From f5b96cc273a01dae5861eda7fa8196bcd680eb1b Mon Sep 17 00:00:00 2001
From: Tomrrr1 <76951517+Tomrrr1@users.noreply.github.com>
Date: Mon, 4 Mar 2024 18:34:29 +0000
Subject: [PATCH] Testing gha

---
 .Rbuildignore                    | 1 +
 .github/workflows/rworkflows.yml | 2 +-
 NAMESPACE                        | 2 ++
 R/conservative_idr.R             | 2 +-
 R/optimal_idr.R                  | 2 +-
 man/conservative_idr.Rd          | 1 -
 man/optimal_idr.Rd               | 1 -
 7 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index e13c405..6b7eebb 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^\.DS_Store$
diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index 8af828e..f953821 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -21,7 +21,7 @@ jobs:
       fail-fast: ${{ false }}
       matrix:
         config:
-        - os: ubuntu-latest # not run on Windows because MACSr is not supported.
+        - os: ubuntu-latest
           bioc: devel
           r: auto
           cont: ghcr.io/bioconductor/bioconductor_docker:devel
diff --git a/NAMESPACE b/NAMESPACE
index b1b8906..9289362 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,12 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
 export(calculate_idr)
+export(conservative_idr)
 export(feature_counts_matrix)
 export(generate_pseudoreplicates)
 export(idr_analysis)
 export(macs_call_peak)
 export(multiple_replicates_chipr)
 export(multiple_replicates_mspc)
+export(optimal_idr)
 import(ChIPpeakAnno)
 import(GenomicAlignments)
 import(GenomicRanges)
diff --git a/R/conservative_idr.R b/R/conservative_idr.R
index ea0b953..2b59f2b 100644
--- a/R/conservative_idr.R
+++ b/R/conservative_idr.R
@@ -12,7 +12,7 @@
 #' @returns A list containing a summary of the IDR analysis along with the path
 #' to the output files.
 #'
-#' @keywords internal
+#' @export
 
 conservative_idr <- function(treat_files,
                              control_files = NULL,
diff --git a/R/optimal_idr.R b/R/optimal_idr.R
index 6a908af..6d1f006 100644
--- a/R/optimal_idr.R
+++ b/R/optimal_idr.R
@@ -12,7 +12,7 @@
 #'
 #' @returns Summary of the IDR output
 #'
-#' @keywords internal
+#' @export
 optimal_idr <- function(treat_files,
                         control_files = NULL,
                         is_paired,
diff --git a/man/conservative_idr.Rd b/man/conservative_idr.Rd
index 5e39479..65b9fa5 100644
--- a/man/conservative_idr.Rd
+++ b/man/conservative_idr.Rd
@@ -117,4 +117,3 @@ to the output files.
 \code{conservative_idr()} performs the conservative IDR analysis as defined
 by ENCODE. The function writes a filtered set of peaks to a desired location.
 }
-\keyword{internal}
diff --git a/man/optimal_idr.Rd b/man/optimal_idr.Rd
index 1cf2c37..11329a6 100644
--- a/man/optimal_idr.Rd
+++ b/man/optimal_idr.Rd
@@ -117,4 +117,3 @@ Summary of the IDR output
 biological replicate BAM files, shuffling reads, splitting into
 pseudoreplicates and calling peaks on the pseudoreplicates.
 }
-\keyword{internal}