rmflight

hrbrmstr, 24 days ago to random

🚨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, 6 months ago to random

Driving companion today. Kids were insistent that I bring a stuffy with me on my solo speed run to Dad's to get stuff that's been sitting in his basement for 13 years.

Doesn't complain about anything, not much for conversation though.

rmflight, 1 month ago to python

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, 9 months ago to random

This will either work great, or be a disaster. Trying something different, and mapping our route out with stops, and making the reservation a day in advance.

So actually shooting for close to 8 hours of driving time tomorrow, stopping in Harrisburg PA tomorrow, and have an actual reservation at a hotel.

#FlightVacation

rmflight, 9 months ago to random

One day down, 1 1/2 to go.

Safe in Pennsylvania for the night. Started at 8am, finally stopped at 6:10pm.

Had an accident to get around on I81N, that added a bit, but wasn't too badly. Maine bound tomorrow I think.

#FlightVacation

rmflight, 7 months ago to random

My search foo is failing me.

@hrbrmstr had a Daily Drop post highlighting a variety of methods for enabling parallel processing not that long ago??

I cannot find the drop in my email, or on substack, or in my bookmarks here, which is really, really odd, b/c I commented on it even.

Help?

rmflight, 4 months ago to random

Finally watched "League of Superpets". Honestly, a better Justice League movie than Joss Whedon's version, and almost up there with Zach Snyder's. I would definitely watch the sequel.

rmflight, 8 months ago to random

Was wondering why every iteration of my #RStats code was spitting out a message in this code:

if (iter %% 1000) {  
 message(...)  
}  

Took forever to realize I wanted:

if ((iter %% 1000) == 0) {  
 message(...)  
}  

🤦‍♂️

rmflight, 8 months ago to random

Anyone else overly amused that the first day of actual #RStats #PositConf2023 talks are on "talk like a pirate day"? 🤣

rmflight, 2 months ago to random

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

Very nice.

rmflight, 10 months ago to random

Definitely an adult. Excited for a new salad spinner after the old one broke.

rmflight, 5 months ago to random

Me, 44 yo, having some ankle issues that have been slowly clearing up.

Spouse says 5's shirt was "criss-cross".

My brain goes: "Kris Kros'll make ya jump, jump", and I jump.

My ankle immediately regrets it. 😭

futurebird, 15 days ago to random

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, 4 months ago to random

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

rmflight, 6 months ago to random

So who is going to give this a try w/ #QuartoPub #RStats 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, 1 year ago to random

Build A Bear has axolotl plushies available now?! I've been tempted by some of the stuff there when we've taken the kiddos there before, but this, this one I want for myself.

https://www.buildabear.com/lavender-axolotl-/031354.html

rmflight, 1 month ago to random

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/

rmflight, 7 months ago to machinelearning

Two new preprints on #MachineLearning and #Metabolomics now available from our lab!

Both are centered around learning / predicting metabolite - to - pathway relationships in KEGG.

A cautionary tale about properly vetting datasets used in supervised learning predicting metabolic pathway involvement
https://www.biorxiv.org/content/10.1101/2023.10.03.560711v1

Benchmark dataset for training machine learning models to predict the pathway involvement of metabolites
https://www.biorxiv.org/content/10.1101/2023.10.03.560715v1

/1

rmflight, 4 months ago to random

For the past 6 months or so, I've just been living with the fact that sourceing my #RStats function file directory takes 90 seconds at the beginning of this analysis.

Today, I got annoyed enough I decided to actually measure the time it takes, and figure out if any specific file was causing the long delay.

Turns out, I had left a data processing script meant to be run once in the function file directory! Moved it out, and now it's 1 second to source everything. 🤦‍♂️

rmflight, 9 months ago to random

I know it's at least 1/2 the #migraine talking, but I'm done with this trip, and so want to turn tail for home instead of my in-laws tomorrow.

One more week, and then maybe (big maybe) a stop at Lego Discovery center just outside DC on our way back home. We are all so tired, and another week is just going to add onto it.

#FlightVacation

hrbrmstr, 2 days ago to random

Drop #469 (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, 6 months ago to random

I'm always surprised by the number of people who assume that permanent residents / landed immigrant / green card holders are allowed to vote (USA).

I like to encourage people I know to go and "vote well, because I can't", and I get funny looks because they are under the impression that I can vote. It gets even better when they discover I pay the same taxes as a citizen, and still can't vote.

Where is this misinformation that non-citizens can legally vote?

rmflight, 8 months ago to random

Unfortunately have to miss @Cmastication keynote: "It's Abstractions All the Way Down"

at #PositConf2023 due to cooking lunch for the fam, but looking forward to checking it out later (hopefully tomorrow sometime after the recording is in the conf portal).

rmflight, 28 days ago to bioinformatics

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

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.

#bioinformatics #RnaSeq