Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

Hi Johannes, Thanks for contacting the developers of the packages affected by this change. FWIW Pbase is also affected (didn't see it in your list): https://bioconductor.org/checkResults/3.5/bioc-LATEST/Pbase/malbec2-buildsrc.html H. On 04/06/2017 01:07 PM, Rainer Johannes wrote: @Florian:

Re: [Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

Hi Maarten, Vince, We need to fix this. The plan is to promote rowRanges to an S4 generic in the DelayedArray package (DelayedArray depends on matrixStats). And to remove the rowRanges S4 generic defined in SummarizedExperiment (SummarizedExperiment depends on DelayedArray). So we'll have only 1

Re: [Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

I'm curious as to why you are looping over the views in the first place. Maybe we could arrive at a vectorized solution, which is often but not always simpler and faster. Michael On Wed, Apr 5, 2017 at 8:13 PM, Pariksheet Nanda wrote: > Hi bioconductor devs, > > The

[Bioc-devel] Bioconductor 3.5 release: April 7 deadlines

Hi, Some recent activity has caused some (red) ripples across the builds and the El Capitan Mac builds are still unsettled. To accommodate, we're extending the deadline to pass R CMD build and check with no errors to next Friday (http://www.bioconductor.org/developers/release-schedule/).

Re: [Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

Hi Pariksheet, This is the expected behavior. Some background: BSgenomeViews are list-like objects where the *list elements* (i.e. the elements one extracts with [[) are the DNA sequences from the views: > views BSgenomeViews object with 2 views and 0 metadata columns: seqnames

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

And by Rainer I mean Johannes. It is late… From: Rainer Johannes Date: Thursday, 6 April 2017 at 22:07 To: "Obenchain, Valerie" Cc: Stian Lågstad , Michael Lawrence ,

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

@Florian: nothing you have to change. I checked all packages and 70 of them have problems related to the relocation of the filters. For 63 of them everything should be fine once the updated versions of biovizBase and ggbio are built. This fixes also Gviz and most of the packages with them. For

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

We've updated the release schedule and moved the deadline for errors to next Friday, April 14. Valerie On 04/06/2017 10:29 AM, Stian Lågstad wrote: > How does the error deadline tomorrow (http://www.bioconductor.org/ > developers/release-schedule/) affect packages that are still red because of

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

I thought that this all originates in biovizBase? So there’s nothing to change in Gviz unless I miss a crucial point here. Florian On 06.04.17, 19:10, "Bioc-devel on behalf of Stian Lågstad" wrote: How does the error

Re: [Bioc-devel] Filter classes moved from ensembldb to AnnotationFilter

How does the error deadline tomorrow (http://www.bioconductor.org/ developers/release-schedule/) affect packages that are still red because of this change? I don't know what else to do other than to wait for changes in Gviz (which my package is dependent on). Thanks. On Tue, Apr 4, 2017 at 10:05

Re: [Bioc-devel] Check error on malbec2

>From the looks of your code, when a user runs the examples/vignette they have >the option of a tempdir() which is what you show and run as default for the >examples, or specifying their own unique directory for the output. The output >directory is passed as an argument to your functions which

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

On Thu, Apr 6, 2017 at 2:59 AM, Martin Morgan wrote: > On 04/06/2017 05:33 AM, Aaron Lun wrote: >>> >>> The tool is not perfect, so assess each report carefully. >> >> >> I also get a warning on almost every C++ function I've written, because >> I use the following

Re: [Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

I am sure there are better responses to come, but here are a few initial comments. On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson wrote: > Dear all, > > SummarizedExperiment and matrixStats both contain a method/function called > rowRanges one operates on a

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

On 04/06/2017 05:33 AM, Aaron Lun wrote: The tool is not perfect, so assess each report carefully. I also get a warning on almost every C++ function I've written, because I use the following code to handle exceptions: SEXP output=PROTECT(allocVector(...)); try { // do

[Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

Dear all, SummarizedExperiment and matrixStats both contain a method/function called rowRanges one operates on a SummarizedExperiment-object the other on a matrix. matrixStats is required by SummarizedExperiment, or a package it is depending on, so rowRanges is masked when loading

Re: [Bioc-devel] PROTECT errors in Bioconductor packages

> The tool is not perfect, so assess each report carefully. I also get a warning on almost every C++ function I've written, because I use the following code to handle exceptions: SEXP output=PROTECT(allocVector(...)); try { // do something that might raise an exception }

[Bioc-devel] PROTECT errors in Bioconductor packages

Bioc developers, Tomas Kalibera has developed an offline bug-finding tool written specifically to detect C PROTECT errors. The tool detects errors in the following Bioconductor packages: affyio affyPLM Biostrings BufferedMatrix chopsticks CNEr crlmm csaw DECIPHER DiffBind diffHic