@Lluis_Revilla@fosstodon.org avatar

Lluis_Revilla

@Lluis_Revilla@fosstodon.org

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

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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 😉

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 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,
@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).

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 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 en 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/

ai4blobcat, to rstats
@ai4blobcat@sigmoid.social avatar

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.

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

sjcowtan, to random
@sjcowtan@mastodon.online avatar

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 ?

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

sjcowtan, to vscode
@sjcowtan@mastodon.online avatar

Can anyone here tell me how to stop the #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.

kupac, to random
@kupac@functional.cafe avatar

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.

brodriguesco, to random
@brodriguesco@fosstodon.org avatar

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

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)

Lluis_Revilla, to random
@Lluis_Revilla@fosstodon.org avatar

CRAN is looking for someone to maintain package:

"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

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

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 #rstats world. who else remembers Revolution R?

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

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@bbolker @benschneider @davidbraze I tried several times to find other reports and I wasn't able. It doesn't seem they are public if they were written. This seems like the old canary document companies used to use, if it is not present you know what it means...

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.

mattcowgill, to random
@mattcowgill@mastodon.social avatar

I’m kind of worried about Posit — and by extension,

From: @zkamvar
https://hachyderm.io/@zkamvar/111699279163834211

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@mattcowgill @zkamvar why are you worried about the language? Does the R community depend so much on those great well-payed developers than the thousands that contribute for free (including R core members and CRAN team)?

Lluis_Revilla,
@Lluis_Revilla@fosstodon.org avatar

@alastairmrushworth @mattcowgill @zkamvar 🤔 Could you (both) elaborate? Thanks! 😃

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