@@ -1,6 +1,6 @@

 Package: ReUseData

 Title: Reproducible and ReUsable Data Resources

-Version: 0.99.18

+Version: 0.99.19

 Authors@R: 

     person(given = "Qian",

            family = "Liu",

@@ -28,10 +28,6 @@

 #'     will also remove those.

 #' @param cloud Whether to return the pre-generated data from Google

 #'     Cloud bucket of ReUseData. Default is FALSE.

-#' @param remote Whether to use the csv file (containing information

-#'     about pre-generated data on Google Cloud) from GitHub, which is

-#'     most up-to-date. Only works when `cloud = TRUE`. Default is

-#'     FALSE.

 #' @param checkData check if the data (listed as "# output: " in the

 #'     yml file) exists. If not, do not include in the output csv

 #'     file. This argument is added for internal testing purpose.

@@ -79,7 +75,7 @@

 #' dataSearch(c("ensembl", "liftover"))  ## both locally generated data and google cloud data! 

 #' 

 dataUpdate <- function(dir, cachePath = "ReUseData", outMeta = FALSE,

-                       keepTags = TRUE, cleanup = FALSE, cloud = FALSE, remote = FALSE, checkData = TRUE) {

+                       keepTags = TRUE, cleanup = FALSE, cloud = FALSE, checkData = TRUE) {

     ## find/create the cache path, and create a BFC object.

     bfcpath <- Sys.getenv("cachePath")

     if(bfcpath != ""){

@@ -106,13 +102,7 @@ dataUpdate <- function(dir, cachePath = "ReUseData", outMeta = FALSE,

     ## append pre-generated cloud data

     if (cloud) {

-        if (remote) {

-            download.file("https://raw.githubusercontent.com/rworkflow/ReUseDataRecipe/master/meta_gcp.csv",

-                          file.path(tempdir(), "meta_gcp.csv"))

-            meta_gcp <- read.csv(file.path(tempdir(), "meta_gcp.csv"))

-        } else {

-            meta_gcp <- read.csv(system.file("extdata", "meta_gcp.csv", package = "ReUseData"))

-        }

+        meta_gcp <- read.csv(system.file("extdata", "meta_gcp.csv", package = "ReUseData"))

         meta <- rbind(meta, meta_gcp)

     }

@@ -9,18 +9,8 @@

 #'     `recipeSearch`, and `recipeLoad`. Default is "ReUseDataRecipe".

 #' @param force Whether to remove existing and regenerate recipes

 #'     cache. Default is FALSE. Only use if any old recipes that have

-#'     been previously cached locally are updated remotely (on GitHub

-#'     `repos`).

-#' @param remote Whether to download the data recipes directly from a

-#'     GitHub repository. Default is FALSE.

-#' @param repos The GitHub repository containing data recipes that are

-#'     to be synced to local cache. Only works when

-#'     `remote=TRUE`. Default is "rworkflows/ReUseDataRecipes" GitHub

-#'     repository where public data recipes are saved, which might be

-#'     more up-to-date than the recipes contained in`ReUseData`

-#'     package. It can also be a private GitHub repository where users

-#'     save their own data recipes.

-#' @return a `recipeHub` object.

+#'     been previously cached locally are updated.

+##' @return a `recipeHub` object.

 #' @importFrom tools R_user_dir

 #' @import BiocFileCache

 #' @import Rcwl

@@ -28,14 +18,11 @@

 #' @export

 #' @examples

 #' recipeUpdate()

-#' recipeUpdate(force=TRUE)

-#' recipeUpdate(force = TRUE, remote = TRUE)

+#' ## recipeUpdate(force=TRUE)

 recipeUpdate <- function(cachePath = "ReUseDataRecipe",

-                         force = FALSE,

-                         remote = FALSE,

-                         repos = "rworkflow/ReUseDataRecipe"){

-    

+                         force = FALSE){

+     

     ## find/create the cache path, and create a BFC object.

     bfcpath <- Sys.getenv("cachePath")

     if(bfcpath != ""){

@@ -47,8 +34,8 @@ recipeUpdate <- function(cachePath = "ReUseDataRecipe",

     }

     bfc <- BiocFileCache(cachePath, ask = FALSE)

-    ## if "force=TRUE", remove local recipes, and reload/update all

-    ## recipes from remote repo.

+    ## if "force=TRUE", remove local cache and reload/update all

+    ## recipes for a new cache.

     if(force){

         message("Warning: existing caches will be removed and regenerated!")

         bfcremove(bfc, bfcinfo(bfc)$rid)

@@ -56,23 +43,12 @@ recipeUpdate <- function(cachePath = "ReUseDataRecipe",

     ## FIXME: CREATE A private github repo for private data recipes. 

     message("Update recipes...")

