Merge pull request #103 from kbroman/master

Fix zip_datafiles() re subdirectories

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qtl2
-Version: 0.18
-Date: 2019-02-08
+Version: 0.19-1
+Date: 2019-02-16
 Title: Quantitative Trait Locus Mapping in Experimental Crosses
 Description: R/qtl2 provides a set of tools to perform quantitative
     trait locus (QTL) analysis in experimental crosses. It is a

NEWS.md

@@ -1,3 +1,11 @@
+## qtl2 0.19-1 (2019-02-16)
+
+### Bug fixes
+
+- Fix bug in `zip_datafiles()` when the files are in a subdirectory.
+  (See [Issue #102](https://github.com/rqtl/qtl2/issues/102).)
+
+
 ## qtl2 0.18 (2019-02-08)
 
 ### New features

R/zip_datafiles.R

@@ -47,8 +47,11 @@ function(control_file, zip_file=NULL, overwrite=FALSE, quiet=TRUE)
 
     dir <- dirname(control_file)
 
-    if(is.null(zip_file))
-        zip_file <- sub("\\.[a-z]+$", ".zip", control_file)
+    move_zip_file <- TRUE
+    if(is.null(zip_file)) {
+        zip_file <- sub("\\.[a-z]+$", ".zip", basename(control_file))
+        move_zip_file <- FALSE
+    }
 
     # read control file
     control <-  read_control_file(control_file)
@@ -96,7 +99,13 @@ function(control_file, zip_file=NULL, overwrite=FALSE, quiet=TRUE)
     }
 
     # do the zipping
-    utils::zip(zip_file, files, flags=zip_flags)
+    utils::zip(basename(zip_file), files, flags=zip_flags)
+
+    # if not being zipped into the data file directory, move it
+    if(move_zip_file) {
+        setwd(cwd)
+        file.rename(file.path(dir, basename(zip_file)), zip_file)
+    }
 
     invisible(zip_file)
 }