changed master -> main branch in MUGAarrays and qtl2data

rqtl · Oct 13, 2021 · 21a1cbf · 21a1cbf
1 parent 3ec082f
commit 21a1cbf
Show file tree

Hide file tree

Showing 8 changed files with 9 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mmconvert
-Version: 0.2-3
-Date: 2021-10-12
+Version: 0.2-4
+Date: 2021-10-13
 Title: Mouse Map Converter
 Description: Function to convert mouse genome positions between the build 39 physical map and the Cox genetic map <doi:10.1534/genetics.109.105486>.
 Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-## mmconvert 0.2-3 (2021-10-12)
+## mmconvert 0.2-4 (2021-10-13)
 
 - Added a dataset with the MUGA array annotations for markers on the
   autosomes or X chromosome, with mouse build GRCm39 positions and

diff --git a/R/cross2_to_grcm39.R b/R/cross2_to_grcm39.R
@@ -24,7 +24,7 @@
 #' @examples
 #' \dontrun{
 #' file <- paste0("https://raw.githubusercontent.com/rqtl/",
-#'                "qtl2data/master/DOex/DOex.zip")
+#'                "qtl2data/main/DOex/DOex.zip")
 #' DOex <- read_cross2(file)
 #' DOex_rev <- cross2_to_grcm39(DOex)
 #' }

diff --git a/README.Rmd b/README.Rmd
@@ -90,7 +90,7 @@ the revised Cox genetic map.
 
 ```{r cross2_to_grcm39, eval=FALSE}
 file <- paste0("https://raw.githubusercontent.com/rqtl/",
-               "qtl2data/master/DOex/DOex.zip")
+               "qtl2data/main/DOex/DOex.zip")
 
 library(qtl2)
 DOex <- read_cross2(file)

diff --git a/README.md b/README.md
@@ -110,7 +110,7 @@ the revised Cox genetic map.
 
 ```r
 file <- paste0("https://raw.githubusercontent.com/rqtl/",
-               "qtl2data/master/DOex/DOex.zip")
+               "qtl2data/main/DOex/DOex.zip")
 
 library(qtl2)
 DOex <- read_cross2(file)

diff --git a/inst/scripts/grab_muga_array_annot.R b/inst/scripts/grab_muga_array_annot.R
@@ -4,7 +4,7 @@
 library(here)
 library(data.table)
 
-url <- "https://raw.githubusercontent.com/kbroman/MUGAarrays/master/UWisc/"
+url <- "https://raw.githubusercontent.com/kbroman/MUGAarrays/main/UWisc/"
 
 files <- c(gm="gm_uwisc_v2.csv",
            mm="mm_uwisc_v2.csv",

diff --git a/man/cross2_to_grcm39.Rd b/man/cross2_to_grcm39.Rd
diff --git a/tests/testthat/test-cross2_to_grcm39.R b/tests/testthat/test-cross2_to_grcm39.R
@@ -7,7 +7,7 @@ test_that("cross2_to_grcm39 works for DOex", {
     skip_if(isnt_karl(), "this test only run locally")
 
     file <- paste0("https://raw.githubusercontent.com/rqtl/",
-                   "qtl2data/master/DOex/DOex.zip")
+                   "qtl2data/main/DOex/DOex.zip")
     DOex <- read_cross2(file)
 
     DOex_rev <- cross2_to_grcm39(DOex)