MASS rename

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: opencpu
 Type: Package
 Title: Embedded Scientific Computing and Reproducible Research with R
-Version: 1.6.6
+Version: 1.6.7
 Author: Jeroen Ooms
-Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
+Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
 License: Apache License 2.0
 URL: https://www.opencpu.org
-    https://github.com/jeroenooms/opencpu#readme
-BugReports: https://github.com/jeroenooms/opencpu/issues
+    https://github.com/jeroen/opencpu#readme
+BugReports: https://github.com/jeroen/opencpu/issues
 Depends:
     R (>= 3.0.0)
 Imports:

LICENSE

@@ -10,4 +10,4 @@ Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
-limitations under the License.
+limitations under the License.

R/bioc_load.R

@@ -54,4 +54,4 @@ bioc_load <- function(pkgname, biocpath){
 
   #return the path 
   return(pkgpath);
-}
+}

R/check.enabled.R

@@ -3,4 +3,4 @@ check.enabled <- function(what){
     return(TRUE);
   }
   stop('The ', what, ' feature has not been enabled on this server.\nAdmin needs to set: {"enable.', what,'":true}');
-}
+}

R/config.R

@@ -19,4 +19,4 @@ config <- local({
 
   #default is get
   get
-})
+})

R/cran_load.R

@@ -48,4 +48,4 @@ cran_load <- function(pkgname){
 
   #return the path 
   return(pkgpath);
-}
+}

R/createconfigfile.R

@@ -14,4 +14,4 @@ createconfigfile <- function(){
       warning("Failed to create new config file: ", configfile, ". Using default config.")      
     };
   }
-}
+}

R/email.R

@@ -7,4 +7,4 @@ email <- function(to, ...){
 
 address <- function(name, mail){
   paste0('"', name, '"<', mail, '>');
-}
+}

R/errorif.R

@@ -6,4 +6,4 @@ errorifnot <- function(condition, msg){
   if(!isTRUE(condition)){
     res$error(msg);
   }
-}
+}

R/eval_fork.R

@@ -16,7 +16,7 @@ eval_fork <- function(..., timeout=60){
   totaltime <- as.numeric(enddtime - starttime, units="secs")
 
   #try to avoid bug/race condition where mccollect returns null without waiting full timeout.
-  #see https://github.com/jeroenooms/opencpu/issues/131
+  #see https://github.com/jeroen/opencpu/issues/131
   #waits for max another 2 seconds if proc looks dead
   while(is.null(myresult) && totaltime < timeout && totaltime < 2) {
     Sys.sleep(.1)

R/execute_function.R

@@ -33,4 +33,4 @@ execute_function <- function(object, requri, objectname="FUN"){
 
   #perform evaluation
   session$eval(mycall, fnargs, storeval=TRUE, format=requri[1])
-}
+}

R/extract.R

@@ -77,4 +77,4 @@ extract <- local({
        "graphics"= extract_graphics(evaluation)
     )  
   }  
-});
+});

R/find_aliases.R

@@ -8,4 +8,4 @@ find_aliases <- function(pkgpath, pkgname) {
   data.frame(name=topic_names, alias=aliasstring, stringsAsFactors = FALSE)  
 }
 
-#links <- names(all_topics)[match(unique(all_topics), all_topics)]
+#links <- names(all_topics)[match(unique(all_topics), all_topics)]

R/from.R

@@ -2,4 +2,4 @@ from <- function (pkg, name) {
   pkg <- as.character(substitute(pkg))
   name <- as.character(substitute(name))
   get(name, envir = asNamespace(pkg), inherits = FALSE)
-}
+}

R/gist_load.R

@@ -53,4 +53,4 @@ gist_load <- function(gistuser, gistid){
 
   #return the path 
   return(gistpath)
-}
+}

R/github_load.R

@@ -49,4 +49,4 @@ github_load <- function(gituser, gitrepo){
 
   #return the path 
   return(pkgpath);
-}
+}

R/httpget_github.R

@@ -27,4 +27,4 @@ httpget_github <- function(uri){
 
   #serve basic files
   httpget_package(pkgpath, reqtail);
-}
+}

R/httpget_info.R

@@ -10,4 +10,4 @@ httpget_info <- function(requri){
     "GET" = httpget_object(myobject, "print", "sessionInfo"),
     stop("invalid method")
   );
-}
+}

R/httpget_package.R

@@ -28,4 +28,4 @@ httpget_package <- function(pkgpath, requri){
     "info" = httpget_package_info(pkgpath),    
     httpget_package_file(pkgpath, requri)     
   );
-}
+}

R/httpget_package_html.R

@@ -28,4 +28,4 @@ httpget_package_html <- function(pkgpath, requri){
   mytmp <- tempfile(fileext=".html");
   tools::Rd2HTML(rdfile, out=mytmp, package=reqpackage, Links=mylinks, stylesheet="R.css");
   res$sendfile(mytmp); 
-}
+}

