diff --git a/.Rbuildignore b/.Rbuildignore index 112ad26..2407d3e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,6 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +^data-raw$ +^cran-comments\.md$ +^LICENSE\.md$ ^\.travis\.yml$ diff --git a/DESCRIPTION b/DESCRIPTION index d8fb70f..1d3cfcb 100644 --- a/DESCRIPTION +++ b/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 -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 = "igor.dolgalev@nyumc.org", 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 , Liberzon et al. 2015 + ) 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) diff --git a/LICENSE b/LICENSE index d456648..a46a21f 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,2 @@ YEAR: 2018 -COPYRIGHT HOLDER: Your name goes here +COPYRIGHT HOLDER: Igor Dolgalev diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..b442934 --- /dev/null +++ b/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. diff --git a/NAMESPACE b/NAMESPACE index 7b8774f..ab1f832 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,5 +1,6 @@ # Generated by roxygen2: do not edit by hand +export("%>%") export(msigdbr) export(msigdbr_show_species) import(dplyr) diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..9a22022 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,4 @@ +# msigdbr 6.1.1 + +* Based on MSigDB v6.1 release. +* Initial CRAN submission. diff --git a/R/functions.R b/R/functions.R index 74ad8ea..9ed8225 100644 --- a/R/functions.R +++ b/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 diff --git a/R/globals.R b/R/globals.R deleted file mode 100644 index 8d68b1e..0000000 --- a/R/globals.R +++ /dev/null @@ -1,5 +0,0 @@ -# fix R CMD Check notes (for CRAN compatibility) -# https://stackoverflow.com/q/9439256/265614 -# https://github.com/r-lib/devtools/issues/1714 -# https://community.rstudio.com/t/tidyeval-equivalent-of-mutate/1295 -utils::globalVariables(c(".", ".data")) diff --git a/R/utils-pipe.R b/R/utils-pipe.R new file mode 100644 index 0000000..9c17c65 --- /dev/null +++ b/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 diff --git a/man/pipe.Rd b/man/pipe.Rd new file mode 100644 index 0000000..b7daf6a --- /dev/null +++ b/man/pipe.Rd @@ -0,0 +1,12 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils-pipe.R +\name{\%>\%} +\alias{\%>\%} +\title{Pipe operator} +\usage{ +lhs \%>\% rhs +} +\description{ +See \code{magrittr::\link[magrittr]{\%>\%}} for details. +} +\keyword{internal}