@Mehrad@fosstodon.org
@Mehrad@fosstodon.org avatar

Mehrad

@Mehrad@fosstodon.org

Bioinformatician🧬 during the day, Data Scientist📈 in the afternoon, and Linux🐧 hobbyist at night. Federation and E2EE advocate. Interested in Data Analysis, Machine Learning, and FOSS/FLOSS.

Languages:
🗣
|_ 🇮🇷: Native
|_ [🇺🇸🇬🇧]: Almost native
|_ 🇫🇮: In Progress 😅

🤖
|_ :rstats: : Primary
|_ :python: : Know my way around
|_ 🐪: Oldie but Goodie (esp. regex)
|_ :rust: : n00b

Some of my interests in machine-readable format:
#Rstats #Bioinformatics #MachineLearning #OpenScience

This profile is from a federated server and may be incomplete. Browse more on the original instance.

coolandnormal, to random
@coolandnormal@aus.social avatar

People who understand R and RStudio, please help me out.

I've been asked to use it for a class that is neither a stats nor an IT unit, so none of us are experienced with the tech.

Here's the issue:

I open RStudio. It shows me a mostly blank screen with the usual row of menus along the top plus the RStudio logo and name. Each menu displays (empty). In a separate window it opens the RStudio logo only.

I can't work out how to make it display menus and the rest of the UI.

It was working normally yesterday.

I have tried turning all aspects of the situation off and on again. I haven't tried downloading RStudio again.

Edit: possibly relevant, it's running on a basic laptop that's over 10yo.

#RStats #RStudio

Mehrad,
@Mehrad@fosstodon.org avatar

@coolandnormal
That looks like a broken install. It should not look like that. I suggest uninstalling it and installing it again. Alternatively you can use other software instead of Rstudio to work with R:
VScode
Rkward
If you are on Windows, R comes with it's own very minimal GUI that some of my colleagues still exclusively use

wlwl, to random

my first rtoot

Mehrad,
@Mehrad@fosstodon.org avatar

@wlwl
Welcome to Fediverse. The "Nicest hashtag in the first post award" should go to you 🏆

brodriguesco, to random
@brodriguesco@fosstodon.org avatar

compiling from source to package it for

Mehrad,
@Mehrad@fosstodon.org avatar

@brodriguesco
Yeah, that takes time 😅 I did that with Guix and I had to also compile some of the dependencies as well. But regardless of the time, it is fun to see everything automatically in Nix or Guix come together in harmony and give a fully functional software.

Mehrad, to KDE
@Mehrad@fosstodon.org avatar

One of the things that I truly miss in @kde is a modern and actively-maintained diff tool. Gnome/GTK has Meld which despite of ugly GTK style, is a very decent diff tool which also allows comparing "blank files" which user can copy-paste snippets from elsewhere. has kdiff3 and kompare, both of which feel and look dated and old-school.

https://invent.kde.org/sdk/kdiff3

thelinuxcast, to random
@thelinuxcast@fosstodon.org avatar

GNOME Took In $556k Last Year While Spending $675.9k | https://www.reddit.com/r/linux/comments/1cmu7jr/gnome_took_in_556k_last_year_while_spending_6759k/

Mehrad, (edited )
@Mehrad@fosstodon.org avatar

@thelinuxcast
For @kde I couldn't find the 2023 financial report, but I managed to find this for 2022 (go to "Financial Working Group" section):

https://ev.kde.org/reports/ev-2022/

Total Income: 285,495.97 €
Total Expenses: 384,604.78 €

jadi, to github
@jadi@bsd.cafe avatar

I was sending a minor PR to the uutils / project regarding a breaking test on and thought its a good opportunity to record a video and:

  • talk about the uutils/coreutils which is a rewrite of coreutils in Rust
  • show the env and do some coding in it
  • Show the flow of sending a PR on

https://youtu.be/5JcaQWGMRVE

Mehrad,
@Mehrad@fosstodon.org avatar

@jadi
Noce motto "Have an hour of fun, maybe a lifetime of jobs" 🤓

Btw, it would have been helpful to the project to add a Github Action for NetBSD. This way every new PR will be checked against NetBSD before being merged. In the long run it would be very beneficial imho.

