httpsgithu · pull · May 20, 2022 · May 20, 2022 · May 20, 2022 · May 20, 2022
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -6,3 +6,4 @@ README.md
 LICENSE
 ^appveyor\.yml$
 ^examples$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-13,        r: 'release'}
+          - {os: macos-14,        r: 'release'}
+          - {os: windows-latest,  r: '4.1'}
+          - {os: windows-latest,  r: '4.2'}
+          - {os: windows-latest,  r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,3 @@
-.*
 !/.gitignore
 !/.Rbuildignore
 !/.travis.yml

diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,12 @@
 Package: opencpu
 Title: Producing and Reproducing Results
-Version: 2.2.8
-Authors@R: person("Jeroen", "Ooms", role = c("aut", "cre"), email = "jeroen@berkeley.edu",
+Version: 2.2.15
+Authors@R: person("Jeroen", "Ooms", role = c("aut", "cre"), email = "jeroenooms@gmail.com",
     comment = c(ORCID = "0000-0002-4035-0289"))
 License: Apache License 2.0
 Encoding: UTF-8
-URL: https://www.opencpu.org (website)
-    https://github.com/opencpu/opencpu (devel)
+URL: https://www.opencpu.org 
+    https://opencpu.r-universe.dev/opencpu
 BugReports: https://github.com/opencpu/opencpu/issues
 Depends: 
     R (>= 3.0.0)
@@ -20,6 +20,9 @@ Imports:
     webutils (>= 0.6),
     curl (>= 4.0),
     rappdirs,
+    rlang,
+    vctrs,
+    methods,
     zip,
     mime,
     protolite,
@@ -30,17 +33,16 @@ Suggests:
     unix (>= 1.5.3),
     haven,
     pander,
-    R.rsp,
     svglite
 SystemRequirements: pandoc, apparmor (optional)
-VignetteBuilder: knitr, R.rsp
-Description: A system for embedded scientific computing and reproducible research with R.
+Description: A system for embedded scientific computing and reproducible research with R 
+    as described in <doi:10.48550/arXiv.1406.4806>.
     The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
     with R. This provides a reliable and scalable foundation for statistical services or 
     building R web applications. The OpenCPU server runs either as a single-user development
     server within the interactive R session, or as a multi-user Linux stack based on Apache2. 
     The entire system is fully open source and permissively licensed. The OpenCPU website
     has detailed documentation and example apps.
 LazyData: yes
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2.9000
 Roxygen: list(markdown = TRUE)
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,opencpu_info)
 export(available_apps)
 export(install_apps)
 export(installed_apps)

diff --git a/NEWS b/NEWS
@@ -1,3 +1,18 @@
+2.2.13
+  - Fix 'anchored' man links for CRAN
+  - Raise default memory limit on cloud server to 1e10 for V8
+
+2.2.11
+  - Errors raised by R now by default include a backtrace if available. You can
+    opt-out by setting 'error.backtrace' to false in your user.conf.
+  - Fix error.showcall to actually show/hide the call from errors.
+
+2.2.10
+  - Fix getRversion type for CRAN
+
+2.2.9
+ - Use packageStartupMessage() for loading messages
+
 2.2.8
  - Fixes for R-4.2 changes in R_LIBS_SITE and R_LIBS_USER
  - Default platform is now Ubuntu-22.04 with R-4.2

diff --git a/R/config.R b/R/config.R
@@ -4,7 +4,7 @@ config <- local({
   confpaths <- character()
 
   load <- function(filepath){
-    message("Loading config from ", filepath)
+    packageStartupMessage("Loading config from ", filepath)
     confpaths <<- c(confpaths, filepath)
     newconf <- as.list(fromJSON(filepath));
     for(i in seq_along(newconf)){

diff --git a/R/evaluate.R b/R/evaluate.R
@@ -2,6 +2,7 @@ evaluate_input <- function(input, args = NULL, storeval = FALSE) {
 
