[R-pkg-devel] Trouble building vignettes with R-devel, can't replicate locally

Greetings I just tried to upload a new version of stationery, my collection of Sweave and markdown templates. CRAN fails to build vignettes, almost certainly a problem in Pandoc (what version is CRAN using?). My experience with markdown in general is that if you don't like the format they

[Rd] Proposed function file.backup

FALSE (default), rename the file. Otherwise, keep old copy. ##' @param verbose If TRUE, list the files in the output directory ##' @author Shadi Pirhosseinloo Paul Johnson ##' @return The name of the newly created file. ##' @importFrom tools file_ext ##' @importFrom tools file_path_sans_ext #

Re: [Rd] unable to load shared object

Hm. I cannot find it now, but I saw notes about problems with Onedrive, maybe also Dropbox, because file paths are not exactly what r expects. Usually I have package library as local folder. Did your R choose that location automatically? Paul Johnson University of Kansas On Fri, Oct 5, 2018, 3

[R-pkg-devel] fate of functions with periods in name

I have not introduced functions with periods in their name before, but recently I wanted to put a new version of "rbind.fill" in my package rockchalk. When I do the package check with R-3.5.1, I see a package build warning: Found the following apparent S3 methods exported but not registered:

Re: [R-pkg-devel] questions about \dontrun{} etc.

I think Ben has a good question and I have a related followup. On Thu, Sep 6, 2018 at 2:07 PM Ben Bolker wrote: > * My preference would be for using \dontrun{} universally (consistent, > readable, mostly avoids accidental runs), but this goes against > (informal?) CRAN policy > > * universal

Re: [R-pkg-devel] Package vignette index

Can one of you confirm this answer: The --as-cran package checker is looking for "build/vignette.rds", not "vignettes/index.html" as I thought. Details below. On Mon, Aug 13, 2018 at 12:20 PM, Paul Johnson wrote: > Can you advise me about this warning in package

[R-pkg-devel] Debian pandoc "\passthrough undefined" error and workaround

Today I saw an error from CRAN that I did not see in Win-builder or on my system with Ubuntu Linux. This is from the CRAN Debian test system: * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ...

[R-pkg-devel] Package vignette index

Can you advise me about this warning in package check: Package has a VignetteBuilder field but no prebuilt vignette index. In my vignette folder, I do have an "index.html" file, the index in the installed package is fine. But I still get this package build warning: I asked same question on

[Rd] package check fail on Windows-release only?

I mistakenly left a write in "/tmp" in the rockchalk package (version 1.8.109) that I uploaded last Friday. Kurt H wrote and asked me to fix today. While uploading a new one, I became aware of a problem I had not seen. The version I uploaded last Friday, 1.8.109, has OK status on all platforms

Re: [Rd] what do you think about write.table(... qmethod = "excel")?

ils write.table ##' @return the return from write.table, using revised quotes ##' @export ##' @author Paul Johnson ##' @examples ##' set.seed(234) ##' x1 <- data.frame(x1 = c("a", "b,c", "b", "The \"Washington, DC\""), ##' x2 = rnorm(4), stringsAs

[Rd] what do you think about write.table(... qmethod = "excel")?

Last week one of our clients reported trouble with a csv file I generated with write.table. He said that columns with quotes for character variables were rejected by their data importer, which was revised to match the way Microsoft Excel uses quotation marks in character variables. I explained

Re: [Rd] Rmpi, openMPI editions.

MPI not to try to use Infiniband at all. pj On Mon, Jun 19, 2017 at 2:34 PM, Paul Johnson <pauljoh...@gmail.com> wrote: > Greetings. > > I see a warning message while compiling OpenMPI and would appreciate > it if you tell me what it means. > > This warning happens wi

Re: [Rd] duplicated factor labels.

uot;The following `from` values were not present in `x`: ", paste(from[!(1:length(from) %in% from_found) ], collapse = ", ")) } x[!mapidxNA] <- to[mapidx[!mapidxNA]] x } In the rockchalk package, I wrote a function called combineLevels that is careful with ordinal variables an

[Rd] arrows: no vectors for "code" and "angle" parameters

I was teaching new R users to make some fun graphs. I had some arrows examples worked up we came across a problem. The arrows function ignores 2nd and following elements of vectors given as code an angle. Would you please consider 1) allowing vectors for code and angle, or 2) returning an error

[Rd] Rmpi, openMPI editions.