R/httpget_session.R

@@ -31,4 +31,4 @@ httpget_session <- function(filepath, requri){
      "tar" = httpget_session_tar(filepath, reqtail),
      stop("invalid session api: /session/",reqhead)
   );  
-}
+}

R/httpget_session_files.R

@@ -1,3 +1,3 @@
 httpget_session_files <- function(filepath, requri){
   httpget_file(c(filepath, requri));  
-}
+}

R/httpget_session_graphics.R

@@ -66,4 +66,4 @@ httpget_session_graphics <- function(filepath, requri){
 
   newfilename <- paste(utils::tail(strsplit(basename(filepath), "_", fixed=TRUE)[[1]], 1), reqplot, sep="_plot");
   httpget_object(myobject, reqformat, newfilename);
-}
+}

R/httpget_session_info.R

@@ -5,4 +5,4 @@ httpget_session_info <- function(filepath, requri){
   #render
   reqformat <- requri[1];
   httpget_object(myinfo, reqformat, "sessionInfo");  
-}
+}

R/httpget_session_source.R

@@ -7,4 +7,4 @@ httpget_session_source <- function(filepath, requri){
   #render
   reqformat <- requri[1];
   httpget_object(mysrc, reqformat, "warnings", "text");
-}
+}

R/httpget_session_warnings.R

@@ -8,4 +8,4 @@ httpget_session_warnings <- function(filepath, requri){
   #render
   reqformat <- requri[1];
   httpget_object(mywarnings, reqformat, "warnings", "text");
-}
+}

R/httpget_static.R

@@ -10,4 +10,4 @@ httpget_static <- function(){
 
   #send it
   res$sendfile(system.file(filepath, package=packagename));    
-}
+}

R/loadsessioninfo.R

@@ -8,4 +8,4 @@ loadsessioninfo <- function(filepath){
 
   #load other pkgs
   lapply(as.list(names(myinfo$otherPkgs)), require, character.only=TRUE);  
-}
+}

R/mimelist.R

@@ -177,4 +177,4 @@ mimelist <- list (
 	"yaml"="text/yaml",
 	"yml"="text/yaml",
 	"zip"="application/zip"
-);
+);

R/parse_arg_prim.R

@@ -22,4 +22,4 @@ parse_arg_prim <- function(x){
   } else {
     return(x)
   }
-}
+}

R/parse_post.R

@@ -56,4 +56,4 @@ parse_post <- function(reqbody, contenttype){
       return(I(x))
     }
   }));  
-}
+}

R/parse_query.R

@@ -14,4 +14,4 @@ parse_query <- function(query){
   ARGS <- lapply(ARGS, function(s) {utils::URLdecode(chartr('+',' ',s))});
   names(ARGS) <- lapply(argslist, "[[", 1);    
   return(ARGS)
-}
+}

R/printwithmax.R

@@ -2,4 +2,4 @@ printwithmax <- function(..., max.print = getOption("max.print")){
   oldopt <- options(max.print=max.print);
   print(...);
   options(max.print=oldopt$max.print)
-}
+}

R/req.R

@@ -86,4 +86,4 @@ req <- local({
   };
 
   environment();
-});
+});

R/res.R

@@ -164,4 +164,4 @@ res <- local({
   };
 
   environment();
-});
+});

R/rhttpdhandler.R

@@ -67,4 +67,4 @@ rhttpdhandler <- function(rootpath){
       "status code" = response$status
     );
   }
-}
+}

R/setLibPaths.R

@@ -12,4 +12,4 @@ setLibPaths <- local({
     newlibs <- newlibs[sapply(newlibs, checkfordir)]
     assign(".lib.loc", newlibs, envir=environment(.libPaths));
   }
-})
+})

R/stub.R

@@ -5,4 +5,4 @@ stub <- function(){
   brew::brew()
   httpuv::runServer()
   knitr::knit()
-}
+}

R/tryCatch_capture_stack.R

@@ -12,4 +12,4 @@ tryCatch_capture_stack <- function(quoted_code, error) {
     withCallingHandlers(eval(quoted_code), error = capture_calls),
     error = error
   )
-}
+}

