Re: [Bioc-devel] TIMEOUTs on Morelia

​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 wrote: > Actually, it does seem like there is a more complicated issue going on. I > will

Re: [Rd] Wrong config check for __libc_stack_end

On Feb 1, 2016, at 12:32 PM, Martin Maechler wrote: >> Simon Urbanek >>on Mon, 1 Feb 2016 08:36:56 -0500 writes: > >> On Feb 1, 2016, at 4:16 AM, Martin Maechler >> wrote: > > [..]

Re: [Bioc-devel] TIMEOUTs on Morelia

I don't see an error, but on linux under valgrind and current R-devel / bioc packages and especially > packageVersion("S4Vectors") [1] '0.9.26' I see > rse[1:2,] # hangs ==23105== Invalid read of size 4 ==23105==at 0xD0B8D4D: int_bsearch (Rle_class.c:606) ==23105==by 0xD0B8C45:

Re: [Bioc-devel] TIMEOUTs on Morelia

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

[Bioc-devel] AnnotationHub server downtime - Friday, Feb 5, 12:00PM-4:00PM PST

We need to take down the AnnotationHub server for scheduled maintenance. This will take place on Friday, February 5th, from 12:00 Noon until 4:00PM Seattle time (PST). We hope the actual downtime will be much shorter. During this time, requests to the AnnotationHub server (from the

Re: [Bioc-devel] TIMEOUTs on Morelia

Hi all, The problem was in S4Vectors where I introduced a regression about 10 days ago. Thanks to Martin for spotting the bug for me. Should be fixed in S4Vectors 0.9.27. Sorry for the inconvenience, H. On 02/01/2016 01:02 PM, Morgan, Martin wrote: I don't see an error, but on linux under

Re: [R-pkg-devel] S3 length method behavior

Hi Nathan, Perhaps if you defined your "length" object as "nbm" (number of binary messages), it would not interfere with the default "length". Jim On Tue, Feb 2, 2016 at 12:46 AM, Georgi Boshnakov < georgi.boshna...@manchester.ac.uk> wrote: > Hi, > > >I have run into an issue while developing

Re: [Bioc-devel] TIMEOUTs on Morelia

Thanks for the quick fix! On Feb 1, 2016 6:36 PM, "Hervé Pagès" wrote: > Hi all, > > The problem was in S4Vectors where I introduced a regression about 10 > days ago. Thanks to Martin for spotting the bug for me. Should be fixed > in S4Vectors 0.9.27. > > Sorry for the

Re: [Rd] Best way for rgl's .onLoad to fail?

> "BH" == Bryan Hanson > on Sun, 31 Jan 2016 09:50:46 -0500 writes: BH> I think the 2nd option will be more palatable to BH> inexperienced users, but both do state the important BH> detail. Bryan >> On Jan 30, 2016, at 4:11 PM, Duncan Murdoch

Re: [Rd] Best way for rgl's .onLoad to fail?

On 01/02/2016 4:26 AM, Martin Maechler wrote: "BH" == Bryan Hanson on Sun, 31 Jan 2016 09:50:46 -0500 writes: BH> I think the 2nd option will be more palatable to BH> inexperienced users, but both do state the important BH> detail. Bryan >> On Jan

Re: [Rd] Wrong config check for __libc_stack_end

> Alba Pompeo > on Fri, 29 Jan 2016 08:23:26 -0200 writes: > Here is my log from 'make check' using an Intel i5 64-bit > processor - http://pastebin.com/raw/N6SYAuFX Here is > Isaac's log from 'make check' using an Intel Atom 32-bit > processor -

Re: [Rd] In plot.ts, las=1 applies to ylab with multiple series and not to axis labels

> Spencer Graves > on Sat, 30 Jan 2016 15:34:36 -0600 writes: > Hello: > In plot.ts, las=1 applies to ylab and not axis labels with > multiple series. The documented behavior is to have las=1 apply to axis > labels and not ylab. >

Re: [Rd] More problems with building R on a musl platform

> Alba Pompeo > on Mon, 1 Feb 2016 15:33:11 -0200 writes: > Here's what I did. > svn checkout https://svn.r-project.org/R/trunk/ > cd ./trunk > aclocal -I m4 && autoconf > tools/rsync-recommended > cd .. > mkdir build > cd build

Re: [Rd] Wrong config check for __libc_stack_end

On Feb 1, 2016, at 4:16 AM, Martin Maechler wrote: >> Alba Pompeo >>on Fri, 29 Jan 2016 08:23:26 -0200 writes: > >> Here is my log from 'make check' using an Intel i5 64-bit >> processor - http://pastebin.com/raw/N6SYAuFX Here is

Re: [Rd] Best way for rgl's .onLoad to fail?

If I recall it correctly, at least on Linux, rgl only needs X11 when rgl.useNULL(FALSE). Is that correct? If so, I would say dependency on X11 is optional and therefore you should be able to load the package even without X11. Or is it that it still requires X11 libs but not an X11 server? My

Re: [Rd] Wrong config check for __libc_stack_end

On Feb 1, 2016, at 9:56 AM, Alba Pompeo wrote: > @Simon. Here's what I did. > I checked out R revision 70059. > Ran export r_cv_libc_stack_end=no. (otherwise it would give that error > we talked about before) No, the whole point was to test this behavior. I see that the

Re: [Rd] More problems with building R on a musl platform

Here is tests/reg-tests-1c.Rout.fail - http://pastebin.com/raw/3QVDUBwT About the libm, I don't know which one R uses. musl has its on libm. http://git.musl-libc.org/cgit/musl/tree/src/math I think I also have openlibm installed, but I don't think that's used. Any more information I can give to

[Bioc-devel] seqlevelsStyle: EnsDb integration with UCSC based annotations

Dear All! Just wanted to let you know that I just pushed the last changes to the ensembldb package (version 1.3.14) that allow an easier integration with non-Ensembl based annotation. In detail, I’ve implemented the seqlevelsStyle and seqlevelsStyle<- method from the GenomeInfoDb and now it’s

Re: [Rd] In plot.ts, las=1 applies to ylab with multiple series and not to axis labels

> On Feb 1, 2016, at 2:55 AM, Martin Maechler > wrote: > >> Spencer Graves >>on Sat, 30 Jan 2016 15:34:36 -0600 writes: > >> Hello: >> In plot.ts, las=1 applies to ylab and not axis labels with >> multiple series. The

Re: [Bioc-devel] TIMEOUTs on Morelia

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" > To: "Hartley, Stephen (NIH/NHGRI) [F]" > Cc: "bioc-devel"

Re: [Rd] Wrong config check for __libc_stack_end

@Simon. Here's what I did. I checked out R revision 70059. Ran export r_cv_libc_stack_end=no. (otherwise it would give that error we talked about before) Ran ./configure --without-recommended-packages. (otherwise it would complain of not finding ./src/library/Recommended/MASS_*.tar.gz) Ran make.

[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,

Re: [Rd] Best way for rgl's .onLoad to fail?

On 01/02/2016 11:46 AM, Henrik Bengtsson wrote: If I recall it correctly, at least on Linux, rgl only needs X11 when rgl.useNULL(FALSE). Is that correct? If so, I would say dependency on X11 is optional and therefore you should be able to load the package even without X11. Or is it that it

Re: [Rd] Wrong config check for __libc_stack_end

But it looks like R is working. I found the R binary on build/bin/R I ran it and it works. Should I be worried about the make check log? @Isaac Dunham Can you please test this on your system too? Maybe R can be packaged soon? Ciao. On Mon, Feb 1, 2016 at 3:33 PM, Alba Pompeo