Greetings. I see a warning message while compiling OpenMPI and would appreciate it if you tell me what it means. This warning happens with any OpenMPI > 1.6.5. Even before starting a cluster, just "sessionInfo" triggers this warning. I'm pasting in the message from R-3.3.2 (this is MRO). Do

Re: [Rd] duplicated factor labels.

On Fri, Jun 16, 2017 at 2:35 AM, Joris Meys wrote: > To extwnd on Martin 's explanation : > > In factor(), levels are the unique input values and labels the unique output > values. So the function levels() actually displays the labels. > Dear Joris I think we agree.

[Rd] duplicated factor labels.

Dear R devel I've been wondering about this for a while. I am sorry to ask for your time, but can one of you help me understand this? This concerns duplicated labels, not levels, in the factor function. I think it is hard to understand that factor() fails, but levels() after does not > x <-

[Rd] syntax difference clusterExport in parallel and snow

We got some errors and eventually figured out that parallel::clusterExport second argument is "varlist" while in snow::clusterExport it is "list". The user had loaded parallel first, but did something else which inadvertently loaded snow, then clusterExport failed because we had "varlist" and not

Re: [Rd] Cluster: Various GCC, how important is consistency?

wrote: > On Tue, Oct 18, 2016 at 1:44 AM, Paul Johnson <pauljoh...@gmail.com> wrote: >> >> Administrator suggested I try to build with the GCC that is provided >> with the nodes, which is gcc-4.4.7. > > Redhat provides an alternative compiler (gcc 5.3 based) in o

[Rd] Cluster: Various GCC, how important is consistency?

On a cluster that is based on RedHat 6.2, we are updating to R-3.3.1. I have, from time to time, run into problems with various R packages and some older versions of GCC. I wish we had newer Linux in the cluster, but with 1000s of nodes running 1000s of jobs, well, they don't want a restart.

[Rd] seq.int does not return a sequence of integers sometimes

I have a script that goes wrong because I assumed that seq.int would return integers. Below please see it does not unless user is super cautious about inserting "L" with inputs. I think seq.int should do coercion for me before returning the sequence. > xx <- seq.int(1,10) > class(xx) [1]

[Rd] Suggestion: pdf.options(embed=TRUE)

I learned last week that I generated a lot of PDFs and forgot to go back and embed the fonts in them. It would be very pleasant for me if pdf.options included an argument to turn on font embedding and have fonts always embedded. Always. Thanks for your time, as always. -- Paul E. Johnson

Re: [Rd] configure statement for R-devel with updated zlib in user account

On Mon, Feb 15, 2016 at 3:28 AM, Jesper Gådin wrote: > Hi Paul, > > This might be what you are looking for. > https://stat.ethz.ch/pipermail/r-devel/2015-April/070951.html > > Jesper > Thanks to help form Wes Mason at KU and Jesper Gadin in r-devel, I compiled R-devel on

[Rd] configure statement for R-devel with updated zlib in user account

I'm aware R-devel no longer includes zlib. This works find on up-to-date Linux systems. On the older Centos 6 cluster at KU, they have zlib tool old for R-devel. The R-devel configure fails thus: checking if zlib version >= 1.2.5... no checking whether zlib support suffices... configure: error:

[Rd] something wrong in package submission procedure/website

mail Submission Information: Submitter: Paul Johnson <paulj...@ku.edu> Package: rockchalk Version: 1.8.97 Note the email has the correct package version 1.8.97, what I uploaded yesterday. The email points to a webpage where I confirm submission. The 3rd box there requires me to agree to "I

[Rd] Package Dependency

Lately, I see a dependency problem with R-3.2 systems. install.packages allows dependencies, but they are not installed so the install fails. I see this a lot with students who are able to install packages like ggplot2 but then can't load it because a dependency "stringi" is missing. Those

Re: [Rd] MKL Acceleration encouraging; need adjust package builds?

