[Bioc-devel] questions about windows build execute permissions and R version dependency

Hi, I have a two questions about the bioconductor build and BiocCheck process when submitting packages. 1) My submitted package ('motifmatchr') returns the following warning on the Windows computer: Warning: file 'motifmatchr/cleanup' did not have execute permissions: corrected How can this

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 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] builds: veracruz2 Mac builder

Minor correction below: On 03/22/2017 12:56 PM, Obenchain, Valerie wrote: > Hi, > > We recently learned that R 3.4.0, to be released on April 21, will use > OS X 10.11 (El Capitan). This means we need a new devel Mac builder up > and running before the next release. toluca2 will also become an

[Bioc-devel] builds: veracruz2 Mac builder

Hi, We recently learned that R 3.4.0, to be released on April 21, will use OS X 10.11 (El Capitan). This means we need a new devel Mac builder up and running before the next release. toluca2 will also become an El Capitan builder but not until after the release. Over the past week, Herve has

[Bioc-devel] Annotation packages maintained by Francesco Ferrari

Hi, We have 24 annotation packages in the repo maintained by Francesco Ferrari, the majority of which are broken (output below). The last time these were updated was for Bioconductor 2.8 (3 years ago). We've tried a number of times to contact Francesco but did not get a response. The plan is 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 '$<-'

- Original Message - > From: "Hervé Pagès" > To: "Martin Morgan" , "lcollado" > , "bioc-devel" > > Cc: "Jeff Leek" , "Andrew Jaffe" > Sent:

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

This is very useful, thank you very much! I will stay tuned for any further advice on this. Thanks, Alina On 22 March 2017 at 16:53, Gabe Becker wrote: > Alina, > > Typically in cases like the one you describe, people want users to use the > paper citation when citing use

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 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 '$<-'

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] Citation of an accompanying paper

You can include both like I do in https://github.com/leekgroup/derfinderPlot/blob/master/inst/CITATION which is similar to what Xie's knitr does. On Wed, Mar 22, 2017 at 12:53 PM, Gabe Becker wrote: > Alina, > > Typically in cases like the one you describe, people want

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

Alina, Typically in cases like the one you describe, people want users to use the paper citation when citing use of the package. Whether this is what they "should" want is somewhat debatable, but at least it seems reasonable, as by using the package users are, assumedly, applying the method your

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

If you do not have a CITATION file, a citation is automatically generated. So yes, effectively it would overwrite. See details in R-exts. On Wed, Mar 22, 2017 at 6:30 AM, Alina Selega wrote: > Hi Monther, > > Thank you for your reply! > > Would that overwrite 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 '$<-'

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] Citation of an accompanying paper

Hi Monther, Thank you for your reply! Would that overwrite the package citation that currently shows up on the page though? My paper doesn't cite the Bioconductor package (as it was accepted before I had a valid link to include), it just refers to the same name of the computational method. Is

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

> 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 '$<-'

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] segfault in csaw native code

Thanks Ryan. I've determined the issue - a rather embarrassing one, actually, where the C array wasn't of the right length - I'm not quite sure why it didn't show up earlier. Anyway, patches have been committed to release and devel. Cheers, Aaron On 22/03/17 01:14, Ryan Thompson wrote: > Hi

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

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