CRAN release 2.0.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rliger
 Version: 2.0.1
-Date: 2024-03-24
+Date: 2024-04-04
 Type: Package
 Title: Linked Inference of Genomic Experimental Relationships
 Description: Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.
@@ -37,7 +37,7 @@ LazyData: true
 RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Encoding: UTF-8
-Additional_repositories: https:/welch-lab.r-universe.dev, https://blaserlab.r-universe.dev
+Additional_repositories: https://welch-lab.r-universe.dev, https://blaserlab.r-universe.dev
 LinkingTo: Rcpp, RcppArmadillo, RcppProgress
 Depends:
     methods,

NAMESPACE

@@ -52,6 +52,7 @@ S3method(writeH5,default)
 S3method(writeH5,dgCMatrix)
 S3method(writeH5,liger)
 S3method(writeH5,ligerDataset)
+export("%<>%")
 export("%>%")
 export("cellMeta<-")
 export("coordinate<-")
@@ -266,6 +267,7 @@ importFrom(Matrix,summary)
 importFrom(Matrix,t)
 importFrom(Rcpp,evalCpp)
 importFrom(ggplot2,fortify)
+importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
 importFrom(methods,new)
 importFrom(methods,show)

NEWS.md

@@ -17,7 +17,7 @@
 
 - Fixed wrong UINMF aborting criteria
 - Fixed example/test skipping criteria for non-existing dependencies
-- Fixed file access issue when checking package on CRAN
+- Fixed file access issue when checking on CRAN
 - Updated installed data file `system.file("extdata/ctrl.h5", "extdata/stim.h5")` to be of standard 10X H5 format
 - Updated `quantileNorm()` automatic reference selection according to #297
 - Other minor fixes (including #308)

R/aaa.R

@@ -10,6 +10,10 @@ NULL
 #' @export
 magrittr::`%>%`
 
+#' @importFrom magrittr %<>%
+#' @export
+magrittr::`%<>%`
+
 scPalette <- c('#E41A1C', '#377EB8', '#4DAF4A', '#FFCF00', '#aa47b9', '#e67c14',
                '#e7a2b4', '#54B0E4', '#9a5831', '#BC9DCC', '#222F75', '#1B9E77',
                '#B2DF8A', '#E3BE00', '#FF6699', '#8f3c4d', '#01e1e6', '#591cc5',

R/import.R

@@ -445,7 +445,7 @@ createH5LigerDataset <- function(
 #' # Save and read regular current-version liger object
 #' tempPath <- tempfile(fileext = ".rds")
 #' saveRDS(pbmc, tempPath)
-#' pbmc <- readLiger(tempPath)
+#' pbmc <- readLiger(tempPath, dimredName = NULL)
 #'
 #' # Save and read H5-based liger object
 #' h5Path <- system.file("extdata/ctrl.h5", package = "rliger")