Re: [Bioc-devel] Suggested edits to support site posting guide

hi Leo, We currently have "Rudeness and ad hominem comments are not acceptable" in the section on replying. This is nice and simple. I think most of the people reading the guide will be first time question-askers, but I'm glad we have the above bulletpoint so we can say someone was breaking the

Re: [Bioc-devel] push access to adaptest

i approve On Mon, Apr 30, 2018 at 11:13 AM Nima Hejazi wrote: > Hello BioC team --- > > Wilson Cai (cc'd) and I are co-developers / co-authors of the adaptest > package that has joined the > Bioconductor ecosystem as of 3.7. I

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Interesting. I tried something like that in the past i.e. start with a unary setClassUnion() but then got into problems when I tried to add new members to the union by **extending** the union class: https://stat.ethz.ch/pipermail/r-devel/2016-March/072489.html So it seems like I should have

Re: [Bioc-devel] Error: node stack overflow

Excellent! Are you planning to commit this to the 3.5 branch too? In that case we'll wait a couple more days before installing R 3.5 patched on the build machines for the BioC 3.8 builds. Thanks, H. On 04/30/2018 01:43 PM, Michael Lawrence wrote: It's checked into devel now. Thanks for the

Re: [Bioc-devel] Error: node stack overflow

I just pushed it to the 3.5 branch. On Mon, Apr 30, 2018 at 2:14 PM, Hervé Pagès wrote: > Excellent! Are you planning to commit this to the 3.5 branch too? > In that case we'll wait a couple more days before installing R 3.5 > patched on the build machines for the BioC 3.8

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

It would be great to be able to define a matrix-like abstraction independent of 'matrix' and 'DelayedMatrix'. It could also encompass objects from the Matrix package and potentially other things. So you could define a parent class of 'matrix' using setClassUnion() and then use setIs() to establish

Re: [Bioc-devel] Error: node stack overflow

It's checked into devel now. Thanks for the well documented examples, Hervé. On Mon, Apr 30, 2018 at 10:26 AM, Michael Lawrence wrote: > I've fixed it and will push to R-devel as soon as it passes checks. > > Michael > > On Sun, Apr 29, 2018 at 9:04 PM, Michael Lawrence

Re: [Bioc-devel] Error: node stack overflow

Great, thanks! I was curious and did: hpages@spectre:~/svn/R/R-3-5-branch$ svn diff -r 74669:74674 src/library/methods/R/methodsTable.R Index: src/library/methods/R/methodsTable.R === --- src/library/methods/R/methodsTable.R

Re: [Bioc-devel] Need some help to submit a R package.

Dear Sir, Please inform me the current status of the package named "sigFeature". The package link is given below. https://github.com/Bioconductor/Contributions/issues/713 Thank you regards Pijush On Fri, Apr 27, 2018 at 7:00 PM, Pijush Das wrote: > > Now it is

[Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Hello, I am trying to extend my package to handle `HDF5Matrix` class ( or more generally `DelayedArray`). I currently have S4 functions for `matrix` class. Usually I have a method for `SummarizedExperiment`, which will call call the method on `assay(x)` and I want the method to be able to deal

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Don't do that. Seriously, just don't. https://github.com/Bioconductor/DelayedArray/issues/16 --t On Mon, Apr 30, 2018 at 10:02 AM, Elizabeth Purdom < epur...@stat.berkeley.edu> wrote: > Hello, > > I am trying to extend my package to handle `HDF5Matrix` class ( or more > generally

[Bioc-devel] Last minute error in the build

Hi, I am the author of *scmeth* package that was submitted during this cycle. I know that there will be a new bioconductor release tomorrow. My package has been passing all the builds until April 27th which is past April 25th, the deadline to pass R CMD check and R CMD build. Now I see errors

Re: [Bioc-devel] Last minute error in the build

The package will have a release version. The branches are frozen now to proceed with the release branching. If the ERROR persists this just means you will have to update your fix on the RELEASE_3_7 branch and the devel (master) branch. There will be an email notification when pushes can

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

But that issue will be fixed, so Tim's advice is inappropriate. On 04/30/2018 10:42 AM, Tim Triche, Jr. wrote: Don't do that. Seriously, just don't. https://github.com/Bioconductor/DelayedArray/issues/16 --t On Mon, Apr 30, 2018 at 10:02 AM, Elizabeth Purdom < epur...@stat.berkeley.edu>

[Bioc-devel] push access to adaptest

Hello BioC team --- Wilson Cai (cc'd) and I are co-developers / co-authors of the adaptest package that has joined the Bioconductor ecosystem as of 3.7. I would like to request push access to this repository on the git server to ensure that we're able

