modify roxygen docs

NAMESPACE

@@ -57,7 +57,6 @@ export(scrapeRemoteFTPFilesTable)
 export(zenodoMetadata)
 import(R6)
 import(checkmate)
-import(httr)
 importFrom(BiocParallel,"bplog<-")
 importFrom(BiocParallel,"bpprogressbar<-")
 importFrom(BiocParallel,"bpworkers<-")
@@ -68,8 +67,6 @@ importFrom(BiocParallel,bpparam)
 importFrom(BiocParallel,bpprogressbar)
 importFrom(BiocParallel,bptry)
 importFrom(BiocParallel,bpworkers)
-importFrom(CoreGx,.errorMsg)
-importFrom(CoreGx,.warnMsg)
 importFrom(R6P,Singleton)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,mcols)

R/getDrugBank.R

@@ -188,12 +188,12 @@ listColToDT <- function(col) {
 }
 
 # Function testing scripts, not run unless this file is called as a script
-if (sys.nframe() == 0) {
-    library(AnnotationGx)
-    library(xml2)
-    library(data.table)
-    library(BiocParallel)
+# if (sys.nframe() == 0) {
+#     library(AnnotationGx)
+#     library(xml2)
+#     library(data.table)
+#     library(BiocParallel)
 
-    drugTargetDT <- getDrugTargets('local_data/drugbank.xml')
+#     drugTargetDT <- getDrugTargets('local_data/drugbank.xml')
 
-}
+# }

R/getPubChem.R

@@ -170,7 +170,7 @@ getRequestPubChem <- function(id, domain='compound', namespace='cid', operation=
 
         if (isTRUE(raw)) return(result)
 
-        .checkThrottlingStatus(result, verbose = verbose)
+        .checkThrottlingStatus(result, throttleMessage = verbose)
 
         canParse <- tryCatch({ parseJSON(result, as='text'); TRUE },
             error=function(e) FALSE)

R/getUniProt.R

@@ -30,25 +30,24 @@ getUniProt <- function(url='') {
 #' @return A httr::response object containing the query results as `format`.
 #'
 #' @import httr
-#' @importFrom CoreGx .errorMsg .warnMsg
 # #' @export
-queryUniProt <- function(query, columns='', limit='', offset='', format='xml',
-        include=TRUE, compress=TRUE, ...,
-        url='https://www.uniprot.org/uniprot') {
-    stop("Not implemented yet!")
-    if (missing(query)) stop(.errorMsg(.context(), 'The query parameter is
-        missing! This parameter is mandatory.'))
+# queryUniProt <- function(query, columns='', limit='', offset='', format='xml',
+#         include=TRUE, compress=TRUE, ...,
+#         url='https://www.uniprot.org/uniprot') {
+#     stop("Not implemented yet!")
+#     if (missing(query)) stop(.errorMsg(.context(), 'The query parameter is
+#         missing! This parameter is mandatory.'))
 
-    ##TODO:: handle more errors
+#     ##TODO:: handle more errors
 
-    # parse parameters
-    include <- if (include) 'yes' else 'no'
-    compress <- if (compress) 'yes' else 'no'
+#     # parse parameters
+#     include <- if (include) 'yes' else 'no'
+#     compress <- if (compress) 'yes' else 'no'
 
-    response <- GET()
-}
+#     response <- GET()
+# }
 
-#'
+# #'
 #'
 #'
 #'