fill out imported fxns from other pkgs in namespace; remove magrittr …

…pipe import

DESCRIPTION

@@ -14,7 +14,6 @@ Description: A repo containing a basic R package for using Cromwell with WDL wor
 Imports:
     httr,
     jsonlite,
-    magrittr,
     dplyr,
     purrr,
     tidyr,

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(cromwell_abort)
 export(cromwell_backends)
 export(cromwell_cache)
@@ -17,7 +16,26 @@ export(cromwell_version)
 export(cromwell_workflow)
 export(workflow_inputs)
 export(workflow_options)
+importFrom(dplyr,"%>%")
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,tibble)
-importFrom(magrittr,"%>%")
+importFrom(httr,GET)
+importFrom(httr,POST)
+importFrom(httr,content)
+importFrom(httr,stop_for_status)
+importFrom(httr,upload_file)
+importFrom(jsonlite,fromJSON)
+importFrom(lubridate,now)
+importFrom(lubridate,with_tz)
+importFrom(lubridate,ymd_hms)
+importFrom(purrr,discard)
+importFrom(purrr,flatten)
+importFrom(purrr,keep)
+importFrom(purrr,map)
+importFrom(purrr,map_dfr)
+importFrom(purrr,pluck)
+importFrom(purrr,reduce)
+importFrom(rlang,is_character)
+importFrom(rlang,is_logical)
 importFrom(rlang,set_names)
+importFrom(tidyr,separate)

R/cromUtils.R

@@ -1,6 +1,7 @@
 #' Pull the workflow options provided for a Cromwell workflow job
 #'
 #' @template workflowid
+#' @importFrom jsonlite fromJSON
 #' @return Returns a data frame of the options for a workflow previously run
 #' @author Amy Paguirigan
 #' @section Important:

R/cromwellCall.R

@@ -3,6 +3,7 @@
 #' Retrieve and process call metadata for a specific workflow.
 #'
 #' @template workflowid
+#' @importFrom tidyr separate
 #' @return Returns a long form data frame of metadata on calls.
 #' NOTE: does not currently support subWorkflows well yet.
 #' @author Amy Paguirigan

R/http.R

@@ -1,3 +1,6 @@
+#' @importFrom httr GET POST stop_for_status content upload_file
+#' @noRd
+#' @keywords internal
 http_get <- function(url, as = NULL, ...) {
   result <- httr::GET(url, ...)
   httr::stop_for_status(result)

R/rcromwell-package.R

@@ -2,6 +2,8 @@
 "_PACKAGE"
 
 ## usethis namespace: start
-#' @importFrom dplyr as_tibble tibble
+#' @importFrom dplyr as_tibble tibble %>%
+#' @importFrom lubridate now with_tz ymd_hms
+#' @importFrom purrr discard flatten keep map map_dfr pluck reduce
 ## usethis namespace: end
 NULL

R/settings.R

@@ -37,6 +37,7 @@ NULL
 #' Cromwell Configuration
 #'
 #' @export
+#' @importFrom rlang is_character is_logical
 #' @param cromwell_url (character) Cromwell server URL. The full url,
 #' for example "http://localhost:8000" or "https://mycromwell.com"
 #' @param verbose (logical) verbose messaging. default: `TRUE`. this