Re: [Bioc-devel] Bioconductor 3.7 release: 3.7 branch created

Awesome! Congrats and thanks to everyone involved in the new release! Best, Leo On Mon, Apr 30, 2018 at 12:49 PM, Obenchain, Valerie wrote: > > The Bioconductor 3.7 branch is now ready. If all goes well over the next 24 > hours we'll announce the official

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

The class union should probably be: setClassUnion("matrixOrDelayed", c("matrix", "DelayedMatrix")) i.e. use DelayedMatrix instead of DelayedArray. So in addition to the class union and to Stephanie's solution, which IMO are both valid solutions, you could also go for something like this:

[Bioc-devel] The following bioconductor packages have duplicate commits

Hi Maintainers, We just concluded the bump in the RELEASE_3_7 branch and master. But, the following packages have a history of duplicate commits and we are leaving it up to the maintainers to fix these duplicate commits. There were 12 software packages that had duplicate commits. Please fix

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Just to mention that the issue with rowSums() on a big DelayedMatrix objects that you are referring to Tim is duly noted and will be one of my first priorities once we're done with the release process. Cheers, H. On 04/30/2018 09:57 AM, Tim Triche, Jr. wrote: much obliged -- and the packages

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Tim: As the developer of DelayedMatrixStats (and enthusiastic 'canary down the coal mine' user-dev of DelayedArray) I'm obviously invested in reducing the confusion around these packages I'm going to write some blog posts-cum-vignettes-cum-F1000 around these issues over the coming weeks, with the

[Bioc-devel] Bioconductor 3.7 release: 3.7 branch created

The Bioconductor 3.7 branch is now ready. If all goes well over the next 24 hours we'll announce the official release tomorrow. You have access to 2 versions of your package in git: the "release" and "devel" versions. The �release� branch is for bug fixes and documentation improvements only. The

Re: [Bioc-devel] Last minute error in the build

Hi Divy, I will take care of this. You don't need to do anything. Cheers, H. On 04/30/2018 07:16 AM, Kangeyan, Divy wrote: Hi, I am the author of *scmeth* package that was submitted during this cycle. I know that there will be a new bioconductor release tomorrow. My package has been

Re: [Bioc-devel] Error: node stack overflow

I've fixed it and will push to R-devel as soon as it passes checks. Michael On Sun, Apr 29, 2018 at 9:04 PM, Michael Lawrence wrote: > Just noticed this thread. I will look into this and hopefully fix it. > > On Sun, Apr 29, 2018 at 6:12 PM, Hervé Pagès

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

Rather than a class union, how about an internal function that is called by the methods for both matrix and DelayedArray: setGeneric("myNewRowMeans", function(x,...) { standardGeneric("myNewRowMeans")}) #' @importFrom DelayedArray rowMeans .myNewRowMeans <- function(x,...){ # a lot of

Re: [Bioc-devel] Last minute error in the build

Done: https://github.com/Bioconductor/HDF5Array/commit/c525570bc927274c37d9f267a2cf194d8e545d91 I also applied the fix to the new RELEASE_3_7 branch of HDF5Array. If you install the latest version of HDF5Array (1.8.0 in the RELEASE_3_7 branch and 1.9.0 in master), that should clear the error

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

But if you merge methods like that, the error method can be that much more difficult to identify. It took a couple of weeks to chase that bug down properly, and it ended up down to rowMeans2 vs rowMeans. I suppose the merged/abstracted method allows to centralize any such dispatch into one place

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

much obliged -- and the packages are terrific, I am not surprised that a big step is accompanied with some growing pains. Thanks to you and Herve and Keegan for enthusiastically chasing down, and spending your time fixing, this and other bugs. Having fiddled with bigMemory and bigMatrix backends

Re: [Bioc-devel] Suggested edits to support site posting guide

Hi Mike, Lori and everyone else, I recently saw this tweet https://twitter.com/aprilwensel/status/989248246878035972 that links to https://medium.com/compassionate-coding/its-time-to-retire-rtfm-31acdfef654f#---0-162 First, I'm curious if you've read it and if you like it. Second, maybe we

Re: [Bioc-devel] Suggested edits to support site posting guide

well, Hadley usually walks people through the steps required to 1) file a bug reproducibly or 2) learn how to do the thing in question organically, and his universe is doing OK, so N=1 in favor of that approach. Also a lot of people helped me learning Perl (!) on Usenet (!!!) so yeah I'm old but

[Bioc-devel] Bioconductor 3.7 release: stop pushes to master

Developers, Today we will create the Bioconductor 3.7 branch from 10am - 1pm EST (2pm - 5pm UTC). At 10am EST, we will block pushes to the master branch. Please stop all pushes to master before this time and do not resume until further notice. Another email will be sent when it is OK to resume