@Lluis_Revilla@fosstodon.org avatar

Lluis_Revilla

@Lluis_Revilla@fosstodon.org

Bioinformatician 📢 about OSS and #rstats, some analysis 📊 & random thoughts and ideas 🎲

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

brodriguesco, to random
@brodriguesco@fosstodon.org avatar

A vulnerability in has been discovered https://nvd.nist.gov/vuln/detail/CVE-2024-27322

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@klmr @brodriguesco I am not sure, but I heard from an R core member that they were getting more security notifications. It could be that they fixed those but not "disclose" them in the NEWS.

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@klmr @joranelias @brodriguesco This might fall into what others have complained about CVE: https://daniel.haxx.se/blog/2023/09/05/bogus-cve-follow-ups/
But here is the extract from Bug Reporting in R: "By default, reports submitted to R’s Bugzilla are public. If you believe your bug is a security vulnerability and should not be public, you may select “Show advanced fields” on the bug submission page, scroll down to the bottom of the page, and check that only members of R-security group are allowed to see the bug. "

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

Submitting to CRAN is daunting and complicated?
Usually packages are accepted on the second attempt! 🙌 💪 🎉

But there are some packages that have a hard time getting in CRAN. 😅 Is your package's case? I'd like to hear what are the biggest roadblocks.🤔

https://llrs.dev/post/2024/01/10/submission-cran-first-try/

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

CRAN is looking for someone to maintain #XML package: #rStats

"So we are looking for a person volunteering to take over 'XML'.
Please let us know if you are interested."

The task is not easy: many thousand of packages depend on it. Anyone taking it will be doing a great service to the R community.

I have a post about the situation they are in but it seems lacking the plots and some content. I'll update this toot once I fix it, to provide a link to it.

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

I am interested in learning more about repositories (not about the packages in them).
I collected some articles and text in this post.
Is it missing something? Let me know!
https://llrs.dev/post/2023/12/09/packaging-r-repositories/

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

While taking a deep breath is a great time to read “Aspects of the Social Organization and Trajectory of the R Project” published at the Journal 15 years ago.
It has great insights on the feelings and opinions of several key members:
https://journal.r-project.org/articles/RJ-2009-014/

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

Do you want to improve messages in your language?
On July 2nd there will be another tutorial about how to translate R the easy way 😄
Is so easy last release includes my contributions in two languages: and Spanish.

If you see some message you want translated in those languages let me know and if you attend the tutorial I'll teach you how (and if not I'll do it myself 😃)

Register for the online : https://events.linuxfoundation.org/user/program/virtual-schedule/

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

Sometimes it is surprising what other people find surprising of something you know: in this case function calls. But I have to admit that I haven't seen or used much "Split-horizon scoping": https://blog.moertel.com/posts/2006-01-20-wondrous-oddities-rs-function-call-semantics.html

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

Recently someone mentioned the difficulty of submitting to CRAN . In close to 4 years of data, I found that 55% of new package submissions fail on the first try (7202 new packages in the period analyzed) .
Overall, ~70% of submissions fail to pass CRAN checks (15926 different versions of packages submitted).
I am checking the data, but I'll post a blog soon. More or less in line with the latest update from CRAN: https://journal.r-project.org/news/RJ-2023-1-cran/

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@Mehrad No, exchanges between CRAN volunteers and maintainers are not public: they can contain sensitive data and are private (GDPR, ...).

If they are about wording and naming they are manual actions, as per the link, but those could also be, fix links, change of maintainers or similar exchanges. I could try to retrieve problems in checks and count that, but the historic archive doesn't have it. I tried to document them via self-reporting some years ago in https://github.com/cranchange/cran_histories/discussions ...

davidbraze, to random
@davidbraze@mstdn.social avatar

within the last year or so @Posit has taken a big tranche of venture capital. VC wants one thing: a massive return, 10x minimum. there are two ways to get that. first is to take a company public. I don't think that's likely here. second is a buy out by a major player like Oracle, Microsoft, Amazon, or another of that ilk. I guess this is what posit's sugar daddy is likely angling for. this isn't unprecedented in the world. who else remembers Revolution R?

https://mastodon.social/@awong234/111751453549394950

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@thomas_mock @bbolker @benschneider @davidbraze Great, thanks for explaining how the reports work for "B Corps". Looking forward to reading the next one.

brodriguesco, to random
@brodriguesco@fosstodon.org avatar

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

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@brodriguesco In a package I built I had also the *.R files which are missing in your case (not sure if it doesn't complain about them or they are missing)

sotneStatue, to bioinformatics
@sotneStatue@fosstodon.org avatar

Today I'll be using #R for RNAseq analysis for the first time, wish me luck

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@sotneStatue Good luck. I'm sure you'll find @Bioconductor packages very helpful! There is also a lot of materials on how to do it.
Pst if you use R the hashtag we use is usually . You might get more help if you post it with that hashtag 😉

sjcowtan, to random

does just what I want, but dare I use it in anything that needs to be maintainable? OO R implementations get replaced so quickly. Is it better to just pretend the only options are and ?

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@sjcowtan They are not replaced quickly, that's why there are so many. But S7 is < 1.0.0 so not quite production ready. There might be some breaking changes down the path.

coolbutuseless, to random
@coolbutuseless@fosstodon.org avatar

Survey: what new bit of syntax would you like in base #RStats?