On Mon, Nov 23, 2015 at 11:39 AM, David Smith wrote: > Hi Paul, > > We've been through this process ourselves for the Revolution R Open project. > There are a number of pitfalls to avoid, but you can take a look at how we > achieved it in the build scripts at: > >

[Rd] MKL Acceleration encouraging; need adjust package builds?

Dear R-devel: The Cluster administrators at KU got enthusiastic about testing R-3.2.2 with Intel MKL when I asked for some BLAS integration. Below I forward a performance report, which is encouraging, and thought you would like to know the numbers. Appears to my untrained eye there are some

[Rd] Proposed change in file.exists() to tolerate Windows

I'm writing to ask if R Core would make file.exists more Windows tolerant when the argument has a trailing slash. This has been discussed by users a few times here, I know it is not a new topic. But it is not a solved problem, yet. I acknowledge that CRAN packages exist which fix this by replacing

[Rd] S3 generic method dispatch on promises

Dear R friends I wanted a function to make a simple percent table that would be easy for students to use. The goal originally was to have a simple thing people would call like this pctable(rowvar, colvar, data) and the things rowvar and colvar might be names of variables in data. I wanted to

[Rd] portableParalleSeeds Package violation, CRAN exception?

I'm writing to ask for a policy exception, or advice on how to make this package CRAN allowable. http://rweb.quant.ku.edu/kran/src/contrib/portableParallelSeeds_0.9.tar.gz Yesterday I tried to submit a package on CRAN and Dr Ripley pointed out that I had not understood the instructions about

[Rd] package compositions removed CRAN. Explain please the output?

I notice compositions was removed on CRAN, that's one I want to try out. I downloaded the last tarball, the build output doesn't look that bad. A warning, no errors. $ R CMD build compositions * checking for file ‘compositions/DESCRIPTION’ ... OK * preparing ‘compositions’: * checking

[Rd] predict.glm line 28. Please explain

I imitated predict.glm, my thing worked, now I need to revise. It would help me very much if someone would explain predict.glm line 28, which says object$na.action - NULL # kill this for predict.lm calls I want to know 1) why does it set the object$na.action to NULL 2) what does the

[Rd] Tab formatting in dummy.coef.R

Happy New Year I recognize this is a low priority issue, but... I'll fix it if you let me. There are some TABs where R style calls for 4 spaces. For example R-3.0.2/src/library/stats/R/dummy.coef.R. I never noticed this until today, when I was stranded on a deserted island with only the R

[Rd] Two R editiosn in Unix cluster systems

Dear R Devel Some of our R users are still insisting we run R-2.15.3 because of difficulties with a package called OpenMX. It can't cooperate with new R, oh well. Other users need to run R-3.0.1. I'm looking for the most direct route to install both, and allow users to choose at runtime. In

Re: [Rd] problem in add1's F statistic when data contains NAs?

Bill I think you are correct, there's something funny in add1, but is it just degrees of freedom? Example below.. On Tue, May 14, 2013 at 2:23 PM, William Dunlap wdun...@tibco.com wrote: Shouldn't the F statistic (and p value) for the x2 term in the following calls to anova() and add1() be

Re: [Rd] Patch proposal for R style consistency (concerning deparse.c)

On Thu, May 2, 2013 at 7:26 AM, Terry Therneau thern...@mayo.edu wrote: I'll be the anybody to argue that } else { is an ugly kludge which you will never find in my source code. Yes, it's necessary at the command line because the parser needs help in guessing when an expression is

Re: [Rd] Patch proposal for R style consistency (concerning deparse.c)

Whoa. Don't let my valuable suggestion get lost. I want } else {. Yihue wants } else {. And I have not heard anybody say they prefer the other way, unless you interpret Duncan's comment that's nonsense as a blanket defense of the status quo. But I don't think he meant that. This is a matter

Re: [Rd] Patch proposal for R style consistency (concerning deparse.c)

OK, I concede that. Now, how about } else { I will provide patch that does only that change. ? On Thu, Apr 18, 2013 at 3:05 AM, peter dalgaard pda...@gmail.com wrote: On Apr 18, 2013, at 05:39 , Paul Johnson wrote: 2 3. I want to omit space after if and for. Since

