@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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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

🚨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

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 python
@rmflight@mastodon.social avatar

Kind of thankful that 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 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.

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

rmflight, to random
@rmflight@mastodon.social avatar

After @njtierney reviewed one of my packages, and commented on 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/

rmflight, to random
@rmflight@mastodon.social avatar

Did something change in 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.

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.

rmflight, to random
@rmflight@mastodon.social avatar

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

Very nice.

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??

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.

LeftistLawyer, to random
@LeftistLawyer@kolektiva.social avatar

Ok, I rarely do this, but for the sake of anecdotal 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.

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??

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.

mbonsma, to random
@mbonsma@mastodon.social avatar

Feeling cute*, might delete later

*like a sleep-deprived chaos monster

rmflight,
@rmflight@mastodon.social avatar

@mbonsma omg, "sleep-deprived chaos monster" feels like the perfect description of being the parent of a newborn.

hrbrmstr, to random
@hrbrmstr@mastodon.social avatar

I honestly did not expect to wake up to the start of the second civil war in 'Murica. At least not this soon in 2024.

rmflight,
@rmflight@mastodon.social avatar

@jt_rebelo @hrbrmstr also, ??

What are you seeing Bob? Could use more info, if you don't mind sharing.

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!

MickaelCanouil, to dashboard
@MickaelCanouil@fosstodon.org avatar

Dashboard, Typst, new cross-reference system allowing more customisation, …
What are you waiting? Time to download, upgrade, and enjoy all these new features (and bug fixes).

https://quarto.org/docs/blog/posts/2024-01-24-1.4-release/

rmflight,
@rmflight@mastodon.social avatar

@MickaelCanouil is one of those big fixes the table cross referencing and captions in Word files?? 🤞

brodriguesco, to random
@brodriguesco@fosstodon.org avatar

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

rmflight,
@rmflight@mastodon.social avatar

@brodriguesco If it's actually the file name issue (and not the file types in the "inst/doc" directory), then adding a leading "v" would likely fix it.

That does seem weird, but also seems like a legacy of not allowing variables to start with a number either.

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

grimalkina, to random
@grimalkina@mastodon.social avatar

A thing I wrote in a recent draft:

"...on the team side, the reality of team practices that claim to be autonomous at large organizations is that supposed independence of action is frequently sustained by senior members or managers “protecting” their teams from external dependencies and taking on the work of advocacy as individual responsibility (Moe et al., 2019; Hicks, et al 2023)."

I think this is a big point with large psychological implications although software journals, alas, did not

rmflight,
@rmflight@mastodon.social avatar

@grimalkina 👋 yes please!

njtierney, to random
@njtierney@aus.social avatar

Hey folks,

Tomorrow at 12pm Sydney/Melbourne time we will be trying out the first round of this live package review. Currently we have myself, @milesmcbain , and @adamhsparks joining for review, which is very exciting!

We will be looking at
@jadeynryan 's
{soils} package: https://github.com/WA-Department-of-Agriculture/soils

And if there is time,
@ngiangre 's {kidsides} package: https://github.com/ngiangre/kidsides

This link will show you what time that is in your timezone: https://www.timeanddate.com/worldclock/fixedtime.html?msg=Twitch+R+package+review&iso=20240121T12&p1=152&ah=1&am=30

Thanks to everyone who has been very helpful with sharing resources and experience and enthusiasm: @tanho, @wviechtb, @michcampbell and @hye
I haven't had as much time to iron out the twitch stream as I would like so hopefully it all works out! I'll post a link here when I've got it working.

Thanks for everyone's help!

rmflight,
@rmflight@mastodon.social avatar

@milesmcbain @jadeynryan @njtierney @adamhsparks @ngiangre @tanho @wviechtb @michcampbell @hye wait, that was today at 8pm EST? I keep forgetting you all are living in the future!?

Will have to watch the recording then.

hrbrmstr, to random
@hrbrmstr@mastodon.social avatar

First image is a fav annual haunt of ours in Southwest Harbor as of yesterday. The second image is the "normal" water level.

Been surveying the damage across the state. This was a truly brutal storm series.

image/png

rmflight,
@rmflight@mastodon.social avatar

@hrbrmstr Best of luck with that! And any impending weather coming your way.

It looks like KY will be spared the weather (yet again), outside of some deep cold.

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