Thanks very much, Hervé, I indeed never noticed the wrong number of elements in my objects.
Best regards, Oleksii On Tue, 6 Apr 2021 at 02:10, Hervé Pagès <hpages.on.git...@gmail.com> wrote: > This is fixed in S4Vectors 0.29.13: > > https://github.com/Bioconductor/S4Vectors/commit/6d79932910af9618465d5f932df5864d0a270e11 > > This new version of S4Vectors should propagate to the build machines and > become available via BiocManager::install() in the next 48h or so. > > Cheers, > H. > > On 4/5/21 3:40 PM, Hervé Pagès wrote: > > Hi Oleksii, > > > > It looks like we have a long-standing bug in the rbind() method for > > DataFrame objects that is somehow surfacing now. Here is a simple > example: > > > > library(IRanges) > > DF1 <- DataFrame(A=I(list(11:12, 21:23))) > > DF2 <- DataFrame(A=IntegerList(31:34, 41:45, 51:56)) > > DF3 <- rbind(DF1, DF2) > > DF3 > > # DataFrame with 3 rows and 1 column > > # A > > # <list> > > # 1 11,12 > > # 2 21,22,23 > > # 3 31,32,33,...,41,42,43,...,51,52,53,... > > > > This result is wrong. We observe this in release and devel. > > > > If you look at the mcols of the GRanges object returned by getAMR() in > > your code below, you'll see that it's actually an invalid DataFrame > > object (its first column has 23 elements but 22 are expected). This is a > > consequence of the above bug. Even though the bug has existed for a long > > time, somehow it was not affecting your code. However this changed > > recently because of some minor refactoring of the rbind() method for > > DataFrame objects that I made a few days ago in S4Vectors. > > > > I'm working on a fix and will let you know when it's ready. > > > > Cheers, > > H. > > > > > > On 4/5/21 1:12 PM, Oleksii Nikolaienko wrote: > >> Dear Bioc team, > >> my package has started to fail during the build check ( > >> http://bioconductor.org/checkResults/devel/bioc-LATEST/ramr/). I tried > to > >> figure out why and it appears that I somehow make GRanges object > >> non-subsettable. Could anyone from "GenomicRanges" developers look at my > >> issue and advise me on a solution, please? > >> > >> To reproduce: > >> > >> library(ramr) > >> data(ramr) > >> amrs <- getAMR(ramr.data, ramr.samples, ramr.method="beta", min.cpgs=5, > >> merge.window=1000, qval.cutoff=1e-3, cores=2) > >> # this works: > >> class(amrs) > >> amrs > >> # error: > >> amrs[2] > >> # suddenly works again: > >> GRangesList(amrs)[[1]][2] > >> > >> > >> Best regards, > >> Oleksii > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> > > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel