From cf5097df635217b1fc46c3b584cd35ad0a0ae823 Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Wed, 29 Nov 2023 17:38:54 +0100
Subject: [PATCH] fix: rm magrittr general import to avoid conflict with
 GenomicRanges::substract

---
 DESCRIPTION             | 2 +-
 NAMESPACE               | 2 +-
 R/fragsize.R            | 2 +-
 R/vmat_utils.R          | 1 -
 man/importPEBamFiles.Rd | 4 ++--
 vignettes/VplotR.Rmd    | 1 -
 6 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index ff3ca06..dc28947 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,6 @@ Description: The pattern of digestion and protection from DNA nucleases such
     over single or aggregated genomic loci of interest.
 URL: https://github.com/js2264/VplotR
 BugReports: https://github.com/js2264/VplotR/issues
-RoxygenNote: 7.1.1
 Depends:
     R (>= 4.0),
     GenomicRanges,
@@ -55,3 +54,4 @@ biocViews:
     ATACSeq, 
     Alignment
 License: GPL (>= 3)
+RoxygenNote: 7.2.3
diff --git a/NAMESPACE b/NAMESPACE
index 7a14c86..a6def14 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -30,11 +30,11 @@ import(RColorBrewer)
 import(Rsamtools)
 import(S4Vectors)
 import(ggplot2)
-import(magrittr)
 import(parallel)
 import(reshape2)
 importFrom(cowplot,plot_grid)
 importFrom(graphics,hist)
+importFrom(magrittr,`%>%`)
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(stats,qt)
diff --git a/R/fragsize.R b/R/fragsize.R
index 2582ed7..90ca38f 100644
--- a/R/fragsize.R
+++ b/R/fragsize.R
@@ -15,10 +15,10 @@
 #' fragment size distribution
 #' @return A list of tbl, one for each .bam file.
 #' 
-#' @import magrittr
 #' @import parallel
 #' @import IRanges
 #' @import GenomicRanges
+#' @importFrom magrittr `%>%`
 #' @importFrom zoo rollmean
 #' @importFrom methods is
 #' @importFrom graphics hist
diff --git a/R/vmat_utils.R b/R/vmat_utils.R
index 9301d62..ffa10b2 100644
--- a/R/vmat_utils.R
+++ b/R/vmat_utils.R
@@ -12,7 +12,6 @@
 #' @param ylims The y limits of the computed Vmat
 #' @return A table object
 #' 
-#' @import magrittr
 #' @import S4Vectors
 #' @import GenomicRanges
 #' @import IRanges
diff --git a/man/importPEBamFiles.Rd b/man/importPEBamFiles.Rd
index 1438c01..90eb844 100644
--- a/man/importPEBamFiles.Rd
+++ b/man/importPEBamFiles.Rd
@@ -18,8 +18,8 @@ importPEBamFiles(
 \item{files}{character vector, each element of the vector is the path 
 of an individual .bam file.}
 
-\item{genome}{character, genome ID (e.g. sacCer3, ce11, dm6, danRer10,
-mm10 or hg38).}
+\item{genome}{character, genome ID (e.g. "sacCer3", "ce11", "dm6", 
+"mm10" or "hg38").}
 
 \item{where}{GRanges, only import the fragments mapping to the 
 input GRanges (can fasten the import process a lot).}
diff --git a/vignettes/VplotR.Rmd b/vignettes/VplotR.Rmd
index bea47c0..38a39c7 100644
--- a/vignettes/VplotR.Rmd
+++ b/vignettes/VplotR.Rmd
@@ -17,7 +17,6 @@ knitr::opts_chunk$set(
 suppressPackageStartupMessages({
     library(GenomicRanges)
     library(ggplot2)
-    library(magrittr)
     library(VplotR)
 })
 ```