What should the following bits of syntax do?

  • ===
  • ++ And --
  • +=
  • //
  • ?
  • {{ }}
  • [[[ ]]]
  • <<==
  • (?: X)
Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@klmr @Mehrad @coolbutuseless could that part be extracted of box? Or used without changing the project to the framework?

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@Mehrad yes, I don't know how {devtools}/{pkgload} displays the development version of the documentation, but I would look more in that direction.
@klmr @coolbutuseless

kupac, to random

Is there something like the Debian package popularity contest, but for packages on CRAN/Bioconductor?

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@kupac CRAN packages served from the Posit mirror or the global mirror are logged so you can use that as a proxy (But how representative the data is is a mystery). See this package to filter the data: https://cran.r-project.org/package=packageRank

Recently for a Rconsortium project @eliocamp was proposing a similar tool to popularity-contest to help detect which help pages are more viewed.

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

Some reflections about repositories: https://llrs.dev/post/2024/05/05/packaging-r-getting-in/
Which definition of cran-like repository do you normally use for R?

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@specphil I might provide some feedback, just the first paragraph lead me to two comments...
You can have a package on CRAN to depend on one that is not there or Bioconductor via Additional_repositories, it is used by several packages (I don't remember if 20 or 200).

But maybe it is me that I started with the z vignette and not the a (while I read @brodriguesco comments and some posts about Nix there is a lot to learn with it).

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@specphil So basically 2 as 2 includes 1.
I don't know much about Nixpkgs. Does it accept R packages outside those two repositories?

Lluis_Revilla, to random Spanish
@Lluis_Revilla@fosstodon.org avatar

El año pasado coorganicé el congreso de de España en Barcelona. Este año será en Sevilla. Si quiere venir a presentar (o no) seréis muy bienvenidos. Podéis presentar talleres, ponencias o posters de cualquier campo! Aunque sea un hobby, ¡¡seguro que alguien va aprender de ti!!
Conocerás a muy buena gente de toda España de todos los sectores.
Si tenéis dudas podéis contactar conmigo o con los organizadores de este año.

http://www.biometricsociety.net/2024/03/27/iii-congreso-xiv-jornadas-de-usuarios-de-r/

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

Aprovecho para remarcar que en una semana tendremos nuestro evento useR de #rstats en #Barcelona espero que sea de interés cómo sacar datos del INE y usarlos.

Más detalles y para inscribirse en https://www.meetup.com/barcelonar/events/300358325/

layal, to random
@layal@fosstodon.org avatar

Do you know what the difference is between nested and packed data? And what does this difference look like in a JSON format? If you're curious about that, please check my last blog post out: https://rdiscovery.netlify.app/posts/2024-05-30_pack-nest/. Cheers😉

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@Mehrad @layal I used nested data.frames when I want to summarize its content based on some other content of the row. It keeps the data in the same data.frame.
I also used it for convenience when wrapping content from APIS serving highly nested JSON. Instead of returning a list I provide a data.frame with some columns being another list with a data.frame

sjcowtan, to vscode

Can anyone here tell me how to stop the #vscode #R linter highlighting lines where I define functions which have a na.rm argument, because it's not snake case? I've read as much as I could find about linter options but couldn't find the right one (camel case option yes, dot case no). The highlighted lines are distracting my brain ferrets, and I won't change the case of the option, because standards are a Thing.

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@sjcowtan Probably you'll need to personalize the linter: https://lintr.r-lib.org/articles/lintr.html#configuring-linters you might need to tweak the object_name_linter linter or a similar one to avoid this. But might be a good point to raise the issue to the maintainers.

ai4blobcat, to rstats

I’m still considering whether to attend posit conference 2024. I’d like to attend the career fair to look for data science related jobs, meanwhile listening some talks. But the ticket is still expensive even for the students, I applied for Opportunity Scholarships but haven’t got any replies from @Posit till now. I doubt is it worthwhile to spend $1198 on a 3-day conference mainly for the career fair? Can anyone have some experiences of posit give some advice? Really appreciate it @rstats

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@ai4blobcat @Posit @rstats I haven't been in such conference. But as a company sponsored conference I think most of the events will be about Posit products. I will attend the conference instead for similar reasons (but it is longer and globally the price will be slightly higher). I too hope it pays off in the long run.

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@grrrck @ai4blobcat Thanks Garrick, the materials are great and I use them to know the latest updates. But in the years I've been following the conference few have been about finding a job or given by recruiters.

  • All
  • Subscribed
  • Moderated
  • Favorites
  • •
  • provamag3
  • InstantRegret
  • mdbf
  • ngwrru68w68
  • magazineikmin
  • thenastyranch
  • rosin
  • khanakhh
  • osvaldo12
  • Youngstown
  • slotface
  • Durango
  • kavyap
  • DreamBathrooms
  • JUstTest
  • GTA5RPClips
  • ethstaker
  • cisconetworking
  • tester
  • modclub
  • everett
  • cubers
  • tacticalgear
  • Leos
  • megavids
  • normalnudes
  • anitta
  • lostlight
  • All magazines
    •