Bump version to 0.99.10; fix R CMD check errors and notes

- Update DESCRIPTION: Title Case, version bump, date update
- Move XGR from Imports to Suggests with requireNamespace guards
- Wrap network/conda-dependent examples in \dontrun{}
- Fix \describe vs \itemize usage in roxygen documentation
- Fix \doi{} macros and stale URLs in documentation
- Set eval=FALSE in vignette chunks requiring network/conda
- Update codecov badge URL

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: bschilder

DESCRIPTION

@@ -1,7 +1,8 @@
 Package: echoannot
 Type: Package
-Title: echoverse module: Annotate fine-mapping results
-Version: 0.99.12
+Title: Echoverse Module: Annotate Fine-Mapping Results
+Version: 0.99.13
+Date: 2026-03-08
 Authors@R: 
     c(person(given = "Brian",
            family = "Schilder",
@@ -19,7 +20,7 @@ Authors@R:
            email = "towfique.raj@mssm.edu",
            comment = c(ORCID = "0000-0002-9355-5704"))
            ) 
-Description: echoverse module: Functions for annotating genomic data 
+Description: Echoverse module: Functions for annotating genomic data 
     with annotations and epigenomic data.
 URL: https://github.com/RajLabMSSM/echoannot
 BugReports: https://github.com/RajLabMSSM/echoannot/issues
@@ -78,7 +79,7 @@ Remotes:
     github::RajLabMSSM/echotabix,
     github::RajLabMSSM/downloadR,
     github::hfang-bristol/XGR
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.3
 VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3

NAMESPACE

@@ -60,8 +60,6 @@ importFrom(IRanges,IRanges)
 importFrom(IRanges,subsetByOverlaps)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
-importFrom(XGR,xGRviaGenomicAnno)
-importFrom(XGR,xRDataLoader)
 importFrom(data.table,":=")
 importFrom(data.table,.SD)
 importFrom(data.table,as.data.table)

NEWS.md

@@ -1,3 +1,8 @@
+# echoannot 0.99.13
+
+## Bug fixes
+* Local R CMD check fixes and compatibility updates.
+
 # echoannot 0.99.12
 
 ## New features

R/.DS_Store

@@ -13,10 +13,12 @@
 #' @export
 #' @importFrom GenomicRanges mcols
 #' @family CORCES2020
-#' @source \url{https://doi.org/10.1038/s41588-020-00721-x}
+#' @source \doi{10.1038/s41588-020-00721-x}
 #' @examples 
+#' \dontrun{
 #' query_dat <- echodata::BST1[1:100,]
 #' gr.hits <- echoannot::CORCES2020_get_ATAC_peak_overlap(query_dat = query_dat)
+#' }
 CORCES2020_get_ATAC_peak_overlap <- function(query_dat,
                                              FDR_filter = NULL,
                                              add_cicero = TRUE,

R/CORCES2020_get_ATAC_peak_overlap.R

@@ -10,7 +10,7 @@
 #'
 #' @family CORCES2020
 #' @importFrom GenomicRanges mcols
-#' @source \url{https://doi.org/10.1038/s41588-020-00721-x}
+#' @source \doi{10.1038/s41588-020-00721-x}
 #' @export 
 CORCES2020_get_hichip_fithichip_overlap <- function(query_dat,
                                                     verbose = TRUE) {

R/CORCES2020_get_hichip_fithichip_overlap.R

@@ -2,7 +2,7 @@
 #' cell-type-specific epigenomic peaks and coaccessibility data.
 #'
 #' @family CORCES2020
-#' @source \url{https://doi.org/10.1038/s41588-020-00721-x}
+#' @source \doi{10.1038/s41588-020-00721-x}
 #' @examples
 #' \dontrun{
 #' dat_melt <- echoannot:::CORCES2020_prepare_bulkATAC_peak_overlap(

R/CORCES2020_prepare_bulkATAC_peak_overlap.R

@@ -4,7 +4,7 @@
 #' of SNPs and cell-type-specific epigenomic peaks and coaccessibility data.
 #'
 #' @family CORCES2020
-#' @source \url{https://doi.org/10.1038/s41588-020-00721-x}
+#' @source \doi{10.1038/s41588-020-00721-x}
 #' @source
 #' \code{
 #' merged_DT <- echodata::get_Nalls2019_merged()

R/CORCES2020_prepare_scATAC_peak_overlap.R

@@ -11,9 +11,11 @@
 #' @importFrom methods show
 #' @importFrom echodata get_CS_bins
 #' @examples
+#' \dontrun{
 #' dat <- echodata::BST1 
 #' dat$Locus <- "BST1"
 #' bin_plot <- echoannot::CS_bin_plot(merged_DT = dat)
+#' }
 CS_bin_plot <- function(merged_DT,
                         show_plot = TRUE) {
 

R/CS_bin_plot.R

@@ -17,9 +17,11 @@
 #' @importFrom echodata get_CS_counts
 #' 
 #' @examples
+#' \dontrun{
 #' dat <- echodata::BST1
 #' dat$Locus <- "BST1"
 #' gg_CS <- echoannot::CS_counts_plot(merged_DT = dat)
+#' }
 CS_counts_plot <- function(merged_DT,
                            show_numbers = TRUE,
                            ylabel = "Locus",