Re: [Bioc-devel] Use set.seed inside function

Thanks, and good to know the with_seed function. best, Chen On 29.11.21 22:43, Henrik Bengtsson wrote: The easiest is to use withr::with_seed(), e.g. withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6)) [1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5" withr::wit

Re: [Bioc-devel] [External] Memory error from sesame build

Thanks Herve. That's super helpful. I will use your trick! Best, Wanding > On Nov 29, 2021, at 5:51 PM, Hervé Pagès wrote: > > On 29/11/2021 09:25, Zhou, Wanding wrote: >> Thanks for the input Herve. I saw your post but can you help me confirm that >> mine is on the 32-bit windows since it sa

Re: [Bioc-devel] [External] Memory error from sesame build

On 29/11/2021 09:25, Zhou, Wanding wrote: Thanks for the input Herve. I saw your post but can you help me confirm that mine is on the 32-bit windows since it says mingw32 (64-bit)? Windows Server 2012 R2 Standard / x64 * using platform: x86_64-w64-mingw32 (64-bit) This shows the Windows arch

Re: [Bioc-devel] Use set.seed inside function

The easiest is to use withr::with_seed(), e.g. > withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6)) [1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5" > withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6)) [1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15

Re: [Bioc-devel] Use set.seed inside function

Thanks. I think it may work in theory, generating "enough" distinct colors is fairly easy. Then the problem will be how to find a subset of colors of size n, and the selected colors are still most distinguishable. I think I will do this with my eyes if no other methods, a tedious job. But at least

[Bioc-devel] Change bioconductor maintainer

Hello, I recently changed my institution and my email address. Could you update the maintainer email address of TOAST (https://bioconductor.org/packages/release/bioc/html/TOAST.html) to zl...@mdanderson.org? Thank you! Ziyi [[alternative HTML version deleted]] _

Re: [Bioc-devel] Use set.seed inside function

It appears that you don't actually want random colors, but instead you want the same colors each time. Why not just generate the vector of 'random distinct colors' one time and save the vector of colors? -Original Message- From: Bioc-devel On Behalf Of Meng Chen Sent: Monday, November 2

[Bioc-devel] Use set.seed inside function

Dear BioC team and developers, I am using BiocCheck to check my package, it returns a warning: " Remove set.seed usage in R code" I am using "set.seed" inside my functions, before calling function distinctColorPalette (randomcoloR package) in order to generate reproducible "random distinct colors

Re: [Bioc-devel] bpparam Non-deterministic Default

This should be solved by the vignette appropriately calling set.seed and explaining why they set the seed and why it is not done automatically. In a visible code chunk. On Sat, Nov 27, 2021 at 7:31 AM Spencer Nystrom wrote: > This GitHub issue, although lengthy, discusses some of the technical >

Re: [Bioc-devel] [External] Memory error from sesame build

Thanks for the input Herve. I saw your post but can you help me confirm that mine is on the 32-bit windows since it says mingw32 (64-bit)? Windows Server 2012 R2 Standard / x64 * using platform: x86_64-w64-mingw32 (64-bit) http://bioconductor.org/checkResults/release/bioc-LATEST/sesame/tokay2-

Re: [Bioc-devel] Memory error from sesame build

Hi Wanding, A process cannot allocate more than 3Gb of memory on 32-bit Windows. See my other post on this list for more information about this: https://stat.ethz.ch/pipermail/bioc-devel/2021-November/018663.html Cheers, H. On 22/11/2021 05:17, Zhou, Wanding wrote: Hi, Recently we are ex

Re: [Bioc-devel] Single Package Builder for New Package Submission

The updates are complete. The Single Package Builder is now using Bioc 3.15 and R 4.2 for new package submissions. We have identified a bug in BiocCheck that will cause current packages to fail in BiocCheckGitClone on the Single Package Builder Report. That looks similar to the following: =

[Bioc-devel] Single Package Builder for New Package Submission

We will be making updates to the Single Package Builder for New Package Submissions throughout the morning. This will cause some intermittent downtime on the build on commit feature of new submission review process. We appreciate your patience while we update. Lori Shepherd Bioconductor Co

Re: [Bioc-devel] Landing page build status different from the build report

The builds reports are not all OK. There is still an ERROR on the windows riesling1 on devel and windows tokay2 in release. Until all are OK it will default to ERROR because there is an ERROR in at least one platform: http://bioconductor.org/checkResults/release/bioc-LATEST/bambu/ http://bio