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

 Package: ReUseData

 Title: Reproducible and ReUsable Data Resources

-Version: 0.99.7

+Version: 0.99.8

 Authors@R: 

     person(given = "Qian",

            family = "Liu",

@@ -28,7 +28,10 @@

 #'     intermediate files that don't match to any data file, `cleanup`

 #'     will also remove those.

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

-#'     Cloud bucket of ReUseData. Default is FALSE. 

+#'     Cloud bucket of ReUseData. 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. 

 #' @details Users can directly retrieve information for all available

 #'     datasets by using `meta_data(dir=)`, which generates a data

 #'     frame in R with same information as described above and can be

@@ -60,7 +63,8 @@

 #' ## newly generated data are now cached and searchable

 #' 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) {

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

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

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

     bfcpath <- Sys.getenv("cachePath")

     if(bfcpath != ""){

@@ -83,7 +87,7 @@ dataUpdate <- function(dir, cachePath = "ReUseData", outMeta = FALSE, keepTags =

     bfcremove(bfc, bfcinfo(bfc)$rid)

-    meta <- meta_data(dir = dir, cleanup = cleanup)

+    meta <- meta_data(dir = dir, cleanup = cleanup, checkData = checkData)

     ## append pre-generated cloud data

     if (cloud) {

@@ -10,7 +10,8 @@ dataUpdate(

   outMeta = FALSE,

   keepTags = TRUE,

   cleanup = FALSE,

-  cloud = FALSE

+  cloud = FALSE,

+  checkData = TRUE

 )

 }

 \arguments{

@@ -45,6 +46,10 @@ will also remove those.}

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

 Cloud bucket of ReUseData. 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.}

 }

 \value{

 a \code{dataHub} object containing the information about local