Incompatibility with the latest GenomicRanges

[lutsik]

Hi,

Thanks for a great set of tools!

There seems to be a problem with disjoinGR and one of the recent GenomicRanges versions. The error and its package-relevant traceback are the following:

Error during wrapup: when 'type' is "any", at least one of 'maxgap' and 'minoverlap' must be set to its default value
....
5: privateUtil.R#102: disjoinGRs(dat)
6: privateUtil.R#88: findOverlaps(.gr, gr, maxgap = 0, minoverlap = 1)
7: findOverlaps(.gr, gr, maxgap = 0, minoverlap = 1)
8: .local(query, subject, maxgap, minoverlap, type, select, ...)
9: findOverlaps_GNCList(query, subject, maxgap = maxgap, minoverlap = minoverl
10: IRanges:::NCList_find_overlaps_in_groups(ranges(query), q_space, q_groups,
11: .Call2("NCList_find_overlaps_in_groups", start(q), end(q), q_space, q_group

Seems to happen with a deliberate GRanges object.

I have just installed the latest source from the master branch, GenomicRanges are 1.30.3, and R is 3.4.3 (2017-11-30).

Best regards,

Pavlo

[mskilab]

Hi Pavlo - I think this is directed to trackViewer package? disjoinGR is not a gUtils function? Best Marcin

…

On Thu, Apr 26, 2018 at 6:55 AM, Pavlo Lutsik ***@***.***> wrote: Hi, Thanks for a great set of tools! There seems to be a problem with disjoinGR and one of the recent GenomicRanges versions. The error and its package-relevant traceback are the following: Error during wrapup: when 'type' is "any", at least one of 'maxgap' and 'minoverlap' must be set to its default value .... 5: privateUtil.R#102: disjoinGRs(dat) 6: privateUtil.R#88: findOverlaps(.gr, gr, maxgap = 0, minoverlap = 1) 7: findOverlaps(.gr, gr, maxgap = 0, minoverlap = 1) 8: .local(query, subject, maxgap, minoverlap, type, select, ...) 9: findOverlaps_GNCList(query, subject, maxgap = maxgap, minoverlap = minoverl 10: IRanges:::NCList_find_overlaps_in_groups(ranges(query), q_space, q_groups, 11: .Call2("NCList_find_overlaps_in_groups", start(q), end(q), q_space, q_group Seems to happen with a deliberate GRanges object. I have just installed the latest source from the master branch, GenomicRanges are 1.30.3, and R is 3.4.3 (2017-11-30). Best regards, Pavlo — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AL-0kXNn_CfUamohknr8jFeiyRIvKtYxks5tsaeagaJpZM4Tk890> .