   #setup handler
   error_object <- NULL
+  cur_env <- rlang::current_env()
   myhandler <- evaluate::new_output_handler(value = function(myval, visible = TRUE){
     if(isTRUE(storeval) && is.null(error_object)){
       assign(".val", myval, sessionenv);
@@ -12,11 +13,14 @@ evaluate_input <- function(input, args = NULL, storeval = FALSE) {
         cat("List of length ", length(myval), "\n")
         cat(paste("[", names(myval), "]", sep="", collapse="\n"))
       } else {
-        getFromNamespace("render", "evaluate")(myval)
+        evaluate_render(myval)
       }
     }
     invisible()
   }, error = function(e){
+    if (isTRUE(config("error.backtrace"))) {
+      e$trace <- rlang::trace_back(top=cur_env)
+    }
     error_object <<- e
   })
 
@@ -37,10 +41,48 @@ evaluate_input <- function(input, args = NULL, storeval = FALSE) {
   }
   res <- evaluate::evaluate(input = input, envir = sessionenv, stop_on_error = 1, output_handler = myhandler)
 
+
+  if(length(error_object) && length(error_object$call) && isTRUE(config("error.backtrace"))){
+    error_object <- clean_trace(error_object)
+  }
+
   # return both
   list (
     res = res,
     sessionenv = sessionenv,
     error = error_object
   )
 }
+
+clean_trace <- function(err){
+  if (!is.null(err$trace)) {
+    tr <- err$trace
+    n <- nrow(tr)
+
+    isErrorHandler <- vapply(tr$call,
+                             function(x) identical(x[[1]], quote(.handleSimpleError)), logical(1))
+    errorHandlerIndex <- min(c(length(isErrorHandler)+1, which(isErrorHandler)))
+
+    isOverheadCall <- tr$namespace[seq_len(errorHandlerIndex - 1)] %in% c("evaluate", "opencpu") # only check before handler
+    lastOverheadIndex <- max(c(0, which(isOverheadCall)))
+
+    trIdx <- rlang::seq2(lastOverheadIndex + 1, errorHandlerIndex-1)
+
+    err$trace <- rlang_trace_slice(tr, trIdx)
+  }
+  return(err)
+}
+
+# Copied from rlang:::trace_slice
+rlang_trace_slice <- function (trace, i) {
+  i <- vctrs::vec_as_location(i, nrow(trace))
+  parent <- match(trace$parent, i, nomatch = 0)
+  out <- vctrs::vec_slice(trace, i)
+  out$parent <- parent[i]
+  out
+}
+
+# Copied from evaluate:::render
+evaluate_render <- function(x){
+  if (isS4(x)) methods::show(x) else print(x)
+}
diff --git a/R/github.R b/R/github.R
@@ -3,7 +3,7 @@ github_prefix <- "ocpu_github"
 getlocaldir <- function(which = 'data'){
   if(is_rapache() || is_admin()){
     return("/usr/local/lib/opencpu")
-  } else if(getRversion() < 4){
+  } else if(getRversion() < "4"){
     rappdirs::user_data_dir('opencpu')
   } else {
     tools::R_user_dir('opencpu', which)

diff --git a/R/httpget_info.R b/R/httpget_info.R
@@ -24,6 +24,7 @@ httpget_info <- function(requri){
   );
 }
 
+#' @export
 print.opencpu_info <- function(x, ...){
   titles <- names(x)
   type <- ifelse(is_rapache(), "Cloud", "Single-User")

diff --git a/R/httpget_webhook.R b/R/httpget_webhook.R
@@ -28,23 +28,23 @@ httpget_webhook <- function(){
 
   #Post-Receive data
   gitref <- payload$ref;
-  giturl <- payload$repository$url;
+  giturl <- payload$repository$clone_url;
   gitrepo <- payload$repository$name;
-  gitmaster <- payload$repository$master_branch;
+  gitmain <- payload$repository$default_branch;
   gituser <- tolower(payload$repository$owner$name);
 
   #Ignore all but master
-  if(is.null(gitref) || is.na(gitref) || !length(gitref) || gitref != paste0("refs/heads/", gitmaster)){
-    res$sendtext(sprintf("Ignoring non-master: %s (default/master branch is '%s')", gitref, gitmaster))
+  if(is.null(gitref) || is.na(gitref) || !length(gitref) || gitref != paste0("refs/heads/", gitmain)){
+    res$sendtext(sprintf("Ignoring non-main: %s (default/master branch is '%s')", gitref, gitmain))
   }
 
