Re: [Bioc-devel] updated BridgeDbR package

On Fri, Apr 29, 2016 at 10:31 PM, Obenchain, Valerie wrote: > It looks like you're one of the authors but not the maintainer. Indeed! Anwesha is finishing her PhD in our group. > If you have svn credentials we can give you write permissions to the repo. If >

Re: [Rd] boxplot with formula involving two-factor levels

> On 29 Apr 2016, at 23:54 , d...@stat.oregonstate.edu wrote: > > Hi, > > I noticed two seemingly equivalent call to boxplot will give different plots > (in the way how the combined factor levels are arranged on the x-axis): > > x = factor(rep(c("a", "b", "c"), each=2)); > y =

Re: [Rd] paths for install and libraries?

On 28 April 2016 at 16:41, Dalthorp, Daniel wrote: | I've written a fairly elaborate package (called "eoa") that relies on | functions from several other packages. I've built the package into a zip | file on Windows using Hadley's devtools::build(binary = T) and have sent | the zip to a couple

Re: [Bioc-devel] some new warnings in a package

On Fri, 29-04-2016, at 23:49, Martin Morgan wrote: > On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote: >> Dear All, >> >> In case it matters, and since we are past the 22, I just noticed that a >> package I maintain (ADaCGH2) is giving warnings in Linux and Mac

Re: [Bioc-devel] some new warnings in a package

On 04/29/2016 05:23 PM, Ramon Diaz-Uriarte wrote: Dear All, In case it matters, and since we are past the 22, I just noticed that a package I maintain (ADaCGH2) is giving warnings in Linux and Mac (e.g., https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html)

[Rd] boxplot with formula involving two-factor levels

Hi, I noticed two seemingly equivalent call to boxplot will give different plots (in the way how the combined factor levels are arranged on the x-axis): x = factor(rep(c("a", "b", "c"), each=2)); y = rep(factor(c("one", "two")), each=3); r = 3; n = r * 6; x = rep(x, 3); y = rep(y, 3); z =

[Bioc-devel] some new warnings in a package

Dear All, In case it matters, and since we are past the 22, I just noticed that a package I maintain (ADaCGH2) is giving warnings in Linux and Mac (e.g., https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/zin2-checksrc.html) that, if I recall correctly, were not being given

Re: [Bioc-devel] updated BridgeDbR package

It looks like you're one of the authors but not the maintainer. If you have svn credentials we can give you write permissions to the repo. If you don't have credentials we can request them for you. If you want the changes in quickly you could ask the maintainer to push them. Valerie On

Re: [Bioc-devel] Spurious errors unit testing on R CMD check

No, those aren't reference classes. There are some reference classes in GenomicFeatures (like TxDb) and BSgenome. I don't think they set explicit finalize methods though. On Fri, Apr 29, 2016 at 12:58 PM, Hector Corrada Bravo wrote: > I've removed all finalizers on these

Re: [Bioc-devel] Spurious errors unit testing on R CMD check

I've removed all finalizers on these classes for this version and are still seeing it. I'll try with gctorture on and see if I can track it down. Any finalizers on GenomicRanges? GNCList or GRanges? On Fri, Apr 29, 2016 at 3:42 PM, Michael Lawrence wrote: > I don't

Re: [Bioc-devel] Spurious errors unit testing on R CMD check

I can look into it. I guess it fails sporadically because of the garbage collector. Activating GC torture might make this easier to reproduce. On Fri, Apr 29, 2016 at 12:06 PM, Hector Corrada Bravo wrote: > I've seen this type of error for a while and have really struggled to

[Bioc-devel] Spurious errors unit testing on R CMD check

I've seen this type of error for a while and have really struggled to track it down. I have a package with unit tests that sporadically fail on R CMD check with errors of this type: --- > test_check("epivizrData") 1. Error: new creates a proper object (@test-creation.R#17)

[Bioc-devel] updated BridgeDbR package

Hi all, I am one of the upstream developers of BridgeDbR and like to see newer version of the package included in Bioconductor. After the pull request I created was closed [0], I realized that was not the right approach. But I also do not have SVN write access, and therefore can not push it like

Re: [Bioc-devel] Found more than one class "Annotated" in cache

Thanks, will fix. On Fri, Apr 29, 2016 at 10:26 AM, davide risso wrote: > Hi all, > > when running R CMD check on our package, we get the following warning: > > checking whether the namespace can be unloaded cleanly ... WARNING > unloading > Error in

Re: [Bioc-devel] Found more than one class "Annotated" in cache

Hi all, when running R CMD check on our package, we get the following warning: checking whether the namespace can be unloaded cleanly ... WARNING unloading Error in .getClassFromCache(what, resolve.confl = "all") : argument "where" is missing, with no default Calls: unloadNamespace ...

Re: [Rd] paths for install and libraries?

> Dalthorp, Daniel > on Thu, 28 Apr 2016 16:41:28 -0700 writes: > I've written a fairly elaborate package (called "eoa") > that relies on functions from several other packages. I've > built the package into a zip file on Windows using > Hadley's

Re: [Bioc-devel] Question: set purification test for overlapped regions between three GRanges object

Dear Jurat, Maybe this would be better asked on support.bioconductor.org. I don't think I fully understand what you intend to do (a fully working example would help), but here are two ideas that could be useful: 1. Maybe a single findOverlaps() will be enough to find all you need: D <-