Re: [R] Regarding Issue Running Parallel Computing on Linux RHEL version 8

2025-01-21 Thread Ivan Krylov via R-help
В Mon, 20 Jan 2025 13:45:25 + "Huseni, Sadamhusen" пишет: > Error in as.data.frame.default(x[[i]], optional = TRUE) : > cannot coerce class ‘"call"’ to a data.frame > Calls: write.table ... data.frame -> as.data.frame -> > as.data.frame.default The underlying issue is that somehow the code

Re: [R] Regarding Issue Running Parallel Computing on Linux RHEL version 8

2025-01-14 Thread Ivan Krylov via R-help
В Tue, 14 Jan 2025 14:23:54 + "Huseni, Sadamhusen" пишет: > ###***Session information from Linux version 8 > R version 4.4.1 (2024-06-14) > Platform: x86_64-redhat-linux-gnu > Running under: Red Hat Enterprise Linux 8.10 (Ootpa) > > Matrix products: default > BLAS/LAPACK: /usr/lib64/libopen

Re: [R] Regarding Issue Running Parallel Computing on Linux RHEL version 8

2025-01-14 Thread Ivan Krylov via R-help
Dear Sadam, В Mon, 13 Jan 2025 14:34:20 + "Huseni, Sadamhusen" пишет: > Issue Observed: The script hangs and does not complete execution > post-update. Previously, it took around two hours; now it runs for > over 17 hours without finishing. Do you still have the RHEL 7 machine? Could you pl

Re: [R] Help Parsing String? From HTML

2025-01-05 Thread Ivan Krylov via R-help
В Sun, 5 Jan 2025 20:03:11 + "Sparks, John via R-help" пишет: > > mystring > {xml_nodeset (1)} > [1] {\n "symbol": "ABI",\n "open": 21.04,\n "high": 21.05,\n > "low": 20.06,\n "close": 20.2,\n "volume": 938700,\n "from": > "2005-01-04"\n} > > But I can't find a way to isolate the ind

Re: [R] mclapply hanging occasionally on macos

2024-12-31 Thread Ivan Krylov via R-help
В Mon, 30 Dec 2024 19:16:11 -0800 Ivo Welch пишет: > useless.function <- function( ) { > y <- rnorm(3); x <- rnorm(3) > summary( lm( y ~ x )) ## useless > NULL > } > > run30 <- function(i) { > message("run30=", i) > useless.function() > } > > run30( 0 ) > message("many mc")

Re: [R] Mutate issue help needed

2024-12-17 Thread Ivan Krylov via R-help
В Tue, 17 Dec 2024 06:44:50 -0700 Neotropical bat risk assessments пишет: > fname <- "Buzz.txt" > All<- fname I think the code needs a call to read.table() or another function to read your data here. 'All' is still a string containing the name of the file, not its contents. > All %>% > mutate

Re: [R] Confirmation of no Electronic Communication functionality

2024-12-13 Thread Ivan Krylov via R-help
Dear Edward Woo, Welcome to R-help! В Fri, 13 Dec 2024 14:24:18 + Edward Woo via R-help пишет: > need an email confirming that r does not include any electronic > communication functionality within the program Could you please provide a definition of electronic communication functionality?

Re: [R] Issue with non-standard file 'vert.txt' in R CMD check

2024-11-20 Thread Ivan Krylov via R-help
Dear Zahra Heidari Ghahfarrokhi, Welcome to R-help! В Mon, 18 Nov 2024 19:48:39 +0330 zahra heidari gh пишет: > A non-standard file named `vert.txt` is being generated in the > check directory, causing a NOTE in the check results. Despite adding > `vert.txt` to `.Rbuildignore`, the file is sti

Re: [R] Invalid term in model formula with gmm after formula.tools is loaded

2024-11-04 Thread Ivan Krylov via R-help
В Sun, 3 Nov 2024 12:53:52 +0100 Elysée Aristide пишет: > Does that mean that I should send a new message? Or is it okay for > this time? No need to post it again. Did it help to replace the as.character() method for formulas provided by 'formula.tools'? I see the problem is already reported to

Re: [R] Invalid term in model formula with gmm after formula.tools is loaded

2024-11-01 Thread Ivan Krylov via R-help
Hi Aristide and welcome to R-help! Your message was a bit mangled [*]. It's best to compose messages to this mailing list in plain text. Otherwise (when composed in HTML), the mailing list eats the HTML part and we're left with the plain text part automatically generated by your mailer, which isn'

Re: [R] The RV coinertia coefficient to interpret multivariate analysis plots

2024-10-15 Thread Ivan Krylov via R-help
В Sun, 13 Oct 2024 13:19:09 +0200 David Bars пишет: > Through different microbiota datasets, I have plotted PCoA, db-RDA and > sPLS-DA using 3 different types of normalization methods (Total sum of > squares, cumulative sum of squares and rarefaction). For each dataset > and multivariate analysis

Re: [R] Warning object has offset 0. PDF file

2024-10-14 Thread Ivan Krylov via R-help
В Sun, 13 Oct 2024 12:45:36 +0200 "Jean-Louis Abitbol" пишет: > WARNING: > /Users/jla/Library/CloudStorage/Dropbox/7cordas/Caio/record/90 NEW > RODA SONG BOOK.pdf (object 254 0): object has offset 0 > > This does not prevent from getting the pages extracted properly and > written to a pdf file w

Re: [R] Time zones in POSIClt objects

2024-10-11 Thread Ivan Krylov via R-help
В Thu, 10 Oct 2024 17:16:52 +0200 Jan van der Laan пишет: > This is where it is unclear to me what the purpose is of the `zone` > element of the POSIXlt object. It does allow for registering a time > zone per element. It just seems to be ignored. I think that since POSIXlt is an interface to wh

Re: [R] apply

2024-10-04 Thread Ivan Krylov via R-help
В Fri, 4 Oct 2024 20:28:01 +0800 Steven Yen пишет: > Suppose I have two vectors, x and y. Is there a way > to do the covariance matrix with “apply”. There is no covariance matrix for just two samples (vectors) 'x' and 'y'. You can only get one covariance value for these. If you had a pair of v

Re: [R] apply

2024-10-04 Thread Ivan Krylov via R-help
В Fri, 4 Oct 2024 19:14:30 +0800 Steven Yen пишет: > I have a vector: > set.seed(123) > n<-3 > x<-rnorm(n); x [1] -0.56047565 -0.23017749 > 1.55870831 > var(x[1]) cov(x[1],x[2]) Are you sure you don't have a matrix? If you type var(x[1]) or cov(x[1],x[2]) into R, you can see that all these are

Re: [R] when installing packages for R on Linux, is it better to use my distro's package manager, or install.packages()?

2024-09-29 Thread Ivan Krylov via R-help
В Sat, 28 Sep 2024 18:05:08 -0400 "Christopher W. Ryan" пишет: > To install a new R package, is it better to use Linux Mint's pacakge > manager (e.g. synaptic, apt-get, or similar), or to install it within > R with install.packages("some_new_package")? Since you've already installed R itself fro

Re: [R] How to install this package

2024-09-25 Thread Ivan Krylov via R-help
В Wed, 25 Sep 2024 18:53:02 +0530 Christofer Bogaso пишет: > Error in dyn.load(dynlib <- getDynlib(dir)) : > > unable to load shared object > '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rgl/libs/rgl.so': > > > dlopen(/Library/Frameworks/R.framework/Versions/4.4-ar

Re: [R] Question about Date Object and time zones

2024-09-25 Thread Ivan Krylov via R-help
24 сентября 2024 г. 17:10:13 GMT+03:00, Luca Brinkmann via R-help пишет: > My current > understanding is, that a Date object does only save the days from the > origin and no more information about timezones or other information > (please correct me if I am wrong). You are correct. > the date o

Re: [R] store list objects in data.table

2024-09-22 Thread Ivan Krylov via R-help
В Sun, 22 Sep 2024 07:44:16 -0400 Naresh Gurbuxani пишет: > carsreg <- carsdt[, .(fit = lm(mpg ~ disp + hp + wt)), by = .(cyl)] > > #I would like a data.table with three rows, one each for "lm" object > corresponding to cyl value > > carsreg[, .N] > #[1] 36 Try wrapping the lm() expression in

Re: [R] "And" condition spanning over multiple columns in data frame

2024-09-12 Thread Ivan Krylov via R-help
В Thu, 12 Sep 2024 09:42:57 +0200 Francesca пишет: > c10Dt <- mutate(c10Dt, exit1= ifelse(is.na(cp1) & id!=1, 1, 0)) > So, I create a new variable, called exit1, in which the program > selects cp1, checks if it is NA, and if it is NA but also the value > of the column "id" is not 1, then it giv

Re: [R] non-conformable arrays

2024-09-11 Thread Ivan Krylov via R-help
В Wed, 11 Sep 2024 17:55:53 +0200 Thierry Onkelinx пишет: > For those how like a fully reproducible example: > the offending line in the code: > https://github.com/inbo/multimput/blob/e1cd0cdff7d2868e4101c411f7508301c7be7482/R/impute_glmermod.R#L65 > a (failing) unit test for the code: > https://

Re: [R] Stop or limit to console printing large list and so on

2024-09-11 Thread Ivan Krylov via R-help
В Wed, 11 Sep 2024 09:44:05 -0400 stephen sefick пишет: > I am having a problem with accidentally typing an object name at the > console that is a very large list and then having to wait for it to be > printed until I can resume my work. Does it help to interrupt the process? https://www.gnu.or

Re: [R] aggregating data with quality control

2024-08-31 Thread Ivan Krylov via R-help
В Sat, 31 Aug 2024 11:15:10 + Stefano Sofia пишет: > Evaluating the daily mean indipendently from the status is very easy: > > aggregate(mydf$hs, by=list(format(mydf$data_POSIX, "%Y"), > format(mydf$data_POSIX, "%m"), format(mydf$data_POSIX, "%d")), > my.mean) > > > Things become more comp

Re: [R] boxplot of raster and shapefile

2024-08-27 Thread Ivan Krylov via R-help
В Mon, 26 Aug 2024 14:33:02 +0200 SIBYLLE STÖCKLI via R-help пишет: > > # Extract raster values within the shapefile > > extracted_values <- extract(raster_file, shape_file) > > # Assuming the shapefile has multiple polygons and you want to > > # create a boxplot for each > > data_list <- lapply

Re: [R] checking for unstated dependencies in examples ... ERROR

2024-08-25 Thread Ivan Krylov via R-help
В Sun, 25 Aug 2024 20:32:07 + Søren Højsgaard via R-help пишет: > checking for unstated dependencies in examples ... ERROR > Warning: parse error in file 'lines': > 77:20) Looks like one of your Rd \examples{} has a syntax error in it. If there is a file gRain.Rcheck/gRain-Ex.R, try to f

Re: [R] paired raster boxplots

2024-08-24 Thread Ivan Krylov via R-help
В Sat, 24 Aug 2024 10:24:36 +0200 пишет: > Yes indeed my raster "s" (the shape file for the boxplot classes) has > several layers. If 's' contains more than one layer, then this already prevents you from giving two names to stack(r, s). > That's way I tried to select a layer by " > s<-sf$Unterr

Re: [R] paired raster boxplots

2024-08-23 Thread Ivan Krylov via R-help
В Fri, 23 Aug 2024 10:15:55 +0200 пишет: > > s<-sf$Unterregio > > r<-allrasters_pres[[1]] > > > > > > rs <- stack(r, s) > > names(rs) <- c('r', 's') > Error in `names<-`(`*tmp*`, value = c("r", "s")) : > incorrect number of layer names It looks like at least one of the rasters 'r' and 's'

Re: [R] Linear regression and stand deviation at the Linux command line

2024-08-23 Thread Ivan Krylov via R-help
В Thu, 22 Aug 2024 13:07:37 -0600 Keith Christian пишет: > I'm interested in R construct(s) to be entered at the command > line that would output slope, y-intercept, and r-squared values read > from a csv or other filename entered at the command line, and the same > for standard deviation calcula

Re: [R] fcaR not for latest R version

2024-08-22 Thread Ivan Krylov via R-help
Dear Peter, В Thu, 22 Aug 2024 16:53:01 +0200 Peter van Summeren пишет: > Did anyone use fcaR for the current version of R/Rstudio on the Mac? Maybe someone hasn't used fcaR on a Mac but can guess a solution to your problem anyway. Maybe someone has, but has no idea how to help you. On mailing

Re: [R] paired raster boxplots

2024-08-22 Thread Ivan Krylov via R-help
В Thu, 22 Aug 2024 08:46:03 +0200 SIBYLLE STÖCKLI via R-help пишет: > rr2s <- stack(r, r2,s) > > names(rs) <- c('r', 's', 'r2') > > Error in `names<-`(`*tmp*`, value = c("r", "s", "r2")) : > > incorrect number of layer names The error must be happening because the variable named 'rs' in y

Re: [R] Force conversion of (POSIXct) time zone with base R

2024-08-22 Thread Ivan Krylov via R-help
В Thu, 22 Aug 2024 08:59:46 + Iago Giné Vázquez пишет: > How should POSIXct time zone be changed without modifying the > specified time (so fix the time zone). Since POSIXct represents the number of seconds since the specified "epoch" moment (beginning of 1970 UTC), fixing the time zone whi

Re: [R] Terminating a cmd windows from R

2024-08-17 Thread Ivan Krylov via R-help
В Sat, 17 Aug 2024 11:47:30 + SIMON Nicolas via R-help пишет: > nmrun <- paste0("cmd.exe /k ",nm_log,".bat ",nmi,".ctl ",nmi,".lst") You are using the /k option that instructs cmd.exe to keep the command prompt open. Does the batch file contain an explicit "exit" to ensure that cmd.exe termi

Re: [R] allequal diff

2024-08-16 Thread Ivan Krylov via R-help
В Fri, 16 Aug 2024 11:32:58 +0200 пишет: > # values and mask r1 > r1 <- getValues(r1) > mask1 <- is.na(r1) > # Do the same for r2 > r2 <- getValues(r2_resampled) > mask2 <- is.na(r2) > > # Combine the masks > all.equal(r1[!(mask1 & mask2)], r2[!(mask1 & mask2)]) Let's consider a more tangible e

Re: [R] allequal diff

2024-08-16 Thread Ivan Krylov via R-help
В Fri, 16 Aug 2024 10:35:35 +0200 пишет: > what do you mean by use is.na() in getValues(). So I need to call > getValues a second time? Not necessarily, but it's one of the options. I was thinking along the lines of: values1 <- getValues(r1) mask1 <- is.na(values1) # Do the same for r2 # Combin

Re: [R] allequal diff

2024-08-16 Thread Ivan Krylov via R-help
В Fri, 16 Aug 2024 07:19:38 +0200 SIBYLLE STÖCKLI via R-help пишет: > Is it possible to consider na.rm=TRUE? > > all.equal(getValues(r1), getValues(r2_resampled), tolerance = 0) > > [1] "'is.NA' value mismatch: 9544032 in current 66532795 in target" Use is.na() on getValues() outputs, combin

Re: [R] Printing

2024-08-11 Thread Ivan Krylov via R-help
В Sun, 11 Aug 2024 22:36:08 +0800 Steven Yen пишет: > All I need is printing by returning out (unless I turn it off). And, > retrieve ap and vap as needed as shown above. Guess I need to read > more about invisible. Perhaps you could print(out) instead of returning it in the if (printing) branc

Re: [R] WDI package commands timing out and not working

2024-08-09 Thread Ivan Krylov via R-help
В Fri, 9 Aug 2024 20:25:51 +0530 Anupam Tyagi пишет: > I am trying this in Bengaluru, India, using R-studio. I tried > downloading a single variable. It happened fast, in less than 5 > seconds. I tried downloading six variables, it took much longer, but > less than a minute. Tried eight variables

Re: [R] WDI package commands timing out and not working

2024-08-09 Thread Ivan Krylov via R-help
В Thu, 8 Aug 2024 12:43:23 +0530 Anupam Tyagi пишет: > In open.connection(con, "rb") : > URL > 'https://api.worldbank.org/v2/en/country/OED/indicator/NY.ADJ.NNAT.GN.ZS?format=json&date=1977:2020&per_page=32500&page=1': > Timeout of 60 seconds was reached If you try to open the link in the brow

Re: [R] Difference between stats.steps() and MuMIn.dredge() to select best fit model

2024-08-01 Thread Ivan Krylov via R-help
В Wed, 31 Jul 2024 11:56:55 + c.bu...@posteo.jp пишет: > step() explore the model space with a step wise approach. > And dredge() try out all possible combinations of the variables. > > But isn't that the same? I might have a mental block on this. > > Which model (formula) would dredge() "tes

Re: [R] Using optim() function to find MLE

2024-07-28 Thread Ivan Krylov via R-help
В Mon, 29 Jul 2024 09:52:22 +0530 Christofer Bogaso пишет: > LL = function(b0, b1) help(optim) documents that the function to be optimised takes a single argument, a vector containing the parameters. Here's how your LL function can be adapted to this interface: LL <- function(par) { b0 <- par[

Re: [R] plotting nnet function....

2024-07-27 Thread Ivan Krylov via R-help
В Sat, 27 Jul 2024 11:00:34 + akshay kulkarni пишет: > My question is : how to plot the final model on the actual data > points? Have you been able to obtain the predictions? What happens if you call predict() on the model object returned to you by train()? Once you have both the data and t

Re: [R] grDevices segfault when building R4.4.0 on RHEL 9.1.

2024-07-17 Thread Ivan Krylov via R-help
В Wed, 17 Jul 2024 02:35:22 + Miguel Esteva пишет: > I replaced the "--with-lapack" flag with "--with-lapack='-lflexiblas > -L/tools/flexiblas/3.4.2/lib64'" and everything built ok. Glad to see you managed to avoid the crash! > From a quick check in my emails, seems the RHEL9 system lapack

Re: [R] reticulate + virtual environments

2024-07-15 Thread Ivan Krylov via R-help
В Mon, 15 Jul 2024 07:56:17 +0200 Sigbert Klinke пишет: > > py_config() > > use_virtualenv("mmstat4.hu.data", required = TRUE) Does it help _not_ to call py_config() before use_virtualenv()? help(py_config) says that it forces the initialization of Python. When you later try to ask for a

Re: [R] Reinterpret data without saving it to a file 1st? Check for integer stopping at 1st decimal?

2024-07-14 Thread Ivan Krylov via R-help
В Sun, 14 Jul 2024 03:16:56 -0400 DynV Montrealer пишет: > Perhaps some way to break the spreadsheet data (eg XLdata <- > read_excel(...)), then put it back together without any writing to a > file (eg XLdataReformed <- reform(XLdata)) ? read_excel() is documented to return objects of class tibb

Re: [R] Problem loading BiodiversityR, Error: package ‘tcltk’ could not be loaded

2024-07-14 Thread Ivan Krylov via R-help
В Sat, 13 Jul 2024 16:04:17 +0100 Adam Hillier пишет: > error: X11 library is missing: install XQuartz from www.xquartz.org Does the problem go away if you install XQuartz from www.xquartz.org? "R installation and administration" section 4 also documents the requirement to have XQuartz instal

Re: [R] Weird R Studio behaviour...

2024-07-09 Thread Ivan Krylov via R-help
В Tue, 9 Jul 2024 13:02:17 + Levent TERLEMEZ via R-help пишет: > System is on W 10, and R 3.4.1 is working with R Studio. R Studio is > updated today https://posit.co/download/rstudio-desktop/ says "RStudio requires R 3.6.0+" so I'm afraid they don't support this configuration any more. --

Re: [R] Bug? plot.formula does need support plot.first / plot.last param in plot.default

2024-07-06 Thread Ivan Krylov via R-help
В Fri, 05 Jul 2024 14:35:40 +0300 "Erez Shomron" пишет: > This works as expected: > with(mtcars, plot(wt, mpg, plot.first = { > plot.window(range(wt), range(mpg)) > arrows(3, 15, 4, 30) > })) I think you meant panel.first, not plot.first. At least I cannot find any mention of plot.first

Re: [R] simple problem with unquoting argument

2024-07-03 Thread Ivan Krylov via R-help
В Wed, 3 Jul 2024 10:13:59 +0200 Troels Ring пишет: > Now e looks right - but I have been unable to find out how to get the > string e converted to the proper argument for sum()  - i.e. what  is > function xx? get(e) will return the value of the variable with the name stored in the variable e.

Re: [R] Referencing Sys.Date to a different time zone

2024-06-28 Thread Ivan Krylov via R-help
В Fri, 28 Jun 2024 18:52:26 +0200 Dennis Fisher пишет: > When I issue the command: > Sys.Date() > I would like to be able to obtain the value for Pacific time (which > differ for the first 9 hours of the day) By the time the value of Sys.Date() is created, it's too late to discern between

Re: [R] Regarding the Security Vulnerability CVE 2024 - 27322

2024-06-27 Thread Ivan Krylov via R-help
В Thu, 27 Jun 2024 11:08:53 + "Priya, Aishwarya" пишет: > Is there a way to patch or upgrade the existing installation to > version 4.4.0, rather than having to uninstall the older version and > then install the latest one? I don't think that there is a supported way to do that. The main pro

Re: [R] Regarding the Security Vulnerability CVE 2024 - 27322

2024-06-26 Thread Ivan Krylov via R-help
Dear Aishwarya Priyadarshini, Welcome to R-help! Most people here aren't affiliated with R Foundation. В Wed, 26 Jun 2024 17:03:37 + "Priya, Aishwarya via R-help" пишет: > I am reaching out to seek your guidance on addressing the security > vulnerability CVE-2024-27322. > To address this i

Re: [R] Naming output file

2024-06-24 Thread Ivan Krylov via R-help
В Mon, 24 Jun 2024 20:16:46 +0800 Steven Yen пишет: > In the call to ame.bopa in a loop, I like inputs in the call to > ame.bopa to be bop1, bop2, bop3,... Thanks. > > for (im in 1:m) { > ame<-ame.bopa(bop,y1.level=y1value,y2.level=y2value,jindex=jindex1,vb.method="invH",joint12=TRUE, >   

Re: [R] Naming output file

2024-06-24 Thread Ivan Krylov via R-help
В Mon, 24 Jun 2024 19:41:10 +0800 Steven Yen пишет: > (2)  name OUTPUT bop1,bop2,bop3. > > I succeeded in line 3 of the code below, > > BUT not line 4. The error message says: > > Error in paste0("bop", im) <- boprobit(eqs, mydata, wt = weight, > method = "NR", : target of assignment expands t

Re: [R] Bug with writeClipboard in {utils}

2024-06-21 Thread Ivan Krylov via R-help
В Thu, 20 Jun 2024 18:39:34 +0300 Ivan Krylov via R-help пишет: > > Is there a way to test this patch or will there soon be a published > > patched R version available for download? > > Not directly. Now that the bug is fixed in R-devel (thanks Tomas!), a Windows build

Re: [R] unable to get barchart of censored subjects from ggsurvplot() in survminer package, if there is no predcitor

2024-06-20 Thread Ivan Krylov via R-help
В Mon, 17 Jun 2024 15:53:16 -0400 "Christopher W. Ryan via R-help" пишет: > Caused by error: > ! Unknown colour name: strata" > about "uknown colour name strata" > ## but there are no strata rlang::last_trace() demonstrates that the error happens because some code receives a string 'strata' and

Re: [R] What is the HEX code for "transparent" color?

2024-06-20 Thread Ivan Krylov via R-help
В Mon, 17 Jun 2024 19:38:21 +0200 Yosu Yurramendi пишет: > output$distPlot <- renderPlot({ > numrows <- 3; numcols <- 3 > a <- c(1,0,1,1,1,1,1,0,1) > pattern <- matrix(a, numrows, numcols, byrow=TRUE) > palette <- c("#", "black") > par(bg="#") > #

Re: [R] Bug with writeClipboard in {utils}

2024-06-20 Thread Ivan Krylov via R-help
В Thu, 20 Jun 2024 13:21:38 + Barthelemy Tanguy пишет: > Is there a way to test this patch or will there soon be a published > patched R version available for download? Not directly. If you're willing to follow the partially manual process yourself, the instructions at [1] describe how to do

Re: [R] Integration of functions with a vector argument

2024-06-20 Thread Ivan Krylov via R-help
В Tue, 18 Jun 2024 23:12:03 + "Levine, Michael" пишет: > I have heard of several packages used for numerical integration in R - > cubature that you mentioned, mvQuad, and pracma. My impression is > that you think that Cubature is the best in your opinion. Is that so? Yes, but the preference

Re: [R] Bug with writeClipboard in {utils}

2024-06-19 Thread Ivan Krylov via R-help
В Tue, 18 Jun 2024 10:12:04 + Barthelemy Tanguy via R-help пишет: > #> [1] "plot(AirPassengers)" "⤀攀" > #> [1] "plot(AirPassengers)" "\u0a00" > #> [1] "plot(AirPassengers)" "\xed\xb0\x80ư" Thanks for showing an example! I was able to reproduce it both with R-4.3.1 on Windows 7 and with a fr

Re: [R] Integration of functions with a vector argument

2024-06-13 Thread Ivan Krylov via R-help
В Wed, 12 Jun 2024 23:42:18 + "Levine, Michael" пишет: > f.int1 <- function(x,y) {Vectorize (function(y) f(c(x,y),H=H,j=j))} Vectorize returns a callable function(y), so wrapping it in a function(x,y) will not work. Since you'd like to integrate over y, we can perform the same transformation

Re: [R] Integration of functions with a vector argument

2024-06-12 Thread Ivan Krylov via R-help
В Tue, 11 Jun 2024 18:44:08 + "Levine, Michael" пишет: > Let us say we have a function > > F <- function(x){ body of the function} > > Where x is, in general, a d by 1 vector with d>1. Now I want to > integrate out some of the coordinates of x, e.g. x[1] or x[2] or both > of them etc. I'm

Re: [R] R Shiny Help - Trouble passing user input columns to emmeans after ANOVA analysis

2024-06-06 Thread Ivan Krylov via R-help
В Wed, 5 Jun 2024 19:07:19 -0500 I B пишет: > However, I am getting the following error: *"Argument is of length > zero."* > if (selected_graph() == cols$column2 | selected_model() == "Main > effects model") { The error must be coming from here. At least one of selected_graph(), cols$colum

Re: [R] Tools to modify highlighted areas in pdf documents?

2024-06-02 Thread Ivan Krylov via R-help
В Sat, 1 Jun 2024 16:16:23 + Leo Mada via R-help пишет: > When highlighting pdf-documents with Microsoft Edge, the bounding box > is sometimes misplaced, and quite ugly so. It also lacks the ability > to draw lines or arrows. > > On the other hand, I did not get used to Acrobat Reader: it us

Re: [R] wrtiteBin in conjunction with seek : the position in the file is not good when writing

2024-05-21 Thread Ivan Krylov via R-help
В Tue, 21 May 2024 11:29:33 +0200 Laurent Rhelp пишет: > pos <- seek(con_in,2,origin="start") > # We have to repeat the command to return the good amount of read > # bytes > print(paste0("pos is not equal to 2, pos = ",pos)) That's because seek() returns the previous position ("before any move",

Re: [R] Description of error is untranslated when R_XLEN_T_MAX is exceeded by only 1 element.

2024-05-13 Thread Ivan Krylov via R-help
Dear Ricardo Villalba, Thank you for spotting this corner case! В Mon, 13 May 2024 11:37:57 -0300 Ricardo Villalba пишет: > I track the messages to be coded here: > https://github.com/r-devel/r-svn/blob/abe625945c4402cd2bb97b5a64e7469db3e904f0/src/main/altclasses.c#L580 > and here > https://git

Re: [R] Is there some way to customize colours for the View output?

2024-05-13 Thread Ivan Krylov via R-help
В Mon, 13 May 2024 06:08:22 -0400 Duncan Murdoch пишет: > The row and column names don't appear to be controllable from that > menu, they seem (on my machine) to be displayed in the same colour as > the background of a dialog box, i.e. some kind of gray. I don't > think R tries to control that c

Re: [R] duplicated() on zero-column data frames returns empty

2024-05-12 Thread Ivan Krylov via R-help
(Sorry for only getting back to this more than a month later.) В Mon, 8 Apr 2024 17:03:00 + Jorgen Harmse пишет: > What is the policy for changing something that is wrong? There is a > trade-off between breaking old code that worked around a problem and > breaking new code written by people

Re: [R] R CMD check vs RStudio check

2024-05-10 Thread Ivan Krylov via R-help
В Fri, 10 May 2024 03:46:54 + "Boylan, Ross" пишет: > The devtools::check() documentation mentions it invoke > pkgbuild::build() and rcmdcheck::rcmdcheck(). Since I'm guessing my > command line build and check invoked those last 2, or at least > operated similarly, they seem less likely suspe

Re: [R] Compilation problems with R4.4.0

2024-05-09 Thread Ivan Krylov via R-help
Glad you got R working! В Thu, 9 May 2024 12:19:49 + Simon Andrews пишет: > Does this need reporting upstream as a bug in R or lapack? Maybe in AlmaLinux (and I think RHEL9 too, but that's up to Miguel Esteva). Best case scenario, they somehow built the reference BLAS and LAPACK packages wi

Re: [R] Using intervals() function for nlme model - Statistics Lab ETHZ

2024-05-09 Thread Ivan Krylov via R-help
Just one more thing: when you do find a solution, can you please share it with us? I do trust nlraa::boot_nlme() as it's been deliberately written for nonlinear mixed-effects models, but the fact that intervals() is inherited from the 'lme' class without any mention of nonlinear models in the manu

Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Ivan Krylov via R-help
В Wed, 8 May 2024 16:59:25 + Simon Andrews пишет: > The lapack libraries are: > > $ rpm -qa | grep lapack > lapack-3.9.0-10.el9.x86_64 > lapack64_-3.9.0-10.el9.x86_64 > lapack64-3.9.0-10.el9.x86_64 > lapack-devel-3.9.0-10.el9.x86_64 Thanks for this information! I figured out I needed to ena

Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Ivan Krylov via R-help
В Wed, 8 May 2024 14:25:08 + Simon Andrews пишет: > #8 0x73f87c0b in dgesv ( > n=12884901891, nrhs=4294967299, > a=, > lda=12884901891, ipiv=..., > b=, > ldb=12884901891, info=0 > ) at /usr/src/debug/lapack-3.9.0-10.el9.x86_64/SRC/dgesv.f:167 > #9 0x750b2a17 in La_solve

Re: [R] Compilation problems with R4.4.0

2024-05-08 Thread Ivan Krylov via R-help
Dear Simon, В Wed, 8 May 2024 10:17:41 + Simon Andrews via R-help пишет: > I'm having a strange problem compiling R4.4.0 on an AlmaLinux9 box. > make[4]: Entering directory '/bi/apps/R/R-4.4.0/src/library/grDevices' > byte-compiling package 'grDevices' > > *** caught segfault *** > address

Re: [R] Problem with creating a PCA graph in a loop

2024-05-08 Thread Ivan Krylov via R-help
В Tue, 7 May 2024 16:57:14 +0200 gavin duley пишет: > aes(label=current_rownames, > colour=wine.data.filt$Treatment > ) As you've noticed, aes() remembers variables by their name and environment, not by value: str(ggplot2::aes(label = foo)) # List of 1 # $ label: language ~foo # <-- variab

Re: [R] Is there some way to customize colours for the View output?

2024-05-07 Thread Ivan Krylov via R-help
В Tue, 7 May 2024 09:51:55 + Iago Giné Vázquez пишет: > In the View help, it is told that: > > On Windows, the initial size of the data viewer window is taken > from the default dimensions of a pager (see Rconsole), but adjusted > downwards to show a whole number of rows and columns. Th

Re: [R] Using intervals() function for nlme model - Statistics Lab ETHZ

2024-05-06 Thread Ivan Krylov via R-help
Dear Tatiana, Marvin & Paul, If you don't get a better answer here, try r-sig-mixed-mod...@r-project.org. On Fri, 3 May 2024 11:29:19 + "Bielakova Tatiana" wrote: > Based on the documentation of nlme package, the function interval is > supported for gls, lme, and lmList classes. Although n

Re: [R] R CMD check vs RStudio check

2024-05-03 Thread Ivan Krylov via R-help
В Fri, 3 May 2024 19:45:08 + "Boylan, Ross via R-help" пишет: > & $R CMD check . > * checking for file './DESCRIPTION' ... ERROR > Required fields missing or empty: > 'Author' 'Maintainer' You're checking a source package directory. This could work, but it's much easier and more reliable

Re: [R] grDevices segfault when building R4.4.0 on RHEL 9.1.

2024-05-03 Thread Ivan Krylov via R-help
Dear Miguel Esteva, I couldn't get a Red Hat "ubi9" container to install enough dependencies to build R. Is there a way to reproduce your setup on a virtual machine somewhere? On Fri, 3 May 2024 00:42:43 + Miguel Esteva via R-help wrote: > *** caught segfault *** > > address 0x1801fa8f70,

Re: [R] strange behavior in base::as.double

2024-05-01 Thread Ivan Krylov via R-help
В Wed, 1 May 2024 11:32:32 -0400 Carl Witthoft пишет: > but as.double('123e') returns 123 -- or whatever the first digit is. Nicely spotted problem! Prof. Brian D. Ripley has fixed it in R-devel revision 86436 [*]. Now as.double('123e') will also return NA. I think that the fix will become part

Re: [R] De-serialization vulnerability?

2024-05-01 Thread Ivan Krylov via R-help
В Wed, 1 May 2024 16:57:18 + "Howard, Tim G \(DEC\) via R-help" пишет: > Is this real? Yes, but with a giant elephant in the room that many are overlooking. It has actually always been much worse. Until R-4.4.0, there used to be a way for readRDS() to return an unevaluated "promise object".

Re: [R] function import file csv Openair

2024-04-30 Thread Ivan Krylov via R-help
Dear Evelina Ballato, В Tue, 30 Apr 2024 10:36:32 + Evelina Ballato пишет: > In the Openair package it is possible to restore the import csv file > function? This question is best addressed to the maintainer of the package (see the output of maintainer("openair")) if not to their GitHub iss

Re: [R] Tidyverse/dplyr solution for filling values of a tibble/dataframe from a column with a nested list.

2024-04-19 Thread Ivan Krylov via R-help
В Thu, 18 Apr 2024 16:31:46 + "Deramus, Thomas Patrick" пишет: > Basically, each list contains a set of doubles, with the first > indicating a specific index (based on the 0 beginning python​ index), > and a certain value (e.g. 0.5). > > What I would like to do is generate set of columns bas

Re: [R] Import multiple tif raster

2024-04-18 Thread Ivan Krylov via R-help
В Thu, 18 Apr 2024 19:04:04 +0200 пишет: > Solution: direct and full path to the .tif files. > I confused back and forward slash Congratulations on solving the problem yourself! Here's a few more options that could be useful in the future: 1. Double the backslashes. Between single quotes ('...

Re: [R] Import multiple tif raster

2024-04-18 Thread Ivan Krylov via R-help
В Thu, 18 Apr 2024 11:08:33 +0200 SIBYLLE STÖCKLI via R-help пишет: > > #to check the index numbers of all imported raster list elements > > allrasters > list() > > > > #call single raster element > > allrasters[[1]] > Error in allrasters[[1]] : subscript out of bounds `allrasters` is an em

Re: [R] Debugging functions defined (locally) inside another functions

2024-04-12 Thread Ivan Krylov via R-help
В Fri, 12 Apr 2024 12:53:02 + Iago Giné Vázquez пишет: > How should I call trace() if f was a function? Let the tracer be quote(debug(g)) and use as.list(body(f)) to determine where it should be injected: f <- function() { message('exists("g") so far is ', exists('g')) g <- function() {

Re: [R] Debugging functions defined (locally) inside another functions

2024-04-12 Thread Ivan Krylov via R-help
В Fri, 12 Apr 2024 12:15:07 + Iago Giné Vázquez пишет: > f <- function(whatever){ >... >g <- function(whatever2){ > ... >} >... > } > > If I wanted to debug some thing directly inside f I would do > debug(f). But this does not go inside g code. On the other hand, > debug

Re: [R] Problem with base::order

2024-04-10 Thread Ivan Krylov via R-help
В Wed, 10 Apr 2024 09:33:19 +0200 Sigbert Klinke пишет: > decreasing=c(F,F,F) This is only documented to work with method = 'radix': >> For the ‘"radix"’ method, this can be a vector of length equal to >> the number of arguments in ‘...’ and the elements are recycled as >> necessary. For the o

Re: [R] How to set the correct libomp for R

2024-04-09 Thread Ivan Krylov via R-help
В Tue, 9 Apr 2024 09:55:06 +0200 gernop...@gmx.net пишет: > If I only move away /usr/local/lib/libomp.dylib, I can still install > it. So it seems that also here the internal libomp.dylib from R is > used. Just the bundled omp files at /usr/local/include (omp-tools.h, > omp.h, ompt.h) seem to be u

Re: [R] CEoptim problems

2024-04-09 Thread Ivan Krylov via R-help
В Tue, 9 Apr 2024 12:04:26 +0200 Adelchi Azzalini пишет: > res <- CEoptim(sumsqrs, f.arg = list(xt), continuous = list(mean = > c(0, 0, 0), sd = rep(1,3), conMat = A, conVec = b), discrete = > list(categories = c(298L, 298L), smoothProb = 0.5),N = 1, rho > = 0.001) > > Error in is.nu

Re: [R] Exceptional slowness with read.csv

2024-04-08 Thread Ivan Krylov via R-help
В Sun, 7 Apr 2024 23:47:52 -0600 Dave Dixon пишет: > > second_records <- read.csv(file_name, skip = 2459465, nrows = 5) It may or may not be important that read.csv defaults to header = TRUE. Having skipped 2459465 lines, it may attempt to parse the next one as a header, so the second call read

Re: [R] How to set the correct libomp for R

2024-04-08 Thread Ivan Krylov via R-help
В Mon, 8 Apr 2024 10:29:53 +0200 gernophil--- via R-help пишет: > I have some weird issue with using multithreaded data.table in macOS > and I am trying to figure out, if it’s connected to my libomp.dylib. > I started using libomp as stated here: > https://mac.r-project.org/openmp/ Does the beha

Re: [R] duplicated() on zero-column data frames returns empty

2024-04-07 Thread Ivan Krylov via R-help
В Fri, 5 Apr 2024 16:08:13 + Jorgen Harmse пишет: > if duplicated really treated a row name as part of the row then > any(duplicated(data.frame(…))) would always be FALSE. My expectation > is that if key1 is a subset of key2 then all(duplicated(df[key1]) >= > duplicated(df[key2])) should alwa

Re: [R] duplicated() on zero-column data frames returns empty vector

2024-04-05 Thread Ivan Krylov via R-help
Hello Mark, В Fri, 5 Apr 2024 03:58:36 + (UTC) Mark Webster via R-help пишет: > I found what looks to me like an odd edge case for duplicated(), > unique() etc. on data frames with zero columns, due to duplicated() > returning a zero-length vector for them, regardless of the number of > rows

Re: [R] Problem with new version of R: Mutated vocals

2024-03-22 Thread Ivan Krylov via R-help
В Fri, 22 Mar 2024 16:11:14 + MACHO Siegfried via R-help пишет: > If I type the command: > Dir <- "C/Users/macho/Documents/_LVn/Experimentelle _bungen" > in the R console there is no problem. However, if I put the same > command into a source file (e.g. Test.r) and call this file from R > (vi

Re: [R] Error message

2024-03-22 Thread Ivan Krylov via R-help
В Fri, 22 Mar 2024 14:52:05 -0500 Val пишет: > : 8d5a 35f8 1ac5 cc14 a04e be5c 572f a3ad .Z5..N.\W/.. > 0010: 6210 7024 9b58 93c7 34d0 acb7 7a82 3f99 b.p$.X..4...z.?. Thank you! This doesn't look like any structured data to me. In particular, it doesn't look like something wri

Re: [R] Error message

2024-03-22 Thread Ivan Krylov via R-help
В Fri, 22 Mar 2024 14:31:17 -0500 Val пишет: > How do I get the first few bytes? What does file.info('X1.RData') say? Do you get any output if you run print(readBin('X1.RData', raw(), 128))? If this is happening on a Linux or macOS machine, the operating system command xxd -l 128 X1.RData wi

Re: [R] Error message

2024-03-22 Thread Ivan Krylov via R-help
В Fri, 22 Mar 2024 14:02:09 -0500 Val пишет: > X2.R > load("X1.RData") > > I am getting this error message: > Error in load("X1.RData", : > bad restore file magic number (file may be corrupted) .. no data > loaded. This error happens very early when R tries to load the file, right at the fir

Re: [R] Building Packages.

2024-03-21 Thread Ivan Krylov via R-help
В Thu, 21 Mar 2024 18:45:35 + Jorgen Harmse via R-help пишет: > The problem may have been that this package is so important to me > that I put it in .Rprofile. The package was not installed for the new > version of R, so every R session started with an annoying error > message. Presumably a s

Re: [R] Building Packages.

2024-03-20 Thread Ivan Krylov via R-help
В Wed, 20 Mar 2024 19:26:53 + Jorgen Harmse пишет: > Thank you. tools:::.install_packages works. I'm glad it works, but it shouldn't be necessary to use (and is not part of the API: not documented to keep working this way). Since you're already using devtools, perhaps devtools::install will

Re: [R] Building Packages.

2024-03-20 Thread Ivan Krylov via R-help
В Wed, 20 Mar 2024 17:00:34 + Jorgen Harmse пишет: > Thank you, but I think I was already using utils. > > Regards, > Jorgen. > > > > environment(install.packages) > > > > > utils::install.packages('/Users/jharmse/Library/CloudStorage/OneDrive-RokuInc/jhBase_1.0.1.tar.gz',type='source

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