@rmflight@mastodon.social avatar

rmflight

@rmflight@mastodon.social

Research parasite* @universityofky. Interested in #openscience, #rstats, bioinformatics, #datavis he/him

*One who uses others data to conduct research, both publicly available data, and those from direct collaborations.

#fedi22

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rmflight, to random
@rmflight@mastodon.social avatar

Does anyone know if there is a built-in size limit on square matrices passed to svd?

I have some 30K x 30K matrices I want the inverse of, and therefore am using stats::svd and some matrix multiplication to do it.

n_val = 30000  
tmp_matrix = matrix(rnorm((n_val ^ 2) / 2), nrow = n_val, ncol = n_val)  
svd_res = svd(tmp_matrix)

I get a segfault, with invalid permissions for the memory. Actual RAM usage seems fine (64 GB machine).

Google (and kagi) aren't helping here.

LeftistLawyer, to random
@LeftistLawyer@kolektiva.social avatar

Ok, I rarely do this, but for the sake of anecdotal #Covid research could you please boost?

  1. Are you O negative blood type?
  2. Have you had covid?

Please chime in with your experience.

rmflight,
@rmflight@mastodon.social avatar

@LeftistLawyer 1. Yes. 2. Yes. Only once. But vaccinated as well as I can, and wear an N95 mask everywhere and avoid eating in public indoors, except for the two times I did (both within a week) and our entire family contracted COVID.

rmflight, to random
@rmflight@mastodon.social avatar

A stuffed Axolotl from my family for Christmas! It's so cute!

rmflight, to bioinformatics
@rmflight@mastodon.social avatar

What RNA-Seq datasets are everyone using for RNA-Seq differential analysis workshops, using {DESeq2} or {limma} ?

Two or three categories, and ideally a good (4 or 5+) number of replicates, human or mouse?

We have some new methods in ontology enrichment, and we really could use some more datasets to try them on.

I've found the {airways} dataset, and lung adenocarcinoma from {recount3} (as an easy pull). Looking for others. TIA.

rmflight, to random
@rmflight@mastodon.social avatar

Looking for recommendations of KN95 / 94 style kids masks (5, 9, 13) that people have used and their kids actually wear? Bonus if they are good at not fogging glasses (9 has glasses now). I've been really happy with 3M Aura for myself, but that's definitely too big for the kiddos.

Going on vacation in a couple weeks, and I know we will be inside with people we don't know way more often than we have been, between hotels and visiting with family.

rmflight, to random
@rmflight@mastodon.social avatar

Did something change in #RStats recently (last couple of years) for comparing two logical vectors?

I'm pretty sure this used to work, and return the expected single value logical:

v1 = c(TRUE, FALSE)  
v2 = c(TRUE, TRUE)

v1 == v2 # FALSE

Now I have to do:

identical(v1, v2)

Like, I'm going to be checking all of my package code to check for logical comparisons using ==, because it's definitely not doing what I expect anymore.

rmflight, to random
@rmflight@mastodon.social avatar

is awesome, and I am finding myself using it more and more over for based reports and documents. I definitely recommend checking out the new features in v 1.4!

https://fosstodon.org/@Posit/111813004531309642

I will note one pain point, and that is tables with captions in Word documents. If you want or need that, it's still not quite there, unfortunately (and it's being worked on, I keep an eye on the issues on GH). Here's hoping we get it in v 1.5!

rmflight, to random
@rmflight@mastodon.social avatar

PLOS-One has a survey about requiring code for publishing articles if you would like to leave feedback.

https://survey.alchemer.com/s3/7500690/Code-Sharing-Policy-Survey-2023-ONE

rmflight, to random
@rmflight@mastodon.social avatar

So who is going to give this a try w/ blogs?

Some neat javascript to use :mastodon: as a comment engine, at these two links.

https://carlschwan.eu/2020/12/29/adding-comments-to-your-static-blog-with-mastodon/

https://anarc.at/blog/2023-01-19-mastodon-comments-in-ikiwiki/

utterances et al already require a GH account, :mastodon: definitely feels like a more natural fit, especially where you use the toot announcing the blog post as the anchor.

Yes, it would potentially require publishing twice (first for link, second to add masto post ID), but 🤷

rmflight, to random
@rmflight@mastodon.social avatar

This is the problem we have today. We continue to favor short term thinking, and leave the next generation to figure it out.

From Holding Back the River, Tyler J Kelley

grrrck, to random
@grrrck@fosstodon.org avatar

I’m learning to accept that is dinner a series of snacks for a group of people who collectively hate everything I’ve made.

rmflight,
@rmflight@mastodon.social avatar

@grrrck 😆 I hear that.

We were spoiled with 13, he will still eat most things.

10, she was picky. It's been years of work (and buying a food guide / program for picky eaters) and she is slowly finding more foods to enjoy.

6, he will throw us for a loop. Won't touch a food they enjoy at one meal, but then devour it at the next, the same day. 🤷‍♂️ And has stopped eating peanut butter from them getting some bread to the roof of their mouth once, six months ago.

hrbrmstr, to random
@hrbrmstr@mastodon.social avatar

🚨Looks like #RStats was not immune to deserialization bugs after all https://hiddenlayer.com/research/r-bitrary-code-execution/

Watch those R Data files (and, we now shld come up with better ways to ensure local R library integrity)!!

CVE-2024-27322

rmflight,
@rmflight@mastodon.social avatar

@hrbrmstr They say that 4.4.0 this particular exploit is fixed. I didn't see anything in the NEWS, but went digging in the source. A commit last month shows that a commit to serialize.c was made, to return an error instead of a promise.