[Rd] Patch proposal for R style consistency (concerning deparse.c)

Hello, everybody. I recognize I'm asking you to deal with a not-very-important problem. But its important to me :) I've noticed a little inconsistency in the print.function() output. I traced the matter to deparse.c, for which I attach a patch that addresses 3 separate things. There's one

[Rd] ifelse can't return a list? Please explain (R-2.15.3)

I hope you are doing well. For me, this was an unexpected problem. I've hoped for quite a few wrong things today, but I'm only asking you about this one. Why does ifelse(1, list(a, b, c), list(x, y, z)) return a list with only a, not list(a, b, c) as I hoped. I wish it would either cause an

Re: [Rd] best practice for packages using mclapply to avoid tcltk

don't follow my suggestion, what do they think they should do instead? pj Cheers, Simon On Feb 2, 2013, at 5:02 PM, Paul Johnson wrote: Dear R-devel friends: I'm back to bother you again about the conflict between mclapply and tcltk. I've been monitoring several packages that want

Re: [Rd] Found explanation for R-2.15.2 slowdown in one case; caution for any users of La_chol

On Sat, Dec 15, 2012 at 11:44 AM, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 14.12.2012 23:31, Paul Johnson wrote: That is the reason why R CMD check gives a WARNING in the checks of your package for quite some time now: checking foreign function calls ... WARNING Foreign

[Rd] Found explanation for R-2.15.2 slowdown in one case; caution for any users of La_chol

2 days ago, I posted my long message about the observed slowdown in a package between R-2.15.0 and R-2.15.2. Uwe Ligges urged me to make a self-contained R example. That was the encouragement I needed. I tracked the problem down to a failing use of a LAPACK routine. R's LAPACK C interface

Re: [Rd] R-2.15.2 changes in computation speed. Numerical precision?

thought of that before, I suppose :) pj Best, Uwe Ligges On 12.12.2012 19:14, Paul Johnson wrote: Speaking of optimization and speeding up R calculations... I mentioned last week I want to speed up calculation of generalized inverses. On Debian Wheezy with R-2.15.2, I see a huge speedup

Re: [Rd] R-2.15.2 changes in computation speed. Numerical precision?

message, but as far as I can see, this is not about base R but the contributed package Amelia: Please discuss possible improvements with its maintainer. Best, Uwe Ligges On 12.12.2012 19:14, Paul Johnson wrote: Speaking of optimization and speeding up R calculations... I mentioned last

[Rd] R-2.15.2 changes in computation speed. Numerical precision?

Speaking of optimization and speeding up R calculations... I mentioned last week I want to speed up calculation of generalized inverses. On Debian Wheezy with R-2.15.2, I see a huge speedup using a souped up generalized inverse algorithm published by V. N. Katsikis, D. Pappas, Fast computing of

[Rd] Changing arguments inside .Call. Wise to encourage const on all arguments?

I'm continuing my work on finding speedups in generalized inverse calculations in some simulations. It leads me back to .C and .Call, and some questions I've never been able to answer for myself. It may be I can push some calculations to LAPACK in or C BLAS, that's why I realized again I don't

Re: [Rd] tcltk capability

Sorry I did not see this sooner. Response below: On Thu, Aug 30, 2012 at 2:48 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: There are quite a few packages that make use of tcltk and although - most R distributions have tcltk capability - its possible to query this via

Re: [Rd] Problem in vignette packaging of Sweave in utils package

On Fri, Jul 27, 2012 at 9:54 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 12-07-27 1:23 AM, Paul Johnson wrote: New help request below On Sat, Jul 7, 2012 at 7:25 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 12-07-03 1:21 PM, Paul Johnson wrote: In ?Sweave, it refers

Re: [Rd] Problem in vignette packaging of Sweave in utils package

New help request below On Sat, Jul 7, 2012 at 7:25 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 12-07-03 1:21 PM, Paul Johnson wrote: In ?Sweave, it refers to Sweave User Manual. In the doc folder of utils package, I see Sweave.pdf. However, I can't find it from within R

[Rd] Are R packages supposed to be relocatable? (avoiding BioConductor scripts...)

