cleanup

.Rbuildignore

@@ -1,3 +1,6 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^data-raw$
+^cran-comments\.md$
+^LICENSE\.md$
 ^\.travis\.yml$

DESCRIPTION

@@ -2,14 +2,16 @@ Package: msigdbr
 Type: Package
 Title: MSigDB for Multiple Organisms in a Tidy Data Format
 Version: 6.1.1
-Author: Who wrote it
-Maintainer: The package maintainer <[email protected]>
-Description: The msigdbr package provides The Molecular Signatures Database
-    (MSigDB) gene sets used with the Gene Set Enrichment Analysis (GSEA)
-    software for various frequently studied model organisms in an R-friendly
-    format.
+Authors@R: person("Igor", "Dolgalev", email = "[email protected]", role = c("aut", "cre"))
+Description: Provides the 'Molecular Signatures Database' (MSigDB) gene sets
+    used with the 'Gene Set Enrichment Analysis' (GSEA) software (Subramanian et
+    al. 2005 <doi:10.1073/pnas.0506580102>, Liberzon et al. 2015
+    <doi:10.1016/j.cels.2015.12.004>) for various frequently studied model
+    organisms in a standard R data frame with key-value pairs.
 License: MIT + file LICENSE
 Encoding: UTF-8
+URL: https://github.com/igordot/msigdbr
+BugReports: https://github.com/igordot/msigdbr/issues
 LazyData: true
 Depends:
     R (>= 3.2.0),
@@ -18,7 +20,8 @@ Depends:
 Imports:
     magrittr,
     rlang
-Suggests: testthat,
+Suggests:
+    testthat,
     knitr,
     rmarkdown
 Roxygen: list(markdown = TRUE)

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2018
-COPYRIGHT HOLDER: Your name goes here
+COPYRIGHT HOLDER: Igor Dolgalev

LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
 export(msigdbr)
 export(msigdbr_show_species)
 import(dplyr)

NEWS.md

@@ -0,0 +1,4 @@
+# msigdbr 6.1.1
+
+* Based on MSigDB v6.1 release.
+* Initial CRAN submission.

R/functions.R

@@ -2,8 +2,6 @@
 #' List the species available in msigdbr.
 #'
 #' @return a vector of possible species
-#' @importFrom magrittr %>%
-#' @importFrom rlang .data
 #' @import dplyr
 #' @export
 msigdbr_show_species <- function() {
@@ -19,8 +17,6 @@ msigdbr_show_species <- function() {
 #' @param subcategory sub-collection, such as CGP, MIR, BP, etc.
 #'
 #' @return a data frame of gene sets with one gene per row
-#' @importFrom magrittr %>%
-#' @importFrom rlang .data
 #' @import tibble
 #' @import dplyr
 #' @export

R/utils-pipe.R

@@ -0,0 +1,12 @@
+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @importFrom rlang .data
+#' @usage lhs \%>\% rhs
+NULL