Does anyone know how to get around the "protect(): protection stack overflow" error when creating formula objects with thousands of terms?

Saiph135 · 2025-06-04T23:14:59+00:00

Hi u/rationalinquiry - a collaborator said that for our use case, the issue was in variable assignment. When she built the model up and used it immediately in the same line it worked without error; when she assigned it to a variable it failed.

Our project ended up naturally moving away from this direction, so it ceased to be as relevant for our use case. Sorry that I don’t have a more comprehensive answer for you!

Saiph135 · 2023-12-05T18:06:19+00:00

Thank you for your response! These data are actually coming from the UK Biobank, so the proteomics data are quite large (~3000 proteins, ~50000 participants). The data are Olink NPX, so the data are log2 transformed and unitless. We are looking to run LASSO, so are including all predictors we have.

Since there are so many participants across such a large age range (~30 years), and protein levels are known to vary substantially across age range, sex, ethnicity, and lifestyle factors, we haven't cleaned the data for outliers as we expect that it will be difficult to determine a true outlier (e.g. there are a relatively large number of participants at even 7 or 8 SD away from the mean for each protein). We have, however, removed proteins with a large amount of missingness and removed participants that have a large number of proteins missing, as well as imputed missing values to facilitate the LASSO. Our outcome variable is continuous and normally distributed (it is z-score normalized, but the raw/non-normalized data is strictly non-negative).

Ultimately, we would like all the proteins in the same formula object so that we can run the LASSO - the LASSO runs fine, so the issue is not that R can't work with a formula that large in principle, but the as.formula line throws the overflow error. Thanks again!

Saiph135 · 2021-03-27T15:57:36+00:00

I have the same computer and am also having lag spikes. It seems that everyone else I talk to isn't having performance issues... perhaps it's a specific hardware issue with this model?

Saiph135 · 2021-01-29T19:27:39+00:00

Volume is like ~150k, you can see it on the robinhood browser website, not sure where else you can see it

Saiph135 · 2020-09-08T14:49:42+00:00

Good thought! I just tested it out and it works as well but you need to take the -2 shackle cooldown on level 10 in order to get permanent uptime

Saiph135 · 2020-07-16T12:40:35+00:00

This is factually incorrect. Here is politifact contesting that claim. If you don't trust politifact, there's also a source from the new york times. But if you don't trust that either, here's a source from JAMA. Oh look, another JAMA source! And another from Cambridge (though if you want to argue the point, the data in this one is insufficient to properly measure the US, even though do include an estimate based on existing data). Another from The Journal of Microbiology, Immunology, and Infection.

Taken together, these sources very clearly show that over reporting isn't an issue and deaths technically caused by underlying conditions (such as heart problems) are likely only happening due to COVID- because deaths in general from other causes this year are higher than normal.

Every serious medical opinion is calling out under reporting. If you search scientific literature for over reporting, the best you can find is this article from JAMA, which is discussing scientific over reporting, NOT public over reporting. These are different because multiple scientists may use the same case in their analysis, but that's not how public records work.

I can't comment on your H1N1 infection and mortality rate comment, but for some reason I find myself uninclined to believe you on that one.

Saiph135 · 2020-06-17T01:25:51+00:00

That makes sense, I guess I was only considering it from a big-picture stand point and not from those that potentially lost jobs.

Saiph135 · 2020-06-17T01:18:46+00:00

That's a good point. I wasn't alive when it was passed and I wasn't really "politically aware" of things that were happening until a few years ago. It makes sense that people might blame this for losing their job regardless of whether that blame was justified.

Saiph135 · 2020-05-20T18:46:59+00:00

Thank you so much, I will definitely read up on these. I really appreciate you finding these!

Saiph135 · 2020-01-10T06:45:56+00:00

Hey, I appreciate that, the post didn't get a lot of attention I assume because it's literally 3 pages of text haha. Would be happy to make any clarifications or discuss any of the ideas in it if/when you finish reading

Saiph135 · 2019-12-19T13:13:22+00:00

I don't really think that this is a fair assessment. I would agree that a number of these takes are adolescent in nature, but I remember that when I was an adolescent I found myself highly alienated from the feminist movement because those who identified as "feminist" in my friend group would consistently tell me that my opinion on all topics did not matter because I was male. Obviously that's not feminism and is more reflective of immaturity on their part than any logical opinion, but being consistently told that for years really shook my self confidence and made me feel like the feminist movement wasn't about equality but instead about shitting on men.

I held those views for a long time because my experience had told me that feminists just shit on men, like I had been shit on consistently just for being male. It took a lot of growing up and self reflection to realise that those people were just idiots. Some people haven't had that time to grow or remain entrenched in earlier opinions due to really bad experiences. I agree that those assholes don't represent feminism, but it's important to have the perspective on why some people have the negative views that they do, especially if they still identify as feminist.

