Re: [R] Number of Cores limited to two in CRAN
Dear Henrik, Thank you! This is quite helpful, especially your longer blog post. Best regards, Ravi From: Henrik Bengtsson Sent: Sunday, July 2, 2023 4:33 AM To: Ravi Varadhan Cc: R-Help Subject: Re: [R] Number of Cores limited to two in CRAN External Email - Use Caution Short answer: You don't want to override that limit in your R package. Don't do it. Long answer: You'll find the reason for this in the 'CRAN Repository Policy' (https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Fpolicies.html=05%7C01%7Cravi.varadhan%40jhu.edu%7Cbf56c90173504853907408db7ad70f08%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C638238836311718317%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=KDB6%2BqMgn4KrKtVEgWezfRY9isT926wLwZGg5yuDKI4%3D=0<https://cran.r-project.org/web/packages/policies.html>). Specifically, the following passage: "Checking the package should take as little CPU time as possible, as the CRAN check farm is a very limited resource and there are thousands of packages. Long-running tests and vignette code can be made optional for checking, but do ensure that the checks that are left do exercise all the features of the package. **If running a package uses multiple threads/cores it must never use more than two simultaneously: the check farm is a shared resource and will typically be running many checks simultaneously.** Examples should run for no more than a few seconds each: they are intended to exemplify to the would-be user how to use the functions in the package." Basically, you can use two cores to demonstrate or validate (e.g. in package tests) that your code *can* run in parallel, but you must not use more than that to demonstrate that your code can "run super fast". Even-longer answer: See my blog post 'Please Avoid detectCores() in your R Packages' (https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jottr.org%2F2022%2F12%2F05%2Favoid-detectcores%2F=05%7C01%7Cravi.varadhan%40jhu.edu%7Cbf56c90173504853907408db7ad70f08%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C638238836311718317%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=xPkA6JCccHZcST76lWa6xFYWWKBOZYQCOezF5t4YVPM%3D=0<https://www.jottr.org/2022/12/05/avoid-detectcores/>) from 2022-12-05 for even more reasons. /Henrik On Sun, Jul 2, 2023 at 9:55 AM Ravi Varadhan via R-help wrote: > > This is the specific error messsage from R CMD check --as-cran > > > Error in .check_ncores(length(names)) : 16 simultaneous processes spawned > Calls: prepost -> makeCluster -> makePSOCKcluster -> .check_ncores > Execution halted > > > Thanks, > Ravi > > > From: Ravi Varadhan > Sent: Saturday, July 1, 2023 1:15 PM > To: R-Help > Subject: Number of Cores limited to two in CRAN > > Hi, > I am developing a package where I would like to utilize multiple cores for > parallel computing. However, I get an error message when I run R CMD check > --as-cran. > > I read that CRAN limits the number of cores to 2. Is this correct? Is there > any way to overcome this limitation? > > Thank you, > Ravi > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help=05%7C01%7Cravi.varadhan%40jhu.edu%7Cbf56c90173504853907408db7ad70f08%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C638238836311873942%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=KTNwXurNvbEhviVf15RF0la%2FvUVGBW60yuyVVy9Umxc%3D=0<https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.html=05%7C01%7Cravi.varadhan%40jhu.edu%7Cbf56c90173504853907408db7ad70f08%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C638238836311873942%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=HvGb20UiUey9O3plynLiRmHQtqpjfrndk2iPfvleT3Q%3D=0<http://www.r-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Number of Cores limited to two in CRAN
This is the specific error messsage from R CMD check --as-cran Error in .check_ncores(length(names)) : 16 simultaneous processes spawned Calls: prepost -> makeCluster -> makePSOCKcluster -> .check_ncores Execution halted Thanks, Ravi From: Ravi Varadhan Sent: Saturday, July 1, 2023 1:15 PM To: R-Help Subject: Number of Cores limited to two in CRAN Hi, I am developing a package where I would like to utilize multiple cores for parallel computing. However, I get an error message when I run R CMD check --as-cran. I read that CRAN limits the number of cores to 2. Is this correct? Is there any way to overcome this limitation? Thank you, Ravi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Number of Cores limited to two in CRAN