I've asked a question in the BioConductor list about package management. My solution depends on your answer to the following question. Are installed R packages relocatable? I mean relocatable in the same sense that files in a RedHat RPM file might be relocatable after compiling

[Rd] Problem in vignette packaging of Sweave in utils package

In ?Sweave, it refers to Sweave User Manual. In the doc folder of utils package, I see Sweave.pdf. However, I can't find it from within R vignette(Sweave User Manual) Warning message: vignette ‘Sweave User Manual’ not found browseVignettes(utils) No vignettes found by browseVignettes(utils)

Re: [Rd] Problem in vignette packaging of Sweave in utils package

On Tue, Jul 3, 2012 at 12:54 PM, Yihui Xie x...@yihui.name wrote: Strange enough; I just noticed the HTML index pages of several base packages were gone (e.g. base, stats, tools, utils) under Ubuntu. Not sure if this is a problem of Debian packages or R itself. It is not only on Debian where

Re: [Rd] stumped on re-building package vignette

On Wed, Jun 6, 2012 at 8:21 AM, Michael Friendly frien...@yorku.ca wrote: [Env: Win Xp / StatET 2.0 / R 2.15.0] In my heplots package I extended the HE-examples.Rnw vignette under inst/doc. The package passes R CMD check on my machine: * using log directory 'C:/eclipse-3.7/heplots.Rcheck'

[Rd] Working on a Vignette called Rcheology

Greetings, R developers Here are my requests today. 1. Would you care to review this vignette http://pj.freefaculty.org/R/Rchaeology.pdf and tell me if you think it is wrong headed, and 2. Supposing you do not think I'm completely wrong, would you care to point me at more examples of R idioms

Re: [Rd] Requests for vignette clarification (re: Writing R Extensions)

On Sun, Jun 3, 2012 at 2:02 PM, Paul Gilbert pgilbert...@gmail.com wrote: I'll make a guess at some parts of this. On 12-06-01 02:53 PM, Paul Johnson wrote: I apologize that these questions are stupid and literal. I write to ask for clarification of comments in the R extensions manual

[Rd] Requests for vignette clarification (re: Writing R Extensions)

I apologize that these questions are stupid and literal. I write to ask for clarification of comments in the R extensions manual about vignettes. I'm not great at LaTeX, but I'm not a complete novice either, and some of the comments are puzzling to me. 1. I'm stumbling over this line: Make

Re: [Rd] Proposal: model.data

On Thu, May 3, 2012 at 12:19 PM, Brian G. Peterson br...@braverock.com wrote: On Thu, 2012-05-03 at 12:09 -0500, Paul Johnson wrote: Greetings: On Thu, May 3, 2012 at 11:36 AM, Brian G. Peterson br...@braverock.com wrote: On Thu, 2012-05-03 at 10:51 -0500, Paul Johnson wrote: If somebody

[Rd] Proposal: model.data

Greetings: I'm still working on functions to make it easier for students to interpret regression predictions. I am working out a scheme to more easily create newdata objects (for use in predict functions). This has been done before in packages like Zelig, Effects, rms, and others. Nothing is

Re: [Rd] Proposal: model.data

Greetings: On Thu, May 3, 2012 at 11:36 AM, Brian G. Peterson br...@braverock.com wrote: On Thu, 2012-05-03 at 10:51 -0500, Paul Johnson wrote: If somebody in R Core would like this and think about putting it, or something like it, into the base, then many chores involving predicted values

[Rd] overriding summary.default or summary.data.frame. How?