Mehrad, to github
@Mehrad@fosstodon.org avatar

I'm frustrated with issue search. I am looking for issues on repo that contains "sort" or "sorting". Github says there is no issue containing "sort" or "sorting"

https://github.com/flatpak/flatpak/issues?q=sorting+

but I have found this:

https://github.com/flatpak/flatpak/issues/4807

Mehrad,
@Mehrad@fosstodon.org avatar

@martinpeck Thanks for trying it out. After some refreshing and trying again, now it works and shows me 2 open and 7 closed. Do you see the same numbers. I wonder what could be the issue. I also don't know how much I can trust the results anymore.

Mehrad, to android
@Mehrad@fosstodon.org avatar

Does anyone know Android app that can get a list of phone numbers, and when any of them call, it picks up the phone, plays a specified audio file (e.g recorded message) and then hang up?

Userfriendliness does not matter.

josi, to random
@josi@fosstodon.org avatar

🪲 R's new vulnerability doesn't scare me.

There are TONS of ways to hide exploits in R code. Want to see how you can abuse:

  • .onLoad()
  • pre-compiled code
  • side effects or
  • hiding in S3 generics?

https://www.youtube.com/watch?v=WGvXEi4nG5k

Mehrad,
@Mehrad@fosstodon.org avatar

@josi
Nice short video. I completely agree with your point, that this CVE was vulnerability, yes, but it doesn't mean it was the only way one could do malicious things. Well said 👍. Blindly using a language is always a risky move.

abmurrow, to random
@abmurrow@fosstodon.org avatar

Oof, guix doesn't seem play nice with foreign distros, even stable ones like Debian. The guix system distro is out of the question because of my WiFi drivers and until nonguix is more mature there really isn't a good alternative for me.

I don't love it but I'll probably have to hop back over to nixos and see how the community changes play out. Good thing it takes like 2 minutes to get my old config back. Still, nix has made it tough to use anything else.

Mehrad,
@Mehrad@fosstodon.org avatar

@abmurrow
Which part of it doesn't play nice with foreign distro? i've used it on Ubuntu 22.04 and also on multiple Manjaro, and I never faced even the slightest issue.

Mehrad,
@Mehrad@fosstodon.org avatar

@abmurrow
When you run a bash script, it is not run with same system environment that you have, instead it creates a subshell. For this reason, most probably you didn't have the profile there at all. One way to bypass that is to use source script.sh instead of bash script.sh to run the content of the script in the current bash.

The way I use guix is to have certain tools and containers in guix on a rolling release distro like Arch or Manjaro as the host.

stux, to random
@stux@mstdn.social avatar

I’m just warming up..

Orange kitty sets its teefs into cardboard

Mehrad,
@Mehrad@fosstodon.org avatar

@stux
The proof that Schrodinger's cat is alive and pissed 😅

Mehrad, to academicchatter
@Mehrad@fosstodon.org avatar

I wonder if it is even ethical to enlist affiliation to the university if my funding comes directly from a funding institute, I'm buying and using my own hardware and software (down to the HDMI cable and mouse), and the data is also coming directly from another organization. The coffee and food is also off my own pocket.

The only things they provide are electricity (computer, coffee), water (coffee), and internet.

Let know your thoughts.

@academicchatter

Mehrad,
@Mehrad@fosstodon.org avatar

@geospacedman Thanks for your questions. The grant was awarded to the PI and he have enlisted me as grantee to the funding institute. We do not ever received any grant writing support. There is no post-grant award support. We are paying the open-access off the funding grant. Office space is provided by university but is not actively used as for certain known reason the team mostly does remote work. As for Office space, as far as I know, university charge PIs if funding overhead cannot be taken.

