Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz

ata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=cTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw%3D&reserved=0 Thanks, H. On 4/23/20 21:55, Bemis, Kylie wrote: That’s interesting. I did: BiocManager::install("Car

Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz

rated on merida1. Then open the vignette via browseVignettes("Cardinal") and check the plots. Do they look ok despite the "semi-transparency" problem? Thanks, H. On 4/23/20 20:39, Bemis, Kylie wrote: I’m now seeing the same "semi-transparency" error on my Mac

Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz

I’m now seeing the same "semi-transparency" error on my Mac builds for Cardinal. My vignettes have used transparency for years now and this has never been an issue before (on merida1 or otherwise). I can reproduce the error locally with an X11() device, but not with quartz(), png(), png(), etc.

[Bioc-devel] set.seed and BiocParallel

Hi all, I remember similar questions coming up before, but couldn’t track any down that directly pertain to my situation. Suppose I want to use bplapply() in a function to fit models to many features, and I am applying over features. The models are stochastic, and I want the results to be repr

Re: [Bioc-devel] Possible to export coerce2() from S4Vectors?

is not well documented. I will try to improve that, as soon as I understand it myself. But no matter what, your cbind() method will need to uplift ordinary DataFrames to IndexedDataFrame. Michael On Wed, Nov 14, 2018 at 7:52 AM Bemis, Kylie mailto:k.be...@northeastern.edu>> wrote: Hi Michael,

Re: [Bioc-devel] Possible to export coerce2() from S4Vectors?

t be possible to fold its logic into as() without breaking too much? Kylie, It would help to see your code, with some pointers to where things break. Michael On Wed, Nov 14, 2018 at 5:36 AM Bemis, Kylie mailto:k.be...@northeastern.edu>> wrote: Hi Herve, Thanks for the detailed reply. Usin

Re: [Bioc-devel] Possible to export coerce2() from S4Vectors?

coerce2() is to support things like [[<- and endoapply(). Once coerce2() works properly, these things work out-of-the-box. So to summarize: just make sure that a DataFrame can be coerced to your DataFrame derivative and [[<- and endoapply() will work out-of-the-box. It could be however that

[Bioc-devel] Possible to export coerce2() from S4Vectors?

Dear all, Are there any plans to export coerce2() from the S4Vectors namespace, like other exported internal utilities such as showAsCell() and setListElement()? I have a couple classes that inherit from DataFrame, and some inherited methods (like [[<-) break in certain situations due to calls

Re: [Bioc-devel] any interest in a BiocMatrix core package?

> wrote: >> >>> I think it makes sense. A lot of sense. Might be useful to involve Henrik >>> (matrixStats) as well. >>> >>> Who are the players, apart from DelayedArray/DelayedMatrixStats and matter? >>> (and some very old stuff in Biobase which shou

Re: [Bioc-devel] any interest in a BiocMatrix core package?

s to foster comparison and informed decisionmaking? @becker.gabe: is ALTREP far enough along that one could contemplate benchmarking with it? On Fri, Feb 24, 2017 at 7:08 PM, Bemis, Kylie mailto:k.be...@northeastern.edu>> wrote: > It’s not there yet, but I plan to expose a C++ API for my

[Bioc-devel] Cardinal duplicate commits

Hi all, I have a problem with duplicate commits in my package “Cardinal”. So far I have avoided making more commits to my other package “matter” until I am sure how to avoid this again. Soon after the git transition, I made a few small commits to the Bioconductor git repo, which I notice now i

Re: [Bioc-devel] Generate valid SSH keys for the bioc-git server!

e: Hi Kylie, Your key shows as accepted. Nitesh On Aug 18, 2017, at 1:28 PM, Bemis, Kylie mailto:k.be...@northeastern.edu>> wrote: Dear Bioc-Devel I am still having trouble fetching from the repository. I’ve tried submitting both my Github username and copy-pasting public SSH key to th

Re: [Bioc-devel] Generate valid SSH keys for the bioc-git server!

Dear Bioc-Devel I am still having trouble fetching from the repository. I’ve tried submitting both my Github username and copy-pasting public SSH key to the Google Form. My public key in ~/.ssh/id_rsa.pub and on Github look similar to the example, so it appears valid to me, but I still get an a

Re: [Bioc-devel] any interest in a BiocMatrix core package?

It’s not there yet, but I plan to expose a C++ API for my disk-backed matrix objects in the next version of my ‘matter’ package. It’s getting easier to interchange matter/HDF5Array/bigmemory/etc. objects at the R level, especially if using a frontend like DelayedArray on top of them, but it wou

Re: [Bioc-devel] Reading and storing single cell ATAC data

Hi Caleb, Per your question on sparse on-disk matrices: is your experimental data coming in some pre-defined text or binary file format, or are you looking to convert to a new, custom format to take advantage of the sparsity? I need to start working on an on-disk sparse matrix implementation so

Re: [Bioc-devel] Updating author/maintainer info

It works now, thanks! Kylie ~~~ Kylie Ariel Bemis Future Faculty Fellow College of Computer and Information Science Northeastern University kuwisdelu.github.io On Sep 22, 2016, at 1:45 AM, Hervé Pagès mailto:hpa...@fredhutch.org>> wrote: Hi Kylie, It seems that

Re: [Bioc-devel] Updating author/maintainer info

Thanks, but when I follow the directions, it doesn’t work: svn: E175013: Commit failed (details follow): svn: E175013: Unable to connect to a repository at URL 'https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/CardinalWorkflows' svn: E175013: Access to 'https://hedgehog.fhcrc.org/bioc-