Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-30 Thread Michael Lawrence
Yea I will have to port the recent fixes. On Wed, Mar 29, 2017 at 11:32 PM, Hervé Pagès wrote: > On 03/27/2017 09:43 AM, Michael Lawrence wrote: >> >> I committed a fix into R trunk with a regression test. > > > Thanks Michael. Any chance you can port the fix to the 3.4

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-30 Thread Hervé Pagès
On 03/27/2017 09:43 AM, Michael Lawrence wrote: I committed a fix into R trunk with a regression test. Thanks Michael. Any chance you can port the fix to the 3.4 branch? H. On Mon, Mar 27, 2017 at 8:41 AM, Michael Lawrence wrote: My bad guys, I'll fix when I get to

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-27 Thread Michael Lawrence
I committed a fix into R trunk with a regression test. On Mon, Mar 27, 2017 at 8:41 AM, Michael Lawrence wrote: > My bad guys, I'll fix when I get to work. > > On Mon, Mar 27, 2017 at 3:59 AM, Martin Morgan > wrote: >> On 03/22/2017 01:12 PM,

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-27 Thread Michael Lawrence
My bad guys, I'll fix when I get to work. On Mon, Mar 27, 2017 at 3:59 AM, Martin Morgan wrote: > On 03/22/2017 01:12 PM, Hervé Pagès wrote: >> >> Hi Martin, >> >> On 03/22/2017 03:17 AM, Martin Maechler wrote: Andrzej Oleś

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-27 Thread Martin Morgan
On 03/22/2017 01:12 PM, Hervé Pagès wrote: Hi Martin, On 03/22/2017 03:17 AM, Martin Maechler wrote: Andrzej Oleś on Wed, 22 Mar 2017 10:29:57 +0100 writes: > Just for the record, on R-3.3.2 Herve's code fails with the following error: > Error in x[TRUE]

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Andrzej Oleś
On Wed, Mar 22, 2017 at 6:12 PM, Hervé Pagès wrote: > > setClass("A", representation(stuff="numeric")) > as.vector.A <- function (x, mode="any") x@stuff > a <- new("A", stuff=c(3.5, 0.1)) > x <- numeric(10) > x[3:4] <- a > > then the code is now valid and we still

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Dan Tenenbaum
- Original Message - > From: "Hervé Pagès" > To: "Martin Morgan" , "lcollado" > , "bioc-devel" > > Cc: "Jeff Leek" , "Andrew Jaffe" > Sent:

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Hervé Pagès
On 03/21/2017 05:28 PM, Martin Morgan wrote: On 03/21/2017 08:21 PM, Hervé Pagès wrote: Hi Leonardo, Thanks for hunting down and isolating that bug! I tried to simplify your code even more and was able to get a segfault with just: setClass("A", representation(stuff="numeric")) x <-

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Leonardo Collado Torres
Awesome, thanks everyone! I'm tempted to write a blog post about this whole story. Best, Leo On Wed, Mar 22, 2017 at 6:36 AM, Martin Morgan wrote: > On 03/22/2017 06:17 AM, Martin Maechler wrote: >>> >>> Andrzej Oleś >>> on

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Martin Morgan
On 03/22/2017 06:17 AM, Martin Maechler wrote: Andrzej Oleś on Wed, 22 Mar 2017 10:29:57 +0100 writes: > Just for the record, on R-3.3.2 Herve's code fails with the following error: > Error in x[TRUE] <- new("A") : > incompatible types (from S4 to

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Martin Maechler
> Andrzej Oleś > on Wed, 22 Mar 2017 10:29:57 +0100 writes: > Just for the record, on R-3.3.2 Herve's code fails with the following error: > Error in x[TRUE] <- new("A") : > incompatible types (from S4 to logical) in subassignment type fix yes,

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Andrzej Oleś
On Wed, Mar 22, 2017 at 10:29 AM, Andrzej Oleś wrote: > Just for the record, on R-3.3.2 Herve's code fails with the following > error: > > Error in x[TRUE] <- new("A") : > incompatible types (from S4 to logical) in subassignment type fix > Quick update: I also get the

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-22 Thread Andrzej Oleś
Just for the record, on R-3.3.2 Herve's code fails with the following error: Error in x[TRUE] <- new("A") : incompatible types (from S4 to logical) in subassignment type fix Cheers, Andrzej On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-21 Thread Martin Morgan
On 03/21/2017 08:21 PM, Hervé Pagès wrote: Hi Leonardo, Thanks for hunting down and isolating that bug! I tried to simplify your code even more and was able to get a segfault with just: setClass("A", representation(stuff="numeric")) x <- logical(10) x[TRUE] <- new("A") I get the

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-21 Thread Hervé Pagès
Hi Leonardo, Thanks for hunting down and isolating that bug! I tried to simplify your code even more and was able to get a segfault with just: setClass("A", representation(stuff="numeric")) x <- logical(10) x[TRUE] <- new("A") I get the segfault about 50% of the time on a fresh R session

[Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-21 Thread Leonardo Collado Torres
Hi bioc-devel, This is a story about a bug that took me a long time to trace. The behaviour was really weird, so I'm sharing the story in case this helps others in the future. I was originally writing it to request help, but then I was able to find the issue ^^. The story ends right now with code