Mehrad,
@Mehrad@fosstodon.org avatar

@geospacedman Actually due to Finland's law, having grant is different from salary and falls under freelancer category. This means that I don't get any of the salary benefits (work insurance, paid vacations, paid pension, automatic taxation, ...), and I have to take care of all that myself. the upside is that I can quit at any given millisecond that I desire. Zero legal obligation to resignation notice and etc.

Mehrad,
@Mehrad@fosstodon.org avatar

@geospacedman About profitability, there are companies which do Bioinformatice, data analysis or even Machine Learning. Among the good ones is IQVIA, but the majority of local companies here are not doing quality work especially when it gets to statistics and Machine Learning (not naming names). That's why it is tempting for PIs to get independent grants and recruite people like me to stear their research.

Do you have any positions? 🤓

nixCraft, (edited ) to linux
@nixCraft@mastodon.social avatar

paste is such a handy #Linux and #Unix command. It saves so much time.

Mehrad,
@Mehrad@fosstodon.org avatar

@glutto
Generally adding a space before command would ignore them from being added to the history. If not, you can add this to your .bashrc or .zshrc

HISTCONTROL=ignorespace

@nixCraft

freemo, to random
@freemo@qoto.org avatar

There are actually people born after 2000 who arent babies right now... I still can not accept this.

Mehrad,
@Mehrad@fosstodon.org avatar

@freemo
Well, then they are 24 years old and can have a 6 years old child as well (assuming having child at 18yo) 😉

indymnv, to random
@indymnv@fosstodon.org avatar

without neofetch how we can rice?

Mehrad,
@Mehrad@fosstodon.org avatar

@indymnv
There are fastfetch, pfetch, nerdfetch, rtfetch ...

jd7h, to random
@jd7h@fosstodon.org avatar
Mehrad,
@Mehrad@fosstodon.org avatar

@jd7h
Accurate🤣, the only thing that bothers me much is the placement of thumbs, when one make a fist, thumb finger points outward (i.e away from each other).

Mehrad, to bioinformatics
@Mehrad@fosstodon.org avatar

>> Chan Zuckerberg CELL by GENE Discover (CZ CELLxGENE) is a collection of free and open-source tools for finding, querying, analysing, downloading and publishing single-cell data. As of April, it includes some 85 million single cells and 1,317 data sets covering 844 cell types, curated and uniformly processed

https://www.nature.com/articles/d41586-024-01217-y

johanv, to random
@johanv@fosstodon.org avatar

I kept needing to look up compatibility for the framework 16 expansion card slots so... label printer to the rescue!

I had to redraw the image in to fit the width of my Brother QL-800, see this short blog post with the details, and image downloads: https://johanv.net/blog/framework16-slot-compatibility-labels/

@frameworkcomputer

Mehrad,
@Mehrad@fosstodon.org avatar

@johanv
I think this is something that @frameworkcomputer should by default ship with their laptop. It is up to the user to attach them or not, but it is completely in the spirit of Framework laptop design.

governa, to github
@governa@fosstodon.org avatar

#Neofetch Development Ends as #GitHub Project Archived

https://www.omgubuntu.co.uk/2024/04/neofetch-system-info-tool-is-dead

Mehrad,
@Mehrad@fosstodon.org avatar

@governa
I was using for years as it was much simpler script. I recently removed then both from my config although I liked the aesthetics.

Anyways, I'm sure soon we will see NeoFetchXC out something like that. There are similar tools that are written in C or Rust, are cross platform and etc, but they are overkill imho. The simplicity and the readability of the script was the main selling point for me. I learnt few useful things along the years from and pfetch.

Mehrad, to random
@Mehrad@fosstodon.org avatar

Almost always videos leave me hung in awe. This last video is no exception, and I strongly suggest watching it especially if you like or curious about quantum physics:

https://youtu.be/6akmv1bsz1M?si=2SckF1yStI4MsI4I

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