I was able to construct a minimal example where it seems the bug originates from SummarizedExperiment:
library(SummarizedExperiment) se <- SummarizedExperiment(matrix(1:6,ncol=2)) rse <- as(se, "RangedSummarizedExperiment") rse[1:2,] # hangs On Mon, Feb 1, 2016 at 2:57 PM, Michael Love <michaelisaiahl...@gmail.com> wrote: > Thanks Stephen and Dan, sorry I haven't chased this down recently. > > I have access to a Mac and will look into it now. > > -Mike > > On Mon, Feb 1, 2016 at 1:45 PM, Dan Tenenbaum <dtene...@fredhutch.org> > wrote: > >> Actually, it does seem like there is a more complicated issue going on. I >> will investigate and report back here. >> >> Thanks, >> Dan >> >> >> ----- Original Message ----- >> > From: "Dan Tenenbaum" <dtene...@fredhutch.org> >> > To: "Hartley, Stephen (NIH/NHGRI) [F]" <stephen.hart...@nih.gov> >> > Cc: "bioc-devel" <bioc-devel@r-project.org> >> > Sent: Monday, February 1, 2016 10:11:54 AM >> > Subject: Re: [Bioc-devel] TIMEOUTs on Morelia >> >> > I think the morelia server was overloaded, so it was restarted >> yesterday around >> > 11PM Seattle time, so I hope we will see fewer TIMEOUTs in today's build >> > report. >> > Dan >> > >> > >> > ----- Original Message ----- >> >> From: "Hartley, Stephen (NIH/NHGRI) [F]" <stephen.hart...@nih.gov> >> >> To: "bioc-devel" <bioc-devel@r-project.org> >> >> Sent: Monday, February 1, 2016 10:06:11 AM >> >> Subject: [Bioc-devel] TIMEOUTs on Morelia >> > >> >> The current devel build for DESeq2 has status TIMEOUT on Morelia. This >> is odd >> >> since the package builder gives it 40 minutes to complete, and it >> finishes in >> >> less than 5 on zin2 and muscato2. >> >> >> >> A bunch of packages that depend on or suggest DESeq2 also timeout on >> Morelia: >> >> DiffBind, derfinder, DChIPRep, gage, phyloseq, rgsepd, systemPipeR, >> and TCC. >> >> All of them time out after 40 minutes, but take less than 10 minutes >> to build >> >> on zin2 and moscato2. >> >> >> >> So I guess the question is: is it DESeq2, or is something wrong with >> the Morelia >> >> server? I don't have an OSX-mavericks machine to test it all out on. >> >> >> >> Is there any way to get previous daily build reports, or are they >> deleted daily? >> >> >> >> -Steve >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> >> Bioc-devel@r-project.org mailing list >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >> > _______________________________________________ >> > Bioc-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