I suppose everybody who makes a package for the first time thinks I can change anything! and then runs into this same question. Has anybody written out information on how a package can override functions in R base in the R 2.14 (mandatory NAMESPACE era)? Suppose I want to alphabetize variables in

[Rd] --as-cran and need to ignore.svn directories

Good morning: I submitted a package update to CRAN and got a bounce because I had not run R CMD check with --as-cran. I'd not heard of that before, but I'm glad to know about it now. I see it warns when my functions do use partial argument matching, and I like that advice very much. Also I see

Re: [Rd] --as-cran and need to ignore.svn directories

On Mon, Mar 12, 2012 at 12:47 PM, Martin Maechler maech...@stat.math.ethz.ch wrote: Jari Oksanen jari.oksa...@oulu.fi [snip]     Paul,     I think the best solution is to 'svn export' svn directory to a     temporary directory/folder: No, I don't think that should not be needed. When

[Rd] Unexpected behavior in factor level ordering

function. To me, this is very bad behavior. Would you agree? # Paul Johnson 2012-02-05 x - c(AD,BC,AD,BC,AD,BC) xf - factor(x, levels=c(BC, AD), labels=c(Before Christ,After Christ)) y - rnorm(6) m1 - lm (y ~ xf ) plot(y ~ xf) abline (m1) ## Just a little problem the line does not go through

Re: [Rd] portable parallel seeds project: request for critiques

Greetings. Answers below. On Tue, Feb 21, 2012 at 7:04 AM, Petr Savicky savi...@cs.cas.cz wrote: Hi. In the description of your project in the file  http://winstat.quant.ku.edu/svn/hpcexample/trunk/Ex66-ParallelSeedPrototype/README you argue as follows  Question: Why is this better

[Rd] portable parallel seeds project: request for critiques

I've got another edition of my simulation replication framework. I'm attaching 2 R files and pasting in the readme. I would especially like to know if I'm doing anything that breaks .Random.seed or other things that R's parallel uses in the environment. In case you don't want to wrestle with

Re: [Rd] portable parallel seeds project: request for critiques

:57 PM, Paul Johnson wrote: I've got another edition of my simulation replication framework.  I'm attaching 2 R files and pasting in the readme. I would especially like to know if I'm doing anything that breaks .Random.seed or other things that R's parallel uses in the environment. In case

Re: [Rd] portable parallel seeds project: request for critiques

On Fri, Feb 17, 2012 at 5:06 PM, Petr Savicky savi...@cs.cas.cz wrote: On Fri, Feb 17, 2012 at 02:57:26PM -0600, Paul Johnson wrote: Hi. Some of the random number generators allow as a seed a vector, not only a single number. This can simplify generating the seeds. There can be one seed

Re: [Rd] tcltk GUIs (was need gui matrix editor: does R Core team have advice on how?)

On Sun, Jan 29, 2012 at 6:10 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 28/01/2012 22:04, John Fox wrote: Dear Paul and Gabor, The Rcmdr GUI uses the tcltk package, so I have some experience with providing an R tcltk-based GUI for various platforms. As Gabor says, everything

[Rd] need gui matrix editor: does R Core team have advice on how?

Dear R-devel: Would R core team consider endorsing a graphical toolkit and trying to facilitate development of little GUI tools? I need a gui matrix editor for users that want to be able to write matrices that are later used to simulate data. Instead of teaching them to write a covariance

[Rd] Last Call: Who says this is not a bug in delete.response()?

On January 5, I posted here concerning this issue (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14767), and I have not heard any answers from people who think this is not a bug, or a simple accident in the delete.response function. The output from delete.response on a terms object alters

[Rd] Example of task seeds with R parallel. Critique?

Greetings: In R parallel's vignette, there is a comment It would however take only slightly more work to allocate a stream to each task. (p.6). I've written down a working example that can allocate not just one, but several separate seeds for each task. (We have just a few project here that need

Re: [Rd] delete.response leaves response in attribute dataClasses

Thanks, Bill Counter-arguments at the end On Thu, Jan 5, 2012 at 3:15 PM, William Dunlap wdun...@tibco.com wrote: My feeling that everyone would index dataClasses by name was wrong.  I looked through the packages that used dataClasses and saw code that would break if the first (response)

[Rd] delete.response leaves response in attribute dataClasses

I posted this one as an R bug (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14767), but Prof. Ripley says I'm premature, and I should raise the question here. Here's the behavior I assert is a bug: The output from delete.response on a terms object alters the formula by removing the

