[Rd] should the top of doc/NEWS.3 mention doc/NEWS.Rd ?

2025-04-13 Thread Benjamin Tyner
Greetings, As of r80088, at the top of doc/NEWS.3 file it says: LATER NEWS:   • News for R 4.x.y can be found in HTML format at doc/html/NEWS.html,     and in text format in file NEWS in the doc directory. However as far as I can tell, neither NEWS nor NEWS.html exists in the R source. Should

[R] reticulate via callr

2025-04-09 Thread Benjamin Tyner
Greetings, I would like to programmatically interact with multiple versions of a given Python module via the reticulate package, without having to restart the R process over and over. (My understanding is reticulate does not provide such a capability by itself, as once reticulate binds to a P

Re: [R] installation: while running make, unable to run pdflatex on 'NEWS.tex'

2024-03-02 Thread Benjamin Tyner
r to that date. On 3/2/24 02:42, Ivan Krylov wrote: В Fri, 1 Mar 2024 10:46:53 -0500 Benjamin Tyner пишет: my platform info: Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.4 LTS Quick things first: have you installed all the build-dependencies? apt build-d

[R] dput(..., file = stderr())

2024-03-01 Thread Benjamin Tyner
Curious to know if this warning is expected behavior, and if so, what is the recommended way instead: > dput(letters, file = stderr()) c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z") Warning messa

[R] installation: while running make, unable to run pdflatex on 'NEWS.tex'

2024-03-01 Thread Benjamin Tyner
A kind member of R-core suggested this is due to a misconfiguration on my system, and to post it to the mailing list for troubleshooting. When trying to build R version 4.3.3, in at least two places during the process it gives LaTeX errors of the form: (example 1) you should 'make docs

[R] .BaseNamespaceEnv locking in non-interactive mode

2022-11-23 Thread Benjamin Tyner
Greetings, Noticed that starting with R version 4.1.0, the base environment is locked by default. So for example in interactive mode, we have > .BaseNamespaceEnv$foo <- "bar" Error in .BaseNamespaceEnv$foo <- "bar" :   cannot add binding of 'foo' to the base environment However it appears tha

[Rd] S4 methods with default argument of NULL

2021-11-06 Thread Benjamin Tyner
Greetings, I noticed that starting with R version 3.5.0, it is now possible to do, for example: setGeneric(name = "foo",    def = function(x, y, ...) standardGeneric("foo"),    valueClass = "fooResult"    ) setMethod(f = "foo",   signature

Re: [R] chaining closure arguments on-the-fly

2020-06-21 Thread Benjamin Tyner
On 6/20/20 5:04 PM, Duncan Murdoch wrote: I think you effectively did that in your original post (all but encapsulating the expression in a function), so yes, it's possible. However, it's a really bad idea.  Why use non-standard evaluation when standard evaluation is fine?  Standard evaluation

Re: [R] chaining closure arguments on-the-fly

2020-06-20 Thread Benjamin Tyner
On 6/20/20 5:49 PM, Bert Gunter wrote: Gents: (with trepidation) f(x = 3, y = g(expr)) **already** evaluates g in the environment of f, **not** in the environment of the caller. (This does not contradict Duncan's example -- 3 is a constant, not a variable). e.g. > f <- function(x = 3, y =

Re: [R] chaining closure arguments on-the-fly

2020-06-20 Thread Benjamin Tyner
On 6/20/20 9:00 AM, Duncan Murdoch wrote: How about g <- function(x, y = x) {   f(x, y) } g(x = 3) or even yEqualsX <- function(f) function(x, y = x) f(x, y) yEqualsX(f)(x = 3) These are a lot like currying, but aren't currying, so they may be acceptable to you.  Personally I'd choose the f

[R] chaining closure arguments on-the-fly

2020-06-20 Thread Benjamin Tyner
Greetings, Occasionally, I desire to call a function with one argument set to equal to another. Here is a toy example:    f <- function(x, y) {        x + y    }    f(x = 3, y = x) # Error in f(x = 3, y = x) : object 'x' not found So far, the most concise way I found to accomplish this is:

[Rd] failed check in reg-tests-1b.R

2020-05-19 Thread Benjamin Tyner
Not certain this is actually a bug, so posting here. I'm on Ubuntu 18.04.4 LTS, building R version 4.0.0. The "configure" and "make" steps are successful, but the "make check" step fails when it gets to this part of ./tests/reg-tests-1b.R:    > ## methods() gave two wrong warnings in some cas

[R-pkg-devel] use of getNativeSymbolInfo

2020-02-09 Thread Benjamin Tyner
Hello, Using package nlme as an example, where there is a registered routine fit_gnls: > library(nlme) > getDLLRegisteredRoutines("nlme")$.C$fit_gnls $name [1] "fit_gnls" $address attr(,"class") [1] "RegisteredNativeSymbol" $dll DLL name: nlme Filename: /home/btyner/R-77784/lib/R/library/nl

