From fddf8b39e8bbfd8576933ac4f609b98fcba6f36a Mon Sep 17 00:00:00 2001
From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com>
Date: Fri, 25 Feb 2022 14:13:05 -0500
Subject: [PATCH] Save NCBI refs to cache dir. Adjust .Rbuildignore for Windows

---
 .Rbuildignore            |  4 ++++
 DESCRIPTION              |  5 +++--
 NAMESPACE                |  1 +
 NEWS.md                  | 10 ++++++++++
 R/get_genomeLocFile.R    |  8 ++++++--
 man/get_genomeLocFile.Rd |  6 +++++-
 6 files changed, 29 insertions(+), 5 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 5c3a56b..2f5b613 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,3 +14,7 @@ Dockerfile
 ^LICENSE\.md$
 inst/hex/
 MAGMA.Celltyping/inst/hex
+
+^node_modules$
+package-lock.json
+package.json
diff --git a/DESCRIPTION b/DESCRIPTION
index 5c1d1dd..cce5d71 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MAGMA.Celltyping
 Type: Package
 Title: Find Causal Cell-Types Underlying Complex Trait Genetics
-Version: 2.0.1
+Version: 2.0.2
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",
@@ -53,7 +53,8 @@ Imports:
     parallel,
     Matrix,
     methods,
-    reshape2
+    reshape2,
+    tools
 Suggests: 
     markdown,
     rmarkdown,
diff --git a/NAMESPACE b/NAMESPACE
index fb72ca4..1b2504e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -83,6 +83,7 @@ importFrom(stats,quantile)
 importFrom(stats,residuals)
 importFrom(stats,setNames)
 importFrom(stringr,str_split)
+importFrom(tools,R_user_dir)
 importFrom(utils,download.file)
 importFrom(utils,read.table)
 importFrom(utils,unzip)
diff --git a/NEWS.md b/NEWS.md
index 9c79846..29f02e1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,13 @@
+# MAGMA.Celltyping 2.0.2
+
+## New features
+
+* `get_genomeLocFile`: Store NCBI ref file in cache dir by default.  
+
+## Bug fixes  
+
+* Add windows-specific files/folders to *.Rbuildignore*.  
+
 # MAGMA.Celltyping 2.0.1  
 
 ## New features
diff --git a/R/get_genomeLocFile.R b/R/get_genomeLocFile.R
index d900fef..d559e04 100644
--- a/R/get_genomeLocFile.R
+++ b/R/get_genomeLocFile.R
@@ -40,8 +40,12 @@
 #' @return File path.
 #' 
 #' @keywords internal
+#' @importFrom tools R_user_dir
+#' @importFrom data.table fread
 get_genomeLocFile <- function(build,
-                              storage_dir = tempdir(),
+                              storage_dir = tools::R_user_dir(
+                                  "MAGMA.Celltyping",
+                                  which="cache"),
                               overwrite = FALSE) {
     build <- toupper(build[1])
     dict <- c(GRCH36 = "NCBI36.3.gene.loc",
@@ -58,7 +62,7 @@ get_genomeLocFile <- function(build,
         overwrite = overwrite
     ) 
     #### Check that download was successful ####
-    d <- data.table::fread(tmp, nrows = 10)
+    d <- data.table::fread(tmp, nrows = 10, nThread = 1)
     if(nrow(d)!=10 || ncol(d)!=6){
         stopper("genomeLocFile did not download properly.",
                 "Please check that you have a stable internet connection, 
diff --git a/man/get_genomeLocFile.Rd b/man/get_genomeLocFile.Rd
index 4bf2d0f..694597c 100644
--- a/man/get_genomeLocFile.Rd
+++ b/man/get_genomeLocFile.Rd
@@ -30,7 +30,11 @@ for(x in names(local_files)){
 }
 }
 \usage{
-get_genomeLocFile(build, storage_dir = tempdir(), overwrite = FALSE)
+get_genomeLocFile(
+  build,
+  storage_dir = tools::R_user_dir("MAGMA.Celltyping", which = "cache"),
+  overwrite = FALSE
+)
 }
 \arguments{
 \item{build}{Genome build. Must be one of: