `quit()` is called.
+
+# The real env is created and attach'ed in the main() via the call to init_shadowenv()!
+init_shadowenv <- function(){
+    .irk.shadowenv <- attach(NULL, name = "jupyter:irkernel")
+
+    add_to_user_searchpath <- function(name, FN, attrs = list()) {
+        assign(name, FN, .irk.shadowenv)
+    }
+
+    # add the accessors to the shadow env to that env, so they are actually accessable 
+    # from everywhere...
+    add_to_user_searchpath(".irk.get_shadowenv", function() {.irk.shadowenv})
+    add_to_user_searchpath(".irk.add_to_user_searchpath", add_to_user_searchpath)
+
+}

R/execution.r

@@ -115,7 +115,7 @@ quit = function(save = 'default', status = 0, runLast = TRUE) {
         if (!is.null(.GlobalEnv$.Last.sys)) .GlobalEnv$.Last.sys()
     }
     if (save) NULL  # TODO: actually save history
-    payload <<- c(payload, list(list(source = 'ask_exit', keepkernel = FALSE)))
+    payload <<- c(.self$payload, list(list(source = 'ask_exit', keepkernel = FALSE)))
 },
 
 handle_error = function(e) {
@@ -215,9 +215,9 @@ execute = function(request) {
     err <<- list()
 
     # shade base::quit
-    assign('quit', .self$quit, envir = .GlobalEnv)
-    assign('q',    .self$quit, envir = .GlobalEnv)
-    
+    .irk.add_to_user_searchpath('quit', .self$quit)
+    .irk.add_to_user_searchpath('q', .self$quit)
+
     # find out stack depth in notebook cell
     # TODO: maybe replace with a single call on first execute and rest reuse the value?
     tryCatch(evaluate(
@@ -250,12 +250,12 @@ execute = function(request) {
     # Workaround to warn user when code contains potential problematic code
     # https://github.com/IRkernel/repr/issues/28#issuecomment-208810772
     # See https://github.com/hadley/evaluate/issues/66
-    if(.Platform$OS.type == 'windows') {
+    if (.Platform$OS.type == 'windows') {
         # strip whitespace, because trailing newlines would trip the test...
         code <- gsub('^\\s+|\\s+$', '', request$content$code)
         real_len <- nchar(code)
         r_len <- nchar(paste(capture.output(cat(code)), collapse = '\n'))
-        if (real_len != r_len){
+        if (real_len != r_len) {
             msg = c('Your code contains a unicode char which cannot be displayed in your ',
                     'current locale and R will silently convert it to an escaped form when the ',
                     'R kernel executes this code. This can lead to subtle errors if you use ',
@@ -264,7 +264,6 @@ execute = function(request) {
             send_error_msg(paste(msg, collapse = '\n'))
         }
     }
-
     tryCatch(
         evaluate(
             request$content$code,

R/kernel.r

@@ -166,7 +166,7 @@ abort_queued_messages = function() {
             c(.pbd_env$ZMQ.PO$POLLIN), # type
             0) # zero timeout, only what's already there
         log_debug('abort loop: after poll')
-        if(bitwAnd(zmq.poll.get.revents(1), .pbd_env$ZMQ.PO$POLLIN)) {
+        if (bitwAnd(zmq.poll.get.revents(1), .pbd_env$ZMQ.PO$POLLIN)) {
             log_debug('abort loop: found msg')
             abort_shell_msg()
         } else {
@@ -343,13 +343,13 @@ run = function() {
         # the easiest seems to be to handle this in a big if .. else if .. else
         # clause...
         # https://github.com/IRkernel/IRkernel/pull/266
-        if(bitwAnd(zmq.poll.get.revents(1), .pbd_env$ZMQ.PO$POLLIN)) {
+        if (bitwAnd(zmq.poll.get.revents(1), .pbd_env$ZMQ.PO$POLLIN)) {
             log_debug('main loop: hb')
             hb_reply()
-        } else if(bitwAnd(zmq.poll.get.revents(2), .pbd_env$ZMQ.PO$POLLIN)) {
+        } else if (bitwAnd(zmq.poll.get.revents(2), .pbd_env$ZMQ.PO$POLLIN)) {
             log_debug('main loop: shell')
             handle_shell()
-        } else if(bitwAnd(zmq.poll.get.revents(3), .pbd_env$ZMQ.PO$POLLIN)) {
+        } else if (bitwAnd(zmq.poll.get.revents(3), .pbd_env$ZMQ.PO$POLLIN)) {
             log_debug('main loop: control')
             handle_control()
         } else {
@@ -381,6 +381,13 @@ main <- function(connection_file = '') {
         connection_file <- commandArgs(TRUE)[[1]]
     }
     log_debug('Starting the R kernel...')
+    # Create the shadow env here
+    # This has to be here so the on.exit can detach the env when main is finished
+    # = available for the whole lifetime of the kernel.
+    init_shadowenv()
+    on.exit({
+        detach("jupyter:irkernel")
+    })
     kernel <- Kernel$new(connection_file = connection_file)
     kernel$run()
 }

cran-comments.md

@@ -0,0 +1,33 @@
+## Release summary
+
+This package is new on CRAN. It contains the R kernel for the Jupyter
+ecosystem. The kernel executes R code, which the frontend (Jupyter Notebook or
+other frontends) submits to the kernel via the network.
+
+## Test environments
+
+* local Win7 64bit install, R 3.2.5, R 3.3.0 and r-devel (3.4)
+* Ubuntu 12.04 (on travis-ci), oldrelease, release, and r-devel
+
+## R CMD check results
+
+There are no WARNINGs and 1 NOTEs.
+
+Note:
+
+* Found the following calls to attach():
+  File 'IRkernel/R/environment.r':
+    attach(NULL, name = "jupyter:irkernel")
+  See section 'Good practice' in '?attach'.
+
+  We use this additional environment to add functions so that regular "stuff"
+  like `quit()` works in the IRkernel environment (in this case to shutdown the
+  kernel). We added the "good practice" `on.exit` call to `detach` in R\kernel.r ->
+  `main()` so that this environment is available as long as the R kernel is running..
+
+## Downstream dependencies
+
+It is assumed that there won't be any code dependencies on this package, as it
+implements an application without any API apart from the startup function and the
+implemented Jupyter Messaging spec. It's usually started as
+`R --slave -e IRkernel::main() --args {connection_file}`.