   #Check for gihtub
   if(!grepl("^https://github.com", giturl)){
-    stop("Currently only Github CI is supported.");
+    stop("Currently only Github CI is supported. Found: ", giturl);
   }
 
   #trigger install and email
-  do.call(webhook_install, c(list(payload = payload), repo = gitrepo, username = gituser, ref = gitmaster, req$get()))
+  do.call(webhook_install, c(list(payload = payload), repo = gitrepo, username = gituser, ref = gitmain, req$get()))
 }
 
 

diff --git a/R/parse_post.R b/R/parse_post.R
@@ -55,7 +55,9 @@ parse_post <- function(reqbody, contenttype){
   }
 
   return(lapply(obj, function(x){
-    if(is.null(x) || isTRUE(is.atomic(x) && length(x) == 1 && !length(dim(x)))){
+    if(is.null(x) ||
+       isTRUE(is.atomic(x) && length(x) == 1 &&
+              !length(dim(x))) && is.null(names(x))){
       #primitives as expressions
       return(deparse_atomic(x))
     } else {
@@ -66,7 +68,7 @@ parse_post <- function(reqbody, contenttype){
 
 # base::deparse() fucks up utf8 strings
 deparse_atomic <- function(x){
-  if(is.character(x)){
+  if(is.character(x) && !is.na(x)){
     str <- jsonlite::toJSON(x)
     str <- sub("^\\[", "c(", str)
     sub("\\]$", ")", str)

diff --git a/R/start.R b/R/start.R
@@ -52,7 +52,7 @@ ocpu_start_server <- function(port = 5656, root ="/ocpu", workers = 2, preload =
   add_workers <- function(n = 1){
     if(length(pool) < workers){
       log("Starting %d new worker(s). Preloading: %s", n, paste(preload, collapse = ", "))
-      cl <- makeCluster(n)
+      cl <- parallel::makeCluster(n)
       lapply(cl, sendCall, fun = function(){
         lapply(preload, getNamespace)
         Sys.getpid()
@@ -195,14 +195,3 @@ ocpu_start_app <- function(app, update = TRUE, ...){
     start_local_app_local(app, ...)
   }
 }
-
-## WORKAROUND: https://github.com/rstudio/rstudio/issues/6692
-## Use 'sequential' setup of PSOCK cluster in RStudio Console on macOS and R 4.0.0
-makeCluster <- function(..., setup_strategy = NULL){
-  if (Sys.getenv("RSTUDIO") == "1" && !nzchar(Sys.getenv("RSTUDIO_TERM")) &&
-      Sys.info()["sysname"] == "Darwin" && getRversion() >= "4") {
-    parallel::makeCluster(..., setup_strategy = "sequential")
-  } else {
-    parallel::makeCluster(...)
-  }
-}
diff --git a/R/utils.R b/R/utils.R
@@ -197,9 +197,10 @@ deparse_query <- function(x){
 
 format_user_error <- function(e){
   errmsg <- e$message;
-  if(length(e$call)){
-    errmsg <- c(errmsg, "", "In call:", deparse(e$call));
-  }
+  if(length(e$call) && isTRUE(config("error.showcall")))
+    errmsg <- c(errmsg, "", "In call:", deparse(e$call), "")
+  if (length(e$trace) && length(e$trace$call) && isTRUE(config("error.backtrace")))
+    errmsg <- c(errmsg, "Backtrace:", format(e$trace))
   return(errmsg)
 }
 

diff --git a/README.md b/README.md
@@ -2,11 +2,8 @@
 
 > Producing and Reproducing Results
 
-[![Build Status](https://travis-ci.org/opencpu/opencpu.svg?branch=master)](https://travis-ci.org/opencpu/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)
 [![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/opencpu/opencpu.svg?style=social&label=Github)](https://github.com/opencpu/opencpu)
 
 A system for embedded scientific computing and reproducible research with R.
 The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
@@ -29,7 +26,7 @@ has detailed documentation and example apps.
 To install the cloud server on Ubuntu Server:
 
 ```sh
-#requires Ubuntu 20.04 (Focal)
+#requires Ubuntu 22.04 (Jammy) or 20.04 (Focal)
 sudo add-apt-repository -y ppa:opencpu/opencpu-2.2
 sudo apt-get update 
 sudo apt-get upgrade