Re: [Bioc-devel] tximport fails to build on Windows

Hi Mike, Here is a more informative error from Stangling and sourcing the vignette on the Windows builder: ... reading in files with read_tsv 1 Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : cannot open file

[Bioc-devel] segfault in csaw native code

Hi Aaron, I'm making a ChIP-Seq analyisis pipeline using csaw, and I'm running into an inconsistent error/segfault. I've reduced it to a test case which you can find here: https://www.dropbox.com/sh/2a2vpb5ek4413fx/AAAXwCaTzsAmfyPefwAbFg8Na?dl=0 The test case consists of my R workspace saved

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

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 '$<-'

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

Re: [Bioc-devel] Citation of an accompanying paper

Hi Alina, I think you need to add a file named CITATION in your package (usually under the inst folder) and use bibentry as follows bibentry(bibtype = "Article", title = "Combining multiple tools outperforms individual methods in gene set enrichment analyses", author =

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

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

Re: [Bioc-devel] Package not being built on Windows or Mac

Thank you all for the explanations, and the assurance that Windows and Mac users should still be able to install it. Robert On Tue, Mar 21, 2017, 2:56 AM Hervé Pagès wrote: > On 03/20/2017 02:31 PM, Dan Tenenbaum wrote: > > As I recall, there were issues building

Re: [Bioc-devel] developing R package for new release

Thanks for taking the time to reply, James. I was confused by the fact that R 3.3.3 was released a few weeks ago and I was thinking that was previously the R-devel… meaning the R version you’re supposed to develop against would have just changed a few weeks ago. I re-read the sentence “R has

Re: [Bioc-devel] Package not being built on Windows or Mac

On 03/20/2017 02:31 PM, Dan Tenenbaum wrote: As I recall, there were issues building RCytoscape (and packages that depend on it) on Mac and Windows. Mostly because this requires a running instance of Cytoscape for each platform (and double that for release + devel). That used too much