Wonder if that's the fix?

https://github.com/wch/r-source/commit/c06f7f2518673a75f9b36f2af9caf7b69ab4952e

BigAngBlack, to random
@BigAngBlack@fosstodon.org avatar

What was your favorite movie that started with this?

New Line Cinema animation

rmflight,
@rmflight@mastodon.social avatar

@BigAngBlack oh man, so many good films from them, hard to pick just one "favorite"

TMNT (1990)
Blade
Lord of The Rings, The Return of the King

hrbrmstr, to random
@hrbrmstr@mastodon.social avatar

Drop (2024-05-20): Make-Up Monday

The late Monday edition of the Drop focuses on productivity tools and news sources. "btw" is a minimalist blogging platform, while the technique of using a calendar for task allocation is recommended for time management. "News Minimalist" uses a rating system for news significance. Additional text-only news sources are suggested for those who prefer lightweight news consumption.

http://dailydrop.hrbrmstr.dev/2024/05/21/drop-469-2024-05-20-make-up-monday/

rmflight,
@rmflight@mastodon.social avatar

@hrbrmstr really liked the idea of calendar planning. @tpoisot had a similar sounding post (geared to researchers writing papers and grants, but still) that was along similar lines.

https://buttondown.email/ctrl-alt-tim/archive/vol-4-a-big-thing-is-just-10000-little-things/

brodriguesco, to random
@brodriguesco@fosstodon.org avatar

R CMD check complains about my vignette names, can't vignettes be numbered? #rstats

rmflight,
@rmflight@mastodon.social avatar

@brodriguesco Yep, vignettes are a special case, it appears.

"To ensure that they can be accessed from a browser (as an HTML index is provided), the file names should start with an ASCII letter and be comprised entirely of ASCII letters or digits or hyphen or underscore."

https://cran.r-project.org/doc/manuals/R-exts.html#Writing-package-vignettes

Cmastication, to random
@Cmastication@mastodon.social avatar

Played around with making generative AI prayer candles:

rmflight,
@rmflight@mastodon.social avatar

@Cmastication is it just me, or is that a likeness of Bruce Springsteen??

futurebird, to random
@futurebird@sauropods.win avatar

I saw these cool golden mirror hexagon stickers and got all excited about making a model of the Webb telescope without thinking about WHY I’d do that so they have been on my desk for a month giving me a mix of vague excitement and slow burn anxiety— I think I will give them to one of the science teachers so I can stop worrying. I already gave them a gyroscope (which they loved)

Alternately I could make a model telescope and hang in the math office and refuse to explain why.

rmflight,
@rmflight@mastodon.social avatar

@futurebird It's a cool piece of engineering, that's why! Seriously, who cares about the "why" if you really want to do it.

hrbrmstr, to random
@hrbrmstr@mastodon.social avatar

Say what I/you will abt this daft twice-yearly manipulation of the time-space continuum, but I'll never not take it being light out at 18:30+ ET.

rmflight,
@rmflight@mastodon.social avatar

@hrbrmstr yes it is nice. But being exhausted that first day b/c you lost an hour of sleep, not fun.

Also, why does the eastern timezone go all the way from Maine to Louisville KY?? What if the real problem with DST is that timezones are just too wide??

rmflight, to python
@rmflight@mastodon.social avatar

Kind of thankful that #RStats is not a system dependency that is pretty much embedded in the OS, and that I can upgrade it even on older software (like running R 4.3.0 on Ubuntu 20 LTS) without worrying about other things depending on it.

In contrast to #python 3.6, that I'm not keen to try and force an upgrade to 3.8 so I can get access to a newer version of SciPy that exposes some underlying functionality that one of our python packages depends on.

rmflight,
@rmflight@mastodon.social avatar

Before anyone suggests Docker or VM, this is already a VM running on top of a cluster of machines, and it has another big project for a manuscript that is currently under review inside of it, so I'm very hesitant to break it in any way before the manuscript is completely done.

So I guess I'm just leaving it be for now.

rmflight,
@rmflight@mastodon.social avatar

@brodriguesco I've done that for packages, but not generally python versions.

Someone else suggested pyenv to give a custom version of python and packages, I will probably end up trying that.

hrbrmstr, to random
@hrbrmstr@mastodon.social avatar

I know I'm "supposed" to hate the live action Avatar (Netflix), but I'm 10-minutes in and it’s…not bad?

rmflight,
@rmflight@mastodon.social avatar

@hrbrmstr I'm on episode 2 after last night, and I agree, this far it's not too bad.

rmflight, to random
@rmflight@mastodon.social avatar

After @njtierney reviewed one of my packages, and commented on #RStats DESCRIPTION white space style, I decided to revisit read.dcf and white space in my pre-commit hooks.

Which also had me reviewing @grrrck modifications to the hooks they had made in a fork to keep automatic from overriding a manual change, and updated the hooks.

Now the hooks live in an actual GH repo instead of gists, hopefully making them easier to find for others.

https://github.com/rmflight/r_git_hooks/

hrbrmstr, to random
@hrbrmstr@mastodon.social avatar

This season of Bad Batch is especially good.

rmflight,
@rmflight@mastodon.social avatar

@hrbrmstr I agree. Youngest is very disappointed we can't watch more episodes until next week.

rmflight, to random
@rmflight@mastodon.social avatar

Oho! I just noticed @phanpy now gives me the option to either "boost" or "quote"!

Very nice.

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