Re: [Rd] informal conventions/checklist for new predictive modeling packages

I agree with almost all, except the last point. Since I have participated in wheel-reinvention lately, I agree with the bulk of your comment. I don't think the fix is as easy as you suspect, RSiteSearch won't help me find a function I need when I don't know the magic words. Some R functions have

Re: [Rd] returning information from functions via attributes rather than return list

On Tue, Jan 3, 2012 at 3:59 PM, Simon Urbanek simon.urba...@r-project.org wrote: Paul, On Jan 3, 2012, at 3:08 PM, Paul Johnson wrote: I would like to ask for advice from R experts about the benefits or dangers of using attr to return information with an object that is returned from

[Rd] returning information from functions via attributes rather than return list

I would like to ask for advice from R experts about the benefits or dangers of using attr to return information with an object that is returned from a function. I have a feeling as though I have cheated by using attributes, and wonder if I've done something fishy. Maybe I mean to ask, where is

[Rd] termplot predict.lm. some details about calculating predicted values with other variables set at the mean

I'm making some functions to illustrate regressions and I have been staring at termplot and predict.lm and residuals.lm to see how this is done. I've wondered who wrote predict.lm originally, because I think it is very clever. I got interested because termplot doesn't work with interactive

[Rd] termplot predict.lm. some details about calculating predicted values with other variables set at the mean

I'm making some functions to illustrate regressions and I have been staring at termplot and predict.lm and residuals.lm to see how this is done. I've wondered who wrote predict.lm originally, because I think it is very clever. I got interested because termplot doesn't work with interactive

[Rd] One step way to create data frame with variable variable names?

Suppose plotx - someName modx - otherName plotxRange - c(10,20) modxVals - c(1,2,3) It often happens I want to create a dataframe or object with plotx or modx as the variable names. But can't understand syntax to do that. I can get this done in 2 steps, creating the data frame and then

[Rd] extra in some lines of R KEYWORDS file

The KEYWORDS file (on R 2.13.1 anyway) , seems to have some extra symbols. Look below at before character complex category and NA ?intentional or mistaken? If not mistaken, what do the mean? Basics sysdataBasic System Variables [!= S] datasets

Re: [Rd] What Calls What diagram. Flow Chart?

On Sun, Oct 9, 2011 at 5:29 PM, mark.braving...@csiro.au wrote: Hi Paul Have you tried mvbutils::foodweb( where=asNamespace( 'lavaan')) (assuming lavaan has a namespace, otherwise where='package:lavaan')? Sounds like it's what you're after-- Mark Thanks, Mark. The foodweb graph for

[Rd] What Calls What diagram. Flow Chart?

I don't know the right computer science words for this question, I'm afraid. Apology in advance. How do you find your way around in somebody else's code? If the user runs a specific command, and wants to know how the data is managed until the result is returned, what to do ? I've tried this

[Rd] Please explain your workflow from R code - package - R code - package

Hi, I'm asking another one of those questions that would be obvious if I could watch your work while you do it. I'm having trouble understanding the workflow of code and package maintenance. Stage 1. Make some R functions in a folder. This is in a Subversion repo R/trunk/myproject Stage 2.

Re: [Rd] Randomness not due to seed

On Tue, Jul 19, 2011 at 8:13 AM, jeroen00ms jeroen.o...@stat.ucla.edu wrote: I am working on a reproducible computing platform for which I would like to be able to _exactly_ reproduce an R object. However, I am experiencing unexpected randomness in some calculations. I have a hard time finding

[Rd] CRAN mirror size mushrooming; consider archiving some?

Hi, everybody I'm setting up a new CRAN mirror and filled up the disk space the server allotted me. I asked for more, then filled that up. Now the system administrators want me to buy an $800 fiber channel card and a storage device. I'm going to do that, but it does make want to suggest to you

[Rd] requesting a mentor for R development

I'd like to learn the process of revising R functions packages and then submitting proposed patches to the R Core team. Would someone be willing to mentor me through one example? For starters, consider an example. I'd like to revise the t.test function to return the stderr value to the user.