-    if (remote) {

-        dlpath <- file.path(cachePath, "recipes.zip")

-        download.file(paste0("https://github.com/", repos,

-                             "/archive/refs/heads/master.zip"),

-                      dlpath)

-        unzip(dlpath, exdir = cachePath)

-        fpath <- list.files(

-            file.path(cachePath, paste0(basename(repos), "-master")),

-            full.names=TRUE)

-        fpath <- fpath[basename(fpath) != "dataGen.R"]

-    } else {

-        rcpfls <- list.files(

-            system.file("extdata/dataRecipes", package = "ReUseData"),

-            full.names = TRUE)

-        file.copy(rcpfls, cachePath)

-        fpath <- list.files(cachePath, pattern = ".R", full.names = TRUE)

-    }

+    rcpfls <- list.files(

+        system.file("extdata/dataRecipes", package = "ReUseData"),

+        full.names = TRUE)

+    file.copy(rcpfls, cachePath)

+    fpath <- list.files(cachePath, pattern = ".R", full.names = TRUE)

+    

     ## add any non-cached recipes to local cache

     if(length(fpath) > 0){

         rnames <- sub(".R$", "", basename(fpath))

@@ -11,7 +11,6 @@ dataUpdate(

   keepTags = TRUE,

   cleanup = FALSE,

   cloud = FALSE,

-  remote = FALSE,

   checkData = TRUE

 )

 }

@@ -47,11 +46,6 @@ will also remove those.}

 \item{cloud}{Whether to return the pre-generated data from Google

 Cloud bucket of ReUseData. Default is FALSE.}

-\item{remote}{Whether to use the csv file (containing information

-about pre-generated data on Google Cloud) from GitHub, which is

-most up-to-date. Only works when \code{cloud = TRUE}. Default is

-FALSE.}

-

 \item{checkData}{check if the data (listed as "# output: " in the

 yml file) exists. If not, do not include in the output csv

 file. This argument is added for internal testing purpose.}

@@ -4,12 +4,7 @@

 \alias{recipeUpdate}

 \title{recipeUpdate}

 \usage{

-recipeUpdate(

-  cachePath = "ReUseDataRecipe",

-  force = FALSE,

-  remote = FALSE,

-  repos = "rworkflow/ReUseDataRecipe"

-)

+recipeUpdate(cachePath = "ReUseDataRecipe", force = FALSE)

 }

 \arguments{

 \item{cachePath}{A character string specifying the name for the

@@ -19,19 +14,7 @@ specified here, must use the same for \code{cachePath} argument in

 \item{force}{Whether to remove existing and regenerate recipes

 cache. Default is FALSE. Only use if any old recipes that have

-been previously cached locally are updated remotely (on GitHub

-\code{repos}).}

-

-\item{remote}{Whether to download the data recipes directly from a

-GitHub repository. Default is FALSE.}

-

-\item{repos}{The GitHub repository containing data recipes that are

-to be synced to local cache. Only works when

-\code{remote=TRUE}. Default is "rworkflows/ReUseDataRecipes" GitHub

-repository where public data recipes are saved, which might be

-more up-to-date than the recipes contained in\code{ReUseData}

-package. It can also be a private GitHub repository where users

-save their own data recipes.}

+been previously cached locally are updated.}

 }

 \value{

 a \code{recipeHub} object.

@@ -43,6 +26,5 @@ repository or user-specified private GitHub repo.

 }

 \examples{

 recipeUpdate()

-recipeUpdate(force=TRUE)

-recipeUpdate(force = TRUE, remote = TRUE)

+## recipeUpdate(force=TRUE)

 }

@@ -40,7 +40,6 @@ test_that("recipe evaluation works", {

 test_that("recipe updating works", {

     rcphub <- recipeUpdate(cachePath = "ReUseDataRecipe",

-                           repos = "rworkflow/ReUseDataRecipe",

                            force = TRUE)

     expect_s4_class(rcphub, "recipeHub")

     expect_vector(recipeNames(rcphub))

@@ -211,11 +211,6 @@ _R_.

 `recipeLoad` and `recipeSearch` functions.

 - use `force=TRUE` when any old recipes that are previously cached are

 updated.

-- use `remote = TRUE`to sync with remote GitHub repositories. By

-  default, it syncs with `ReUseDataRecipe` GitHub

-  repository](https://github.com/rworkflow/ReUseDataRecipe) for

-  public, pre-built data recipes. `repo` can also be a private GitHub

-  repository.

 ```{r}

 ## First time use

@@ -225,13 +220,6 @@ recipeUpdate(cachePath = "ReUseDataRecipe",

 recipeUpdate()

 ```

-To sync the local recipe cache with remote GitHub repository.  

-

-```{r, eval=FALSE}

-recipeUpdate(remote = TRUE,

-             repos = "rworkflow/ReUseDataRecipe")  ## can be private repo

-```

-

 `recipeUpdate` returns a `recipeHub` object with a list of all

 available recipes. One can subset the list with `[` and use getter

 functions `recipeNames()` to get the recipe names which can then be