Re: [Rd] [External] Re: rpois(9, 1e10)

2020-01-23 Thread Benjamin Tyner
On 1/20/20 12:33 PM, Martin Maechler wrote: It's really something that should be discussed (possibly not here, .. but then I've started it here ...). The NEWS for R 3.0.0 contain (in NEW FEATURES) : * Functions rbinom(), rgeom(), rhyper(), rpois(), rnbinom(), rsignrank() and rwil

Re: [Rd] [External] Re: rpois(9, 1e10)

2020-01-20 Thread Benjamin Tyner
On 1/20/20 4:26 AM, Martin Maechler wrote: Coming late here -- after enjoying a proper weekend ;-) -- I have been agreeing (with Spencer, IIUC) on this for a long time (~ 3 yrs, or more?), namely that I've come to see it as a "design bug" that rpois() {and similar} must return return typeof() "i

Re: [Rd] rpois(9, 1e10)

2020-01-19 Thread Benjamin Tyner
Adler wrote: Maybe there should be code for 64 bit R to use long long or the like? On Sun, Jan 19, 2020 at 10:45 AM Spencer Graves mailto:spencer.gra...@prodsyse.com>> wrote: On 2020-01-19 09:34, Benjamin Tyner

Re: [Rd] rpois(9, 1e10)

2020-01-19 Thread Benjamin Tyner
Hello, All:   Consider: Browse[2]> set.seed(1) Browse[2]> rpois(9, 1e10) NAs produced[1] NA NA NA NA NA NA NA NA NA   Should this happen?   I think that for, say, lambda>1e6, rpois should return rnor

[R] safest way to subset (and replace) a data.table

2019-12-07 Thread Benjamin Tyner
Hi I would like to replace a data.table 'DT' with a subset of itself, where the subset is determined by an expression 'expr' which evaluates to logical. Thus far I've been using:    DT <- DT[expr, ] however this frequently results in a SIGABRT from glibc of the form:    "double free or corr

Re: [Rd] Error in close.connection(p) : ignoring SIGPIPE signal

2019-12-06 Thread Benjamin Tyner
redirected to /dev/null. Try p <- pipe("cat > /dev/null", open = "w") instead. Regards, Andreas 2019-12-06 02:46 GMT+01:00 Benjamin Tyner: Not sure if this is a bug, so posting here first. If I run:    cnt <- 0L    while (TRUE) {        cnt <- cnt + 1L

[Rd] Error in close.connection(p) : ignoring SIGPIPE signal

2019-12-05 Thread Benjamin Tyner
Not sure if this is a bug, so posting here first. If I run:    cnt <- 0L    while (TRUE) {        cnt <- cnt + 1L        p <- pipe("echo /dev/stdin > /dev/null", open = "w")        writeLines("foobar", p)        tryCatch(close(p), error = function(e) { print(cnt); stop(e)})    } then once cnt ge

Re: [Rd] BUG?: A copy of base::`+` (primitive) is not a clone but a "pointer"

2019-11-25 Thread Benjamin Tyner
For what it's worth, the current behavior seems to have begun starting with version 3.6.0. If I run in version 3.5.3: > p1 <- .Primitive('+') ; p2 <- p1 ; attr(p1, "myattr") <- 1 ; p2 function (e1, e2)  .Primitive("+") On 11/18/19 10:45 AM, Martin Maechler wrote: >>/Tomas Kalibera />>

Re: [Rd] Should slot<-() alter its first argument?

2019-09-20 Thread Benjamin Tyner
It appears this started with R version 3.5.0. Under R 3.4.4 we have: > setClass("Z", rep=representation(x="character")) > z <- new("Z", x="orig") > `@<-`(z, "x", value="newer") An object of class "Z" Slot "x": [1] "newer" > z An object of class "Z" Slot "x": [1] "newer" > `slot<-`(z, "x", value

[R] Matrix::bdiag doesn't like being given a single named argument

2019-05-31 Thread Benjamin Tyner
Hello, Perhaps not a bug, but interesting because the error only happens when there is a single named argument.    > m <- matrix(1, 1, 1)    > library(Matrix)    > bdiag(m)    1 x 1 sparse Matrix of class "dgCMatrix"    [1,] 1    > bdiag(a = m)    Error in is.list(...) : supplied argument nam

Re: [Rd] R-devel (rev 76409) fails 'make check': non-generic function 'isSymmetric' given to findMethods()

2019-04-23 Thread Benjamin Tyner
Looks fixed as of revision 76417; thanks Brian! On 4/21/19 9:02 PM, Benjamin Tyner wrote: Duncan that does indeed look to be the case. Many thanks! In particular, tests/reg-tests-1d.R optionally loads the Matrix namespace which allows the test to succeed. Compare:    ~/R-rc_2019-04

Re: [Rd] R-devel (rev 76409) fails 'make check': non-generic function 'isSymmetric' given to findMethods()

2019-04-21 Thread Benjamin Tyner
Duncan that does indeed look to be the case. Many thanks! In particular, tests/reg-tests-1d.R optionally loads the Matrix namespace which allows the test to succeed. Compare: ~/R-rc_2019-04-21_r76409/bin/Rscript -e "options(warn=2); library(Matrix); res <- findMethods('isSymmetric'); pri

[Rd] R-devel (rev 76409) fails 'make check': non-generic function 'isSymmetric' given to findMethods()

2019-04-21 Thread Benjamin Tyner
Hello, Most likely I'm doing something wrong, but am at a loss as to what the issue is. I have a clean checkout of trunk here:    ~/svn/r-devel/R$ svn info    Path: .    Working Copy Root Path: /home/btyner/svn/r-devel/R    URL: https://svn.r-project.org/R/trunk    Relative URL: ^/trunk    Rep

Re: [Rd] longint

2018-08-15 Thread Benjamin Tyner
n Murdoch wrote: On 15/08/2018 7:08 AM, Benjamin Tyner wrote: Hi In my R package, imagine I have a C function defined: void myfunc(int *x) {     // some code } but when I call it, I pass it a pointer to a longint instead of a pointer to an int. Could this practice potentially result i

[Rd] longint

2018-08-15 Thread Benjamin Tyner
Hi In my R package, imagine I have a C function defined:    void myfunc(int *x) {   // some code    } but when I call it, I pass it a pointer to a longint instead of a pointer to an int. Could this practice potentially result in a segfault? Regards Ben __

Re: [Rd] Library lib.loc Option Ignored for Dependencies

2018-07-25 Thread Benjamin Tyner
On 07/25/2018 04:28 AM, Uwe Ligges wrote: Not sure if this is a bug: where is it documented that this works not as above (which is what I would expect)? The documentation doesn't say one way or the other. But the fact remains that base:::.getRequiredPackages2, when provided a non-null lib.lo

Re: [Rd] Library lib.loc Option Ignored for Dependencies

2018-07-24 Thread Benjamin Tyner
On 07/24/2018 07:50 AM, Martin Maechler wrote: Benjamin Tyner on Sat, 21 Jul 2018 13:42:43 -0400 writes: > Not sure whether it is the same issue as was raised here: > https://stat.ethz.ch/pipermail/r-devel/2010-October/058729.html > but in any case perhaps th

Re: [Rd] Should there be a confint.mlm ?

2018-07-22 Thread Benjamin Tyner
BTW --- and this is a diversion --- This is nice mathematically (and used in other places, also in "base R" I think) but in principle is a waste: Computing a full k x k matrix and then throwing away all but the length-k diagonal ... In the past I had contemplated but never RFC'ed or really

Re: [Rd] Library lib.loc Option Ignored for Dependencies

2018-07-21 Thread Benjamin Tyner
e package On 07/21/2018 12:34 PM, Martin Maechler wrote: Benjamin Tyner on Fri, 20 Jul 2018 19:42:09 -0400 writes: > Here's a trick/workaround; if lib.loc is the path to your > library, then prior to calling library(), >> environment(.libPaths)$.lib.loc <-

Re: [Rd] Library lib.loc Option Ignored for Dependencies

2018-07-20 Thread Benjamin Tyner
Here's a trick/workaround; if lib.loc is the path to your library, then prior to calling library(), > environment(.libPaths)$.lib.loc <- lib.loc Good day, If there's a library folder of the latest R packages and a partic

[Rd] missing news entry?

2018-07-18 Thread Benjamin Tyner
Hi, Unless I am mistaken, this enhancement to gc(): r73749 | luke | 2017-11-18 13:26:25 -0500 (Sat, 18 Nov 2017) | 2 lines Added 'full' argument to gc() with default 'TRUE' for now. ---

Re: [R] undo compile? (or: remove bytecode from closure)

2018-07-16 Thread Benjamin Tyner
pe this helps, Rui Barradas Às 03:25 de 16-07-2018, Benjamin Tyner escreveu: Hi Given a closure which has been compiled, what's the recommended way to recover the original? For example,       > f <- function(x) x+1       > fc <- cmpfun(f)       > rm(f)       > fc       funct

[R] undo compile? (or: remove bytecode from closure)

2018-07-15 Thread Benjamin Tyner
Hi Given a closure which has been compiled, what's the recommended way to recover the original? For example,     > f <- function(x) x+1     > fc <- cmpfun(f)     > rm(f)     > fc     function(x) x+1     what's the best way to recover f from fc ? Regards Ben ___

[R] system() or pipe(..., open = "r") without child process?

2018-05-22 Thread Benjamin Tyner
Greetings On linux, is it possible to invoke an OS command from within R without spawning a child process? If not, is it possible to avoid copying the "parts of the caller's context" that are mentioned on the clone manpage?  ENOMEM Cannot  allocate  sufficient memory to allocate a task struct

Re: [R] rJava garbage collect

2018-02-06 Thread Benjamin Tyner
esolve the issue. Regards Ben On 6 February 2018 at 04:34, Benjamin Tyner https://stat.ethz.ch/mailman/listinfo/r-help>> wrote: >/Hi />//>/Does rJava offer a way to instruct the JVM to perform a garbage col

Re: [R] rJava garbage collect

2018-02-06 Thread Benjamin Tyner
Thanks Jeff; indeed it works:    .jcall("java/lang/System", method = "gc") On 02/05/2018 11:53 PM, Jeff Newmiller wrote: rJava offers a mechanism to call arbitrary methods in Java. Wouldn't you use that mechanism to call whatever you would call if you were programming in Java (e.g. System.gc

[R] rJava garbage collect

2018-02-05 Thread Benjamin Tyner
Hi Does rJava offer a way to instruct the JVM to perform a garbage collection? Regards Ben __ 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

[R] setSessionLimit

2018-01-19 Thread Benjamin Tyner
Hello The doc/NEWS.2 file mentions a setSessionLimit function, added with version 2.8.0     o   setTimeLimit() function to set limits on the CPU     and/or elapsed time for each top-level computation, and     setSessionLimit() to set limits for the rest of the session. However, I no l

Re: [Rd] OpenBLAS in everyday R?

2018-01-11 Thread Benjamin Tyner
condition? On 01/11/2018 07:56 AM, Ista Zahn wrote: On Jan 10, 2018 8:24 PM, "Benjamin Tyner" <mailto:bty...@gmail.com>> wrote: Thanks Keith. We checked, and indeed libopenblas is not linked against libomp nor libgomp. We suspect this is because we used con

Re: [Rd] OpenBLAS in everyday R?

2018-01-10 Thread Benjamin Tyner
On Jan 9, 2018, at 11:01 PM, Benjamin Tyner wrote: I didn't do the compile; is there a way to check whether that was used? If not, I'll inquire with our sysadmin and report back. In any case, my suggestion was motivated by the fact that some parts of R use OpenMP while others do n

Re: [Rd] OpenBLAS in everyday R?

2018-01-09 Thread Benjamin Tyner
r OpenBLAS omelet without breaking the OpenMP eggs, so to speak. On 01/09/2018 06:41 PM, Keith O'Hara wrote: Do those issues still arise when OpenBLAS is compiled with USE_OPENMP=1 ? Keith On Jan 9, 2018, at 6:03 PM, Benjamin Tyner wrote: Please pardon my ignorance, but doesn't OpenB

Re: [Rd] OpenBLAS in everyday R?

2018-01-09 Thread Benjamin Tyner
Please pardon my ignorance, but doesn't OpenBLAS still not always play nicely with multi-threaded OpenMP? (for example, don't race conditions sometimes crop up)? If so, it might be nice to have the ability to temporarily disable multi-threaded OpenMP (effectively: omp_set_num_threads(1)) for th

Re: [Rd] Coping with non-standard evaluation in R program analysis

2018-01-03 Thread Benjamin Tyner
Evan, The pryr package provides some utilities which may be handy here. In particular see the function: is_promise. Also, next time please post in plaintext. Regards Ben Hello R experts, I plan to develop a tool for dynamic analysis of R programs. I would like to trace function calls at r

Re: [R] read.table(..., header == FALSE, colClasses = )

2017-10-24 Thread Benjamin Tyner
, colClasses = c(y = "character", x = "numeric"), col.names = c("foo", "bar"))      foo  bar    1   a 3.14 so I agree it is good that we are checking for that now. Regards Ben On 10/24/2017 08:55 AM, Martin Maechler wrote: Benjamin Tyner

Re: [R] read.table(..., header == FALSE, colClasses = )

2017-10-24 Thread Benjamin Tyner
Jeff, Thank you for your reply. The intent was to construct a minimum reproducible example. The same warning occurs when the 'file' argument points to a file on disk with a million lines. But you are correct, my example was slightly malformed and in fact gives an error under R version 3.2.2.

[R] read.table(..., header == FALSE, colClasses = )

2017-10-23 Thread Benjamin Tyner
Hello I noticed that starting with R version 3.3.0 onward, this generates a warning:    > txt <- c("a", "3.14")    > read.table(file = textConnection(txt), header = FALSE, colClasses = c(x = "character", y = "numeric")) the warning is "not all columns named in 'colClasses' exist" and I gues

Re: [Rd] force promises inside lapply

2017-07-31 Thread Benjamin Tyner
: $ evaled: logi FALSE $ value : NULL > str(f(log(-1), force=TRUE)) List of 4 $ code : language log(-1) $ env : NULL $ evaled: logi TRUE $ value : num NaN Warning message: In log(-1) : NaNs produced

Re: [Rd] force promises inside lapply

2017-07-28 Thread Benjamin Tyner
E $ value : NULL > str(f(log(-1), force=TRUE)) List of 4 $ code : language log(-1) $ env : NULL $ evaled: logi TRUE $ value : num NaN Warning message: In log(-1) : NaNs produced Can you give a concrete example of what you are try to accomplish? Bill Dunlap TIBCO Software wdunlap tibco.com

[Rd] force promises inside lapply

2017-07-28 Thread Benjamin Tyner
Hi, I thought I understood the change to lapply semantics resulting from this, https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16093 However, would someone care to explain why this does not work? > L <- list(a=1, b=2, c=3) > str(lapply(L, function(x){ y <- substitute(x); force(x);

[R] flushing on.exit prior to q()

2017-02-21 Thread Benjamin Tyner
Hi, When using a custom error function that calls q(), what is the recommended way to "flush" the calling function's on.exit ? For example, say I have a script: #!/usr/bin/Rscript --no-init-file options(error = function() { cat("on error message\n", file = stderr()) q(sav

Re: [Rd] package load altering RNG state

2017-02-07 Thread Benjamin Tyner
Martin, Outstanding! This is a most welcome enhancement. Regards Ben On 02/07/2017 09:59 AM, Martin Maechler wrote: Henric Winell on Tue, 7 Feb 2017 13:37:42 +0100 writes: > Hi, On 2017-02-07 13:12, Benjamin Tyner wrote: >> Hello >> >> When l

[Rd] package load altering RNG state

2017-02-07 Thread Benjamin Tyner
Hello When loading a package, I'm wondering if it's frowned upon for the package to alter the state of the random number generator? I guess not, since the parallel package does it? > set.seed(6860) > old.seed <- .GlobalEnv$.Random.seed > library(parallel) > new.seed <- .GlobalEnv$

Re: [R] [FORGED] file.exists() on device files

2017-01-13 Thread Benjamin Tyner
Thank you for the insights, Rolf and Henrik. To give another example, this time in non-interactive mode, Rscript -e "file.exists(commandArgs(TRUE))" <(echo "Hi") [1] TRUE versus Rscript -e "normalizePath(commandArgs(TRUE))" <(echo "Hi") [1] "/dev/fd/63" Warning message: In n

[R] file.exists() on device files

2017-01-11 Thread Benjamin Tyner
Hi, On my linux machine (Ubuntu, and also tested on RHEL), I am curious to know what might be causing file.exists (and also normalizePath) to not see the final device file here: > list.files("/dev/fd", full.names = TRUE) [1] "/dev/fd/0" "/dev/fd/1" "/dev/fd/2" "/dev/fd/3" > file.exis

Re: [R] modify the imported version of a function

2016-12-19 Thread Benjamin Tyner
= FALSE, dotall = FALSE, ...) { options <- stri_opts_regex(case_insensitive = ignore_case, multiline = multiline, comments = comments, dotall = dotall, ...) structure(pattern, options = options, class = c("regex", "patt

[R] modify the imported version of a function

2016-12-16 Thread Benjamin Tyner
Hi I saw on the assignInNamespace help page, that it changes "the copy in the namespace, but not any copies already exported from the namespace, in particular an object of that name in the package (if already attached) and any copies already imported into other namespaces." So now I'm wonder

[R] R_DirtyImage and Rprof

2016-05-11 Thread Benjamin Tyner
Hello, I have some code which was running in interactive mode while Rprof(..., line.profiling = TRUE). Near the end of my script, it opens up a pipe(..., open = "w") to a perl script, and at that point the execution gets stuck using 100% cpu. (The perl script itself never showed up in pstree

Re: [R] choropleth packages (US)

2015-12-10 Thread Benjamin Tyner
ec 7, 2015 at 9:34 AM, Erich Neuwirth wrote: ggplot2 also can do this with fortify geom_polygon Von meinem iPad gesendet Am 06.12.2015 um 21:03 schrieb Benjamin Tyner : Hi I wish to draw a basic choropleth (US, by state) and am wondering if anyone has any recommendations? I've t

Re: [Rd] For integer vectors, `as(x, "numeric")` has no effect.

2015-12-07 Thread Benjamin Tyner
Perhaps it is not that surprising, given that > mode(1L) [1] "numeric" and > is.numeric(1L) [1] TRUE On the other hand, this is curious, to say the least: > is.double(as(1L, "double")) [1] FALSE Here's the surprising behavior: x <- 1L xx <- as(x, "numeric")

[R] choropleth packages (US)

2015-12-06 Thread Benjamin Tyner
Hi I wish to draw a basic choropleth (US, by state) and am wondering if anyone has any recommendations? I've tried the following thus far: 1. choroplethr: this works, but required installation of 30+ dependencies. I would prefer something with fewer dependencies. 2. tmap: this also seems prom

[R] efficiently multiply each column of a sparse Matrix by a sparse vector

2015-11-28 Thread Benjamin Tyner
Hi, Say I have a sparse Matrix X, and a sparse vector (stored as a 1-column sparse Matrix A), with X and A having the same number of rows, and I wish to multiply each column of X by A, but would like the operation to take full advantage of the sparseness of both X and A. In other words I want

Re: [R] backsolve, chol, Matrix, and SparseM

2015-09-25 Thread Benjamin Tyner
path in the first place. By the way, is R-forge still the correct place to report bugs in package:Matrix? Regards Ben On 09/25/2015 04:25 AM, Martin Maechler wrote: > Dear Ben, > >>>>>> Benjamin Tyner >>>>>> on Thu, 24 Sep 2015 13:47:58 -0400 writes:

[R] backsolve, chol, Matrix, and SparseM

2015-09-24 Thread Benjamin Tyner
Hi I have some code which does (on a symmetric matrix 'x') backsolve(chol(x), diag(nrow(x))) and I am wondering what is the recommended way to accomplish this when x is also sparse (from package:Matrix). I know that package:Matrix provides a chol method for such matrices, but not a backsolve

[R] Rprof and system

2015-08-11 Thread Benjamin Tyner
Hi I have an R script which invokes WriteXLS() (from the package of the same name) which as you may know, calls perl via system(). I've noticed that when I enable profiling using Rprof(), when the script gets to the part where perl is called, it gets "stuck": it just sits there using 99-100% CPU a

Re: [R] package implementing continuous binomial?

2015-05-07 Thread Benjamin Tyner
Thanks David! I'll take a look at zipfR. Regards Ben On 05/07/2015 03:10 PM, David Winsemius wrote: > On May 6, 2015, at 7:00 PM, Benjamin Tyner wrote: > >> Hi >> >> I'm wondering if anyone is aware of an R package implementing (i.e., >> providing a pdf

[R] package implementing continuous binomial?

2015-05-06 Thread Benjamin Tyner
Hi I'm wondering if anyone is aware of an R package implementing (i.e., providing a pdf, cdf, and/or quantile function) for the continuous binomial distribution? Specifically the one characterized here: http://www2.math.uni-paderborn.de/fileadmin/Mathematik/AG-Indlekofer/Workshop/Satellite_meetin

Re: [R] non-terminal token lacking children from utils::getParseData

2015-05-02 Thread Benjamin Tyner
Thank you Yihui for also reporting the bug here: https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16354 and thank you Duncan for finding the issue and fixing it! I definitely like your idea to report a summary message instead of the long text string. Regards Ben > I tried to reduce the offen

Re: [Rd] iterated lapply

2015-02-25 Thread Benjamin Tyner
Actually, it depends on the number of cores: > fun1 <- function(c){function(i){c*i}} > fun2 <- function(f) f(2) > sapply(mclapply(1:4, fun1, mc.cores=1L), fun2) [1] 8 8 8 8 > sapply(mclapply(1:4, fun1, mc.cores=2L), fun2) [1] 6 8 6 8 > sapply(mclapply(1:4, fun1, mc.core

Re: [R] non-terminal token lacking children from utils::getParseData

2015-02-19 Thread Benjamin Tyner
I tried to reduce the offending portion as best I could to a more-or-less minimal example (1136 bytes), which can be downloaded via: wget https://www.dropbox.com/s/74rgxr5x2aalr99/badstring.R then once in R, > b <- parse(file = "~/badstring.R", keep.source = TRUE) > d <- getParseData

[R] quadprog::solve.QP sometimes returns NaNs

2014-09-26 Thread Benjamin Tyner
Hello, Here is an example; hopefully it is reproducible on others' platform: library(quadprog) n <- 66L set.seed(6860) X <- matrix(1e-20, n, n) diag(X) <- 1 Dmat <- crossprod(X) y <- seq_len(n) dvec <- crossprod(X, y) Amat <- diag(n) bvec <- y + runif(n)

[R] scaling of Amat still recommended for quadprog::solve.QP ?

2014-09-25 Thread Benjamin Tyner
Greetings, I ran across this recommendation, to keep the norms of the columns of the Amat on similar scales, https://stat.ethz.ch/pipermail/r-help/2007-September/141335.html However, when I looked at the code, I noticed that the norms are already being calculated: c c calculate the

Re: [R] from cut.Date

2014-09-17 Thread Benjamin Tyner
t; args(cut.Date) function (x, breaks, labels = NULL, start.on.monday = TRUE, right = FALSE, ...) I suppose the latter does make sense, given that days, months, years etc are right-continuous functions of time. Regards Ben > On 17/09/2014 12:04, Benjamin Tyner wrote: > >/ Hello, > />/

[R] from cut.Date

2014-09-17 Thread Benjamin Tyner
Hello, I'm wondering if this is expected? > cut(structure(1, class="Date"), structure(c(11100,1), class="Date")) [1] Levels: 2000-05-23 The help page says that "for ‘"Date"’ objects, only ‘"day"’, ‘"week"’, ‘"month"’, ‘"quarter"’ and ‘"year"’ are allowed" [for the 'breaks' a

Re: [R] lattice: packet.number() versus panel.number()

2014-08-27 Thread Benjamin Tyner
On 08/27/2014 02:10 AM, David Winsemius wrote: > On Aug 26, 2014, at 3:25 PM, Benjamin Tyner wrote: > >> Hi, >> >> According to >> https://svn.r-project.org/R-packages/trunk/lattice/R/print.trellis.R, >> >>"[panel.number] is usually the same as, bu

[R] lattice: packet.number() versus panel.number()

2014-08-26 Thread Benjamin Tyner
Hi, According to https://svn.r-project.org/R-packages/trunk/lattice/R/print.trellis.R, "[panel.number] is usually the same as, but can be different from packet.number" and I had been under the impression that as long as the user is not using a custom index.cond nor perm.cond, the panel.numbe

Re: [Rd] could not find function "anyNA" when building tools package in R 3.1.1

2014-08-13 Thread Benjamin Tyner
I figured out what I did wrong. The end of my $LDFLAGS contained "-Wl,-rpath,/path/to/an/old/R/installation/lib64/R/lib" (which predated anyNA) and I was also using --enable-R-shlib, so possibly related to PR#15790 (I say possibly, because I was not using "make install-libR").

[Rd] could not find function "anyNA" when building tools package in R 3.1.1

2014-08-08 Thread Benjamin Tyner
Hello, When building R from source, during the part where the 'tools' package is built, I get: make[6]: Entering directory `/home/btyner/R-3.1.1/src/library/tools/src' make[6]: Leaving directory `/home/btyner/R-3.1.1/src/library/tools/src' make[5]: Leaving directory `/home/btyner/R-3.1.1/src/libr

Re: [R] non-interactive subset, `$`, and quotes

2014-06-26 Thread Benjamin Tyner
Duncan, How embarrassing! Thanks. -Ben On 06/26/2014 10:25 PM, Duncan Murdoch wrote: > On 27/06/2014, 4:08 AM, Benjamin Tyner wrote: >> Hi >> >> I know that subset() is not intended for use in programming. However I >> am still curious to learn why, in non-inter

[R] non-interactive subset, `$`, and quotes

2014-06-26 Thread Benjamin Tyner
Hi I know that subset() is not intended for use in programming. However I am still curious to learn why, in non-interactive mode, if I take away the quotes around 'bar' Rscript -e "foo <- list(bar = iris); head(subset(foo$'bar', Species=='setosa'))" Sepal.Length Sepal.Width Petal.Length P

Re: [R] detecting the sourcing of site profile on Startup versus post-Startup

2014-04-24 Thread Benjamin Tyner
- > Sent from my phone. Please excuse my brevity. > > On April 23, 2014 6:11:09 PM PDT, Benjamin Tyner wrote: >> Thanks Duncan! Yes, I considered taking advantage of .First, but was >> concerned that the .First defined by the site profile could be masked &

Re: [R] detecting the sourcing of site profile on Startup versus post-Startup

2014-04-23 Thread Benjamin Tyner
gave was a simplifying assumption, sorry about that). On 04/23/2014 06:55 AM, Duncan Murdoch wrote: On 22/04/2014, 8:59 PM, Benjamin Tyner wrote: Greetings, Is there any way to programmatically detect whether a piece of code is being run within the initial (Startup) sourcing o

[R] detecting the sourcing of site profile on Startup versus post-Startup

2014-04-22 Thread Benjamin Tyner
Greetings, Is there any way to programmatically detect whether a piece of code is being run within the initial (Startup) sourcing of the site profile? For example, say I have a site profile, "/path/to/Rprofile.site". Is there any function "my_func" which would return different values for these tw

Re: [R] package environment versus namespace environment

2014-03-09 Thread Benjamin Tyner
earch path, then functions in the base namespace would no longer be able to see objects in utils? (I realize the answer may be vacuous, since library() does not honor pos=1). Regards, Ben On 03/09/2014 09:09 AM, Duncan Murdoch wrote: On 14-03-08 6:42 PM, Benjamin Tyner wr

Re: [R] package environment versus namespace environment

2014-03-08 Thread Benjamin Tyner
es back in alphabetical order.) Regards Ben On 03/07/2014 11:46 AM, Duncan Murdoch wrote: On 07/03/2014 10:16 AM, Benjamin Tyner wrote: Hello, I realize that a function in (for example, function "head1" below) is unable to see (without resorting to "::", anyw

[R] package environment versus namespace environment

2014-03-07 Thread Benjamin Tyner
Hello, I realize that a function in (for example, function "head1" below) is unable to see (without resorting to "::", anyway) objects in utils (for example, "head" below), since package:base is after package:utils on the search path. However, I'm wondering what is the machinery that allows a fu

[Kernel-packages] [Bug 1049466] Re: Need support of Ralink RT3290 wifi support

2013-09-21 Thread Benjamin Tyner
I'm running ubuntu 13.04 and this wireless card was working until a few days ago; now it is no longer working. my configuration is broadcast=yes driver=rt2800pci driverversion=3.8.0-30-generic firmware=0.37 latency=0 link=no multicast=yes wireless=IEEE 802.11bgn Any advice? Thanks -- You receiv

[Bug 1049466] Re: Need support of Ralink RT3290 wifi support

2013-09-21 Thread Benjamin Tyner
I'm running ubuntu 13.04 and this wireless card was working until a few days ago; now it is no longer working. my configuration is broadcast=yes driver=rt2800pci driverversion=3.8.0-30-generic firmware=0.37 latency=0 link=no multicast=yes wireless=IEEE 802.11bgn Any advice? Thanks -- You receiv

Re: [R] retaining comments within functions defined in Rprofile.site

2013-05-25 Thread Benjamin Tyner
gt; > > On Fri, May 24, 2013 at 5:46 PM, Benjamin Tyner <mailto:bty...@gmail.com>> wrote: > > Hi, > > I have some functions defined within etc/Rprofile.site which contain > embedded comments, but it seems the comments get stripped out when the > site

[Rd] segfault when using browser() in Rprofile.site

2013-05-24 Thread Benjamin Tyner
Hi. It seems that if I put a browser() in my Rprofile.site, I get a segfault. This happens on several machines, several versions of R. Here it the valgrind output when using revision 62797: ==31314== Memcheck, a memory error detector ==31314== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Se

[R] retaining comments within functions defined in Rprofile.site

2013-05-24 Thread Benjamin Tyner
Hi, I have some functions defined within etc/Rprofile.site which contain embedded comments, but it seems the comments get stripped out when the site profile is sourced into the base namespace. I'm thinking I need to enable options(keep.source=TRUE) somewhere prior to the actual sourcing of the sit

Re: [Rcpp-devel] non-empty character argument expected

2013-05-17 Thread Benjamin Tyner
Thank you Dirk; how embarrassing! Regards, Ben On 05/16/2013 11:13 PM, Dirk Eddelbuettel wrote: > Instead of > >time.f1 <- system(x2 <- f1(input=x, parms=p)) > > you probably meant > >time.f1 <- system.time(x2 <- f1(input=x, parms=p)) > > Also see the rbenchmark and microbenchmark packag

[Rcpp-devel] non-empty character argument expected

2013-05-16 Thread Benjamin Tyner
Hello, I'm getting an error that I'm at a loss to explain; here is my code: # library(inline) f1 <- cxxfunction(signature(input = "numeric", parms = "list" ), plugin = "Rcpp",

[Bug 1049466] Re: Need support of Ralink RT3290 wifi support

2013-04-18 Thread Benjamin Tyner
Sorry to ask a dumb question, but now that the bug is fixed, what is the best way for one to download and install the fixed linux-firmware and get wireless going? I am running Ubuntu 12.10. Regards, Ben -- You received this bug notification because you are a member of Ubuntu Bugs, which is subsc

Re: [R] holding argument(s) fixed within lapply

2013-03-22 Thread Benjamin Tyner
ple: > > ret2 <- lapply(X=mylist2, >FUN=do.call, >what=function(...) f2(y=Y, ...)) > > Best, > Nello > > -Original Message- > Date: Tue, 12 Mar 2013 22:37:52 -0400 > From: Benjamin Tyner > To: r-help@r-project.org > Subject: Re: [R] hold

Re: [R] holding argument(s) fixed within lapply

2013-03-14 Thread Benjamin Tyner
inal Message- > Date: Tue, 12 Mar 2013 22:37:52 -0400 > From: Benjamin Tyner > To: r-help@r-project.org > Subject: Re: [R] holding argument(s) fixed within lapply > Message-ID: <513fe680.2070...@gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > >

Re: [R] holding argument(s) fixed within lapply

2013-03-12 Thread Benjamin Tyner
Apologies; resending in plain text... Given a function with several arguments, I would like to perform an lapply (or equivalent) while holding one or more arguments fixed to some common value, and I would like to do it in as elegant a fashion as possible, without resorting to wrapping a separate w

[R] holding argument(s) fixed within lapply

2013-03-12 Thread Benjamin Tyner
|Hello, Given a function with several arguments, I would like to perform an lapply (or equivalent) while holding one or more arguments fixed to some common value, and I would like to do it in as elegant a fashion as possible, without resorting to wrapping a separate wrapper for the function if pos

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