README.md

@@ -2,12 +2,12 @@
 
 ##### *A System for Embedded Scientific Computing and Reproducible Research with R*
 
-[![Build Status](https://travis-ci.org/jeroenooms/opencpu.svg?branch=master)](https://travis-ci.org/jeroenooms/opencpu)
-[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/jeroenooms/opencpu?branch=master&svg=true)](https://ci.appveyor.com/project/jeroenooms/opencpu)
-[![Coverage Status](https://codecov.io/github/jeroenooms/opencpu/coverage.svg?branch=master)](https://codecov.io/github/jeroenooms/opencpu?branch=master)
+[![Build Status](https://travis-ci.org/jeroen/opencpu.svg?branch=master)](https://travis-ci.org/jeroen/opencpu)
+[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/jeroen/opencpu?branch=master&svg=true)](https://ci.appveyor.com/project/jeroen/opencpu)
+[![Coverage Status](https://codecov.io/github/jeroen/opencpu/coverage.svg?branch=master)](https://codecov.io/github/jeroen/opencpu?branch=master)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/opencpu)](http://cran.r-project.org/package=opencpu)
 [![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/opencpu)](http://cran.r-project.org/web/packages/opencpu/index.html)
-[![Github Stars](https://img.shields.io/github/stars/jeroenooms/opencpu.svg?style=social&label=Github)](https://github.com/jeroenooms/opencpu)
+[![Github Stars](https://img.shields.io/github/stars/jeroen/opencpu.svg?style=social&label=Github)](https://github.com/jeroen/opencpu)
 
 > The OpenCPU system exposes an http API for embedded scientific
   computing with R. The server can run either as a single-user development
@@ -22,7 +22,7 @@
  - Official [API documentation](https://www.opencpu.org/api.html)
  - Paper: [Towards a Universal Interface for Scientific Computing through Separation of Concerns](http://arxiv.org/abs/1406.4806) 
  - Example [apps](https://www.opencpu.org/apps.html)
- - JavaScript client: [opencpu.js](https://github.com/jeroenooms/opencpu.js)
+ - JavaScript client: [opencpu.js](https://github.com/jeroen/opencpu.js)
  - Server manual: [PDF](http://jeroenooms.github.com/opencpu-manual/opencpu-server.pdf)
 
 ## Cloud Server

inst/test/index.html

@@ -75,7 +75,7 @@
             <li><a target="_blank" href="https://www.opencpu.org/apps.html">Example Apps</a></li>
             <li><a target="_blank" href="https://www.opencpu.org/jslib.html">JavaScript Client</a></li>
             <li><a target="_blank" href="http://jeroenooms.github.com/opencpu-manual/opencpu-server.pdf">PDF manual</a></li>
-						<li><a target="_blank" href="http://github.com/jeroenooms/opencpu">Source Code</a></li>
+						<li><a target="_blank" href="http://github.com/jeroen/opencpu">Source Code</a></li>
 					</ul>
 				</div>
 				<!--/.nav-collapse -->

teststuff/testpayload.R

@@ -142,4 +142,4 @@ payload <- fromJSON('{
                     "url":"https://github.com/octokitty/testing",
                     "watchers":1
                     }
-                    }')
+                    }')

teststuff/testpayload_json.R

@@ -8,14 +8,14 @@ payload <- '{
 "created": false,
 "deleted": false,
 "forced": false,
-"compare": "https://github.com/jeroenooms/jsonlite/compare/035269431ef2...fafc4c046ab6",
+"compare": "https://github.com/jeroen/jsonlite/compare/035269431ef2...fafc4c046ab6",
 "commits": [
 {
 "id": "fafc4c046ab6973dafbbfad51c46a095f53d0129",
 "distinct": true,
 "message": "Trigger build",
 "timestamp": "2014-06-17T16:13:29-07:00",
-"url": "https://github.com/jeroenooms/jsonlite/commit/fafc4c046ab6973dafbbfad51c46a095f53d0129",
+"url": "https://github.com/jeroen/jsonlite/commit/fafc4c046ab6973dafbbfad51c46a095f53d0129",
 "author": {
 "name": "Jeroen",
 "email": "jeroenooms@gmail.com",
@@ -42,7 +42,7 @@ payload <- '{
 "distinct": true,
 "message": "Trigger build",
 "timestamp": "2014-06-17T16:13:29-07:00",
-"url": "https://github.com/jeroenooms/jsonlite/commit/fafc4c046ab6973dafbbfad51c46a095f53d0129",
+"url": "https://github.com/jeroen/jsonlite/commit/fafc4c046ab6973dafbbfad51c46a095f53d0129",
 "author": {
 "name": "Jeroen",
 "email": "jeroenooms@gmail.com",
@@ -66,7 +66,7 @@ payload <- '{
 "repository": {
 "id": 13305534,
 "name": "jsonlite",
-"url": "https://github.com/jeroenooms/jsonlite",
+"url": "https://github.com/jeroen/jsonlite",
 "description": "A smarter JSON encoder/decoder for R",
 "homepage": "http://arxiv.org/abs/1403.2805",
 "watchers": 40,
@@ -100,4 +100,4 @@ req = POST (
   add_headers("Content-Type" = "application/json")
 )
 
-print(req)
+print(req)