Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix rdevel build #310

Merged
merged 2 commits into from
Jan 17, 2024
Merged

Fix rdevel build #310

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ed0b089
check for empty elements using is.null instead of isEmpty
alexg9010 Jan 16, 2024
79e7705
drop isEmpty from Namespace
alexg9010 Jan 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 0 additions & 1 deletion NAMESPACE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,6 @@ importFrom(S4Vectors,"elementMetadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,elementMetadata)
importFrom(S4Vectors,isEmpty)
importFrom(S4Vectors,levels)
importFrom(S4Vectors,subjectHits)
importFrom(data.table,":=")
Expand Down
5 changes: 2 additions & 3 deletions R/tabix.functions.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -297,7 +297,6 @@ checkTabixHeader <- function(tbxFile,message=NULL) {
#' @param slotList list of slot items with respective values
#' @noRd
#'
#' @importFrom S4Vectors isEmpty
makeTabixHeader <- function(slotList) {
# first we query each slots and ...
tabixHead <- sapply(names(slotList),
Expand All @@ -311,7 +310,7 @@ makeTabixHeader <- function(slotList) {
}
)
# then we remove slots we don't need in the header (as the @.Data slot)
tabixHead <- tabixHead[!S4Vectors::isEmpty(tabixHead)]
tabixHead <- tabixHead[!is.null(tabixHead)]

return(tabixHead)

Expand Down Expand Up @@ -388,7 +387,7 @@ readTabixHeader <- function(tbxFile) {
}
)

headerVals <- headerVals[!isEmpty(headerVals)]
headerVals <- headerVals[!is.null(headerVals)]

# parse the object class
class <- unlist(sapply((strsplit(gsub("#", "", h),split = ":")), function(x) if(x[1]=="Class") return(x[2])))
Expand Down