These issues were caused by changes in the S4Vectors, IRanges, and
GenomicRanges packages that happened over the last 3 months.
... | ... |
@@ -210,7 +210,7 @@ setMethod("[", "SplicingGraphs", |
210 | 210 |
seqx <- seq_along(x_genes) |
211 | 211 |
names(seqx) <- names(x_genes) |
212 | 212 |
i <- seqx[i] |
213 |
- ii <- unlist(IRanges(PartitioningByEnd(x_genes))[i], use.names=FALSE) |
|
213 |
+ ii <- IRanges:::unlist_as_integer(IRanges(PartitioningByEnd(x_genes))[i]) |
|
214 | 214 |
x@genes <- x_genes[i] |
215 | 215 |
x@in_by_tx <- x@in_by_tx[ii] |
216 | 216 |
x |
... | ... |
@@ -501,6 +501,7 @@ setMethod("show", "SplicingGraphs", |
501 | 501 |
{ |
502 | 502 |
if (!is(x, "GRangesList")) |
503 | 503 |
stop("'x' must be a GRangesList object") |
504 |
+ metadata(x) <- list() |
|
504 | 505 |
if (is.null(grouping)) { |
505 | 506 |
if (!identical(min.ntx, 2) || !identical(max.ntx, NA)) |
506 | 507 |
stop("the 'min.ntx' and 'max.ntx' args are not supported ", |