Fix #15 and release 1.2.8

Minor update

DESCRIPTION

@@ -36,5 +36,5 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.0
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -3,6 +3,7 @@
 ## Bug fixes
 
 * #14 fixed
+* #15 fixed
 
 # v1.2.7
 

R/XenaDownload.R

@@ -57,7 +57,7 @@ XenaDownload <- function(xquery,
   xquery$destfiles <- file.path(destdir, xquery$fileNames)
 
   if (!dir.exists(destdir)) {
-    dir.create(destdir, recursive = TRUE)
+    dir.create(destdir, recursive = TRUE, showWarnings = FALSE)
   }
 
   message("All downloaded files will under directory ", destdir, ".")
@@ -66,30 +66,33 @@ XenaDownload <- function(xquery,
     message("The 'trans_slash' option is FALSE, keep same directory structure as Xena.")
     message("Creating directories for datasets...")
     for (i in dir_names) {
-      dir.create(i, recursive = TRUE)
+      dir.create(i, recursive = TRUE, showWarnings = FALSE)
     }
   }
 
   apply(xquery, 1, function(x) { # nocov start
-    tryCatch({
-      if (!file.exists(x[5]) | force) {
-        message("Downloading ", x[4])
+    tryCatch(
+      {
+        if (!file.exists(x[5]) | force) {
+          message("Downloading ", x[4])
+          download.file(x[3], destfile = x[5], ...)
+        } else {
+          message(x[5], ", the file has been download!")
+        }
+      },
+      error = function(e) {
+        message(
+          "Can not find file",
+          x[4],
+          ", this file maybe not compressed."
+        )
+        x[3] <- gsub(pattern = "\\.gz$", "", x[3])
+        x[4] <- gsub(pattern = "\\.gz$", "", x[4])
+        x[5] <- gsub(pattern = "\\.gz$", "", x[5])
+        message("Try downloading file", x[4], "...")
         download.file(x[3], destfile = x[5], ...)
-      } else {
-        message(x[5], ", the file has been download!")
       }
-    }, error = function(e) {
-      message(
-        "Can not find file",
-        x[4],
-        ", this file maybe not compressed."
-      )
-      x[3] <- gsub(pattern = "\\.gz$", "", x[3])
-      x[4] <- gsub(pattern = "\\.gz$", "", x[4])
-      x[5] <- gsub(pattern = "\\.gz$", "", x[5])
-      message("Try downloading file", x[4], "...")
-      download.file(x[3], destfile = x[5], ...)
-    })
+    )
   }) # nocov end
 
   if (trans_slash) {

R/XenaHub-class.R

@@ -305,6 +305,8 @@ XenaDataUpdate <- function(saveTolocal = TRUE) { # nocov start
   }
 }
 
-utils::globalVariables(c(".p_dataset_metadata",
-                         ".p_all_cohorts",
-                         ".p_dataset_list"))
+utils::globalVariables(c(
+  ".p_dataset_metadata",
+  ".p_all_cohorts",
+  ".p_dataset_list"
+))

R/api_higher.R

@@ -6,24 +6,27 @@
 ##' @return a character vector contains hosts
 ##' @export
 ##' @examples xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); hosts(xe)
-hosts <- function(x)
+hosts <- function(x) {
   unname(slot(x, "hosts"))
+}
 ##' Get cohorts of XenaHub object
 ##' @param x a [XenaHub] object
 ##' @return a character vector contains cohorts
 ##' @importFrom methods slot
 ##' @export
 ##' @examples xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); cohorts(xe)
-cohorts <- function(x)
+cohorts <- function(x) {
   slot(x, "cohorts")
+}
 ##' Get datasets of XenaHub object
 ##' @param x a [XenaHub] object
 ##' @return a character vector contains datasets
 ##' @importFrom methods slot
 ##' @export
 ##' @examples xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); datasets(xe)
-datasets <- function(x)
+datasets <- function(x) {
   slot(x, "datasets")
+}
 
 ##' Get Samples of a XenaHub object according to 'by' and 'how' action arguments
 ##'

R/api_inner.R

@@ -14,8 +14,9 @@
 
 .null_cohort <- "(unassigned)"
 
-.quote <- function(s)
+.quote <- function(s) {
   paste0('"', s, '"')
+}
 
 .quote_cohort <- function(cohort) {
   ifelse(cohort == .null_cohort, "nil", .quote(cohort))
@@ -25,8 +26,9 @@
   paste0(.quote(l), collapse = collapse)
 }
 
-.collapse_cohort <- function(cohorts, collapse = " ")
+.collapse_cohort <- function(cohorts, collapse = " ") {
   paste0(.quote_cohort(cohorts), collapse = collapse)
+}
 
 .arrayfmt <- function(l, collapse = .collapse) {
   paste0("[", collapse(l), "]")
@@ -83,7 +85,7 @@
 
 ## samples
 
-.samples_any_query <- function(what)
+.samples_any_query <- function(what) {
   paste0(
     "\n        (map :value\n        (query {\n        :select [:%distinct.value]\n        :from [:dataset]\n        :join [:field [:= :dataset.id :dataset_id]\n        :code [:= :field_id :field.id]]\n        :where [:and\n        [:in ",
     what,
@@ -92,8 +94,9 @@
         }))
         '
   )
+}
 
-.samples_all_query <- function(where, what, n) # nocov start
+.samples_all_query <- function(where, what, n) { # nocov start
   paste0(
     "\n        (map :value\n        (query {\n        :select [:value] :from [{\n        :select [",
     where,
@@ -109,7 +112,8 @@
         :having [:= :%count.value ',
     n,
     "]\n        }))\n        "
-  ) # nocov end
+  )
+} # nocov end
 
 
 ##
@@ -120,13 +124,16 @@
 # host --------------------------------------------------------------------
 
 .host_is_alive <- function(host) {
-  tryCatch({
-    result <- .xena_post(host, "(+ 1 2)")
-    stop_for_status(result)
-    TRUE
-  }, error = function(...) {
-    FALSE
-  })
+  tryCatch(
+    {
+      result <- .xena_post(host, "(+ 1 2)")
+      stop_for_status(result)
+      TRUE
+    },
+    error = function(...) {
+      FALSE
+    }
+  )
 }
 
 .host_cohorts <- function(hosts) {
@@ -227,8 +234,9 @@
     how,
     each = x,
     any = unique(unlist(x, use.names = FALSE)),
-    all = Reduce(function(x, y)
-      x[x %in% y], x)
+    all = Reduce(function(x, y) {
+      x[x %in% y]
+    }, x)
   )
 }