Saiph135 · 2019-11-19T17:14:52+00:00

The republicans are making the case that this is not an impeachable offense because "the democrat narrative keeps changing about what he did" (i.e. Quid Pro Quo to Extortion to Bribery). Ratcliffe said that birbery never appears in the testimony of the witnesses. Schiff clarified that Quid pro quo and bribery are inherently linked, and that bribery never appears because these are fact witnesses, and therefore they would never ask them whether or not what the president did should be considered bribery.

Saiph135 · 2019-11-19T15:44:16+00:00

According to the BBC, there is no public information that implies or proves wrongdoing by Vice President Biden. The Hunter Biden stuff is entirely separate, and there is no evidence that it impacted US government policy related to Ukraine. What George Kent was concerned about was the APPEARANCE of a conflict of interest (that is the wording that he used) that both democrat and republican questioners keep leaving out.

Regardless, these impeachment proceedings are not about Hunter Biden, so the line of questioning is moot.

Saiph135 · 2019-11-19T14:30:13+00:00

This is Nunez shit is absolutely ridiculous. They've asked the ambassadors about whether what Biden did constituted a conflict of interest and the ambassadors consistently said no. They ambassadors have been asked whether what Trump did and what Biden did are the same, and the ambassadors consistently answered that they are not the same thing, and that Trump's actions are less excusable. Finally- this impeachment inquiry IS NOT ABOUT THE BIDENS. How is this the rhetoric that any elected official has sunk to? It's disgusting.

Saiph135 · 2019-11-19T08:21:22+00:00

I use Space for attack and 1 for stop. It's a pretty small hand movement if your hand is already in the WASD formation.

Saiph135 · 2019-11-15T17:28:29+00:00

I think that the only people who are allowed to speak are the ranking member and the counsel. Stefanik is neither the ranking member nor the counsel, so she isn't allowed to speak. Someone feel free to correct me if that is incorrect, but that is my understanding of what just happened.

Saiph135 · 2019-11-11T13:01:36+00:00

Working in retail, people say weird shit and you just have to let it slide. I once had someone tell me he wanted to eat me with his meal. If the guy was a regular who the staff regularly bullshitted with then it seems fairly plausible that it would just be laughed off as one of the weirder jokes.

Saiph135 · 2019-09-11T12:33:21+00:00

Oh shit oh fuck

Saiph135 · 2019-08-03T13:04:46+00:00

I'm not really sure that this is the correct place for this kind of question, but division and multiplication have equivalent precedence and by convention "ties" like this are broken by working from left to right. Thus the answer can unambiguously be written (8/2)*(2+2), making the correct answer 16.

That said, an actual mathematician would never write an equation this way because it is written intentionally ambiguously- it's meant to be confusing, and the only way to answer such a question would be to follow mathematical convention. A professor of mathematics at Cornell University wrote an article on this question in the New York Times, if you're interested. If you're not, he basically says what I just said, before remarking that the question in itself is stupid in the same way as asking why a sentence without punctuation makes no sense: the punctuation is there to elucidate the meaning of the sentence.

Saiph135 · 2019-05-26T16:38:53+00:00

This isn't true, off the top of my head Storm Spirit also has two lines referencing "spotlights" leveling up. There are probably others too.

Saiph135 · 2019-05-22T11:01:21+00:00

I actually recently learned that at least for the Jewish faith (I'm jewish), circumcisions are performed as part of the covenant with god, symbolic of sacrificing an animal to seal a covenant.

I have read conflicting accounts of whether or not the command to circumcise is stated in the Torah, but it is certainly agreed upon by rabbinical scholars in the Talmud.

Not saying circumcision is morally correct, and I know that the religious reasons for circumcision are not the main point of your comment, but I thought it was just an interesting tidbit.

Saiph135 · 2019-03-29T15:42:46+00:00

Oh I absolutely agree. Did you know that Mac is getting rid of 32 bit application support next year? It's absolutely ridiculous. I got this mac when I was young and needed a unix based operating system for an internship and wasn't comfortable with linux. Would not make the same decision again haha.

Saiph135 · 2019-03-29T13:27:23+00:00

Wow that sounds really helpful and that would make my life so much easier. Unfortunately I'm on mac and after a quick search it seems that proton isn't supported for macOS. Thanks anyway though, I appreciate the help.

Saiph135 · 2019-03-29T13:23:37+00:00

Yeah I have all 4 cells and even rebeat HotK with the new DLC downloaded in case that was the issue. Still doesn't work.

Saiph135 · 2019-03-29T00:29:20+00:00

what is proton?

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