Remove getwd occurrences

bzhanglab · Jun 25, 2024 · 61ecfea · 61ecfea
1 parent 00cdb46
commit 61ecfea
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Showing 4 changed files with 7 additions and 9 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.4
-Date: 2024-06-18 18:58:59 UTC
-SHA: 584cc5189e1e0674fdbb7b28fedda3b4de5a2d87
+Version: 1.0.5
+Date: 2024-06-24 15:36:09 UTC
+SHA: 00cdb469de694c5f9742ef1cc9cbf2f293296775
diff --git a/R/clinicalomicsdbR.R b/R/clinicalomicsdbR.R
@@ -78,8 +78,7 @@ clinicalomicsdbR <- R6Class("clinicalomicsdbR", list(
   #' @param output_dir Directory to download files to.
   #' @return unmodifed clinicalomicsdbR object
   download = function(output_dir) {
-    cidr <- getwd()
-    dir.create(file.path(cidr, output_dir), recursive = TRUE, showWarnings = FALSE)
+    dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
     for (study_id in self$study_list) {
       dl_url <- self$get_download_url(study_id)
       message(paste0("Downloading study ", study_id, " from ", dl_url))
@@ -94,8 +93,7 @@ clinicalomicsdbR <- R6Class("clinicalomicsdbR", list(
   #' @param output_dir Directory to download files to.
   #' @return unmodifed clinicalomicsdbR object
   download_from_id = function(study_id) {
-    cidr <- getwd()
-    dir.create(file.path(cidr, output_dir), recursive = TRUE, showWarnings = FALSE)
+    dir.create(output_dir, recursive = TRUE, showWarnings = FALSE)
     dl_url <- self$get_download_url(study_id)
     tryCatch(
       {

diff --git a/README.Rmd b/README.Rmd
@@ -50,7 +50,7 @@ See Examples below to see how to use.
 - `new()` - Create new clinicalomicsdbR object. Needed before any other
   function
 - `filter(drugs, cancers)` - filters studies matching provided
-  arugments. `drugs` is a list and can be individual drugs or
+  arguments. `drugs` is a list and can be individual drugs or
   combinations. See the ClinicalOmicsDB website for all options.
   `cancers` can contain multiple cancers.
 - `download(output_dir)` - downloads all studies from `filter()` into

diff --git a/README.md b/README.md
@@ -44,7 +44,7 @@ See Examples below to see how to use.
 - `new()` - Create new clinicalomicsdbR object. Needed before any other
   function
 - `filter(drugs, cancers)` - filters studies matching provided
-  arugments. `drugs` is a list and can be individual drugs or
+  arguments. `drugs` is a list and can be individual drugs or
   combinations. See the ClinicalOmicsDB website for all options.
   `cancers` can contain multiple cancers.
 - `download(output_dir)` - downloads all studies from `filter()` into