Hi, I am developing a package where I would like to utilize multiple cores for parallel computing. However, I get an error message when I run R CMD check --as-cran. I read that CRAN limits the number of cores to 2. Is this correct? Is there any way to overcome this limitation? Thank you, Ravi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to use ifelse without invoking warnings
Thank you to Bert, Sarah, and John. I did consider suppressing warnings, but I felt that there must be a more principled approach. While John's solution is what I would prefer, I cannot help but wonder why `ifelse' was not constructed to avoid this behavior. Thanks & Best regards, Ravi From: John Fox Sent: Thursday, October 7, 2021 2:00 PM To: Ravi Varadhan Cc: R-Help Subject: Re: [R] How to use ifelse without invoking warnings External Email - Use Caution Dear Ravi, It's already been suggested that you could disable warnings, but that's risky in case there's a warning that you didn't anticipate. Here's a different approach: > kk <- k[k >= -1 & k <= n] > ans <- numeric(length(k)) > ans[k > n] <- 1 > ans[k >= -1 & k <= n] <- pbeta(p, kk + 1, n - kk, lower.tail=FALSE) > ans [1] 0.0 0.006821826 0.254991551 1.0 BTW, I don't think that you mentioned that p = 0.3, but that seems apparent from the output you showed. I hope this helps, John -- John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada web: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsocialsciences.mcmaster.ca%2Fjfox%2Fdata=04%7C01%7Cravi.varadhan%40jhu.edu%7Cfd882e7c4f4349db34e108d989bc6a9f%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637692265160038474%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000sdata=Q33yXm36BwEVKUWO72CWFpSUx7gcEEXhM3qFi7n78ZM%3Dreserved=0 On 2021-10-07 12:29 p.m., Ravi Varadhan via R-help wrote: > Hi, > I would like to execute the following vectorized calculation: > >ans <- ifelse (k >= -1 & k <= n, pbeta(p, k+1, n-k, lower.tail = FALSE), > ifelse (k < -1, 0, 1) ) > > For example: > > >> k <- c(-1.2,-0.5, 1.5, 10.4) >> n <- 10 >> ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse >> (k < -1, 0, 1) ) > Warning message: > In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced >> print(ans) > [1] 0.0 0.006821826 0.254991551 1.0 > > The answer is correct. However, I would like to eliminate the annoying > warnings. Is there a better way to do this? > > Thank you, > Ravi > > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-helpdata=04%7C01%7Cravi.varadhan%40jhu.edu%7Cfd882e7c4f4349db34e108d989bc6a9f%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637692265160048428%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000sdata=FXX%2B4zNT0JHBnDFO5dXBDQ484oQF1EK5%2Fa0dG9P%2F4k4%3Dreserved=0 > PLEASE do read the posting guide > https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.htmldata=04%7C01%7Cravi.varadhan%40jhu.edu%7Cfd882e7c4f4349db34e108d989bc6a9f%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637692265160048428%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000sdata=ss2ohzJIY6qj0eAexk4yVzTzbjXxK5VZNors0GpsbA0%3Dreserved=0 > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to use ifelse without invoking warnings
Hi, I would like to execute the following vectorized calculation: ans <- ifelse (k >= -1 & k <= n, pbeta(p, k+1, n-k, lower.tail = FALSE), ifelse (k < -1, 0, 1) ) For example: > k <- c(-1.2,-0.5, 1.5, 10.4) > n <- 10 > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse (k > < -1, 0, 1) ) Warning message: In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced > print(ans) [1] 0.0 0.006821826 0.254991551 1.0 The answer is correct. However, I would like to eliminate the annoying warnings. Is there a better way to do this? Thank you, Ravi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