Re: [Rd] median and data frames

On Wed, Apr 27, 2011 at 12:44 PM, Patrick Burns pbu...@pburns.seanet.com wrote: Here are some data frames: df3.2 - data.frame(1:3, 7:9) df4.2 - data.frame(1:4, 7:10) df3.3 - data.frame(1:3, 7:9, 10:12) df4.3 - data.frame(1:4, 7:10, 10:13) df3.4 - data.frame(1:3, 7:9, 10:12, 15:17) df4.4 -

[Rd] Wish R Core had a standard format (or generic function) for newdata objects

Is anybody working on a way to standardize the creation of newdata objects for predict methods? When using predict, I find it difficult/tedious to create newdata data frames when there are many variables. It is necessary to set all variables at the mean/mode/median, and then for some variables of

[Rd] Wish there were a strict mode for R interpreter. What about You?

Years ago, I did lots of Perl programming. Perl will let you be lazy and write functions that refer to undefined variables (like R does), but there is also a strict mode so the interpreter will block anything when a variable is mentioned that has not been defined. I wish there were a strict mode

Re: [Rd] Standalone C++ application for processing R parser output(SEXP)

On Wed, Mar 23, 2011 at 6:35 PM, Rob Anderson rkjan...@gmail.com wrote: Hi All, I am trying to write a source-to-source compiler for R. I am trying to leverage the R parser code for the purpose. I am trying to transform the SEXP returned from the parser into an AST for our own Ruby embedded

Re: [Rd] function call overhead

Snipping down to bare minimum history before comment: On Wed, Feb 16, 2011 at 4:28 PM, Olaf Mersmann ol...@statistik.tu-dortmund.de wrote: Dear Hadly, dear list, On Wed, Feb 16, 2011 at 9:53 PM, Hadley Wickham had...@rice.edu wrote: system.time(replicate(1e4, base::print))   user  system

Re: [Rd] Set up new CRAN mirror; but have questions before finalizing.

On Sat, Feb 19, 2011 at 12:43 AM, Friedrich Leisch friedrich.lei...@stat.uni-muenchen.de wrote: On Fri, 18 Feb 2011 22:00:28 -0600, Paul Johnson (PJ) wrote:   Hi, everybody   Maybe you might try it and see?  It has updated several times, no   trouble I can see in that.   I have a couple

[Rd] Set up new CRAN mirror; but have questions before finalizing.

Hi, everybody I have an account on Dreamhost.com and when I renewed it recently, their message said my usage of storage and bandwidth had been reasonably low. In an idle moment about 3 weeks ago, I followed your instructions to set up a CRAN mirror on their server. Here it is:

[Rd] Request: Suggestions for good teaching packages, esp. with C code

Hello, I am looking for CRAN packages that don't teach bad habits. Can I have suggestions? I don't mean the recommended packages that come with R, I mean the contributed ones. I've been sampling a lot of examples and am surprised that many ignore seemingly agreed-upon principles of R coding.

[Rd] environment question

Hello, everybody. I'm putting together some lecture notes and course exercises on R programming. My plan is to pick some R packages, ask students to read through code and see why things work, maybe make some changes. As I look for examples, I'm running up against the problem that packages use

Re: [Rd] 'libRblas.so' missing in R 2.12.1

On Thu, Dec 16, 2010 at 7:31 AM, Christian Kohler christian.koh...@klinik.uni-regensburg.de wrote: Dear R developers, I just compiled the latest version of R (2.12.1) and noticed that 'libRblas.so' is missing in the '/x86_64/src/extra/blas' subdirectory of my R-installation. Did I miss

Re: [Rd] How do you make a formal feature request?

On Sat, Aug 21, 2010 at 10:41 AM, Donald Winston satchwins...@yahoo.com wrote: Who decides what features are in R and how they are implemented? If there is someone here who has that authority I have this request: A report() function analogous to the plot() function that makes it easy to

Re: [Rd] No RTFM?

to that section by name/number, rather than duplicate. I'm torn here, because people often assume that if you give them a link, it must not be important (thats why you left it out). pj On Sat, Aug 21, 2010 at 6:04 PM, Ben Bolker bbol...@gmail.com wrote: Paul Johnson pauljohn32 at gmail.com writes

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