Re: [Rd] xtabs(), factors and NAs

Le vendredi 20 janvier 2017 à 18:59 +0100, Martin Maechler a écrit : > > > > > > > > > > > > Milan Bouchet-Valat > > > > > > on Thu, 19 Jan 2017 13:58:31 +0100 writes: > > Hi all, > > I know this issue has been discussed a few

[Rd] xtabs(), factors and NAs

Hi all, I know this issue has been discussed a few times in the past already, but Martin Maechler suggested in a bug report [1] that I raise it here. Basically, there is no (easy) way of printing NAs for all variables when calling xtabs() on factors. Passing 'exclude=NULL, na.action=na.pass' work

[Rd] Bounds error when indexing a matrix with NA_character_

Hi! I've just got a bounds error when trying to index a matrix with NA_character_: > y <- matrix(1:4, 2, 2, dimnames = list(A=c("a", "b"), B=c("a", "b"))) > y[NA,]   B A   a  b   NA NA   NA NA > y[NA_integer_,]  a   b  NA NA  > y[NA_character_,] Error in y[NA_character_, ] : index out

Re: [Rd] Bugzilla activity?

Le mercredi 17 juin 2015 à 07:58 -0300, Duncan Murdoch a écrit : > On 16/06/2015 4:18 PM, Milan Bouchet-Valat wrote: > > Hi! > > > > I was wondering whether anybody was looking at the bugs on Bugzilla. I'm > > asking because I've seen bugs tackled on the ma

Re: [Rd] Bugzilla activity?

been able to reproduce it.) Regards > > The second bug you reported I can reproduce. > > > Cheers > > Joris > > > On Tue, Jun 16, 2015 at 9:18 PM, Milan Bouchet-Valat > wrote: > Hi! > > I was wondering whether anybody was looking

[Rd] Bugzilla activity?

Hi! I was wondering whether anybody was looking at the bugs on Bugzilla. I'm asking because I've seen bugs tackled on the mailing list quite quickly, but two fully reproducible reports I've filed on Bugzilla haven't triggered any reaction in several weeks (for the older one). FWIW, these are: - L

Re: [Rd] Formula evaluation, environments and attached packages

t; In the meantime, I think the following will work: > > Mult <- gnm::Mult > f <- Freq ~ Eye + Hair + Mult(Eye, Hair) > gnm::gnm(f, family=poisson, data=dat) Indeed, that's a good trick, waiting for a more general solution. Regards > Hope that helps, > > Heather

[Rd] Formula evaluation, environments and attached packages

Hi! Some time ago, I replaced calls to library() with calls to requireNamespace() in my package logmult, in order to follow the new CRAN policies. But I just noticed it broke jackknife/bootstrap using several workers via package parallel. The reason is that I'm running model replicates on the wor

Re: [Rd] xtabs and NA

Le lundi 09 février 2015 à 14:52 +0100, Kirill Müller a écrit : > Hi > > > I haven't found a way to produce a tabulation from factor data with NA > values using xtabs. Please find a minimal example below, it's also on > R-pubs [1]. Tested with R 3.1.2 and R-devel r67720. > > It doesn't seem to

Re: [Rd] Making iconv portable?

n1. > > > > (2) Delete any new \” added by iconv. > > > > The whole point of translit is to create combinations of ASCII > characters that represent the unicode characters, so " is just one > many characters that can be used. But it's quite unexpe

Re: [Rd] Writing UTF8 on Windows

Le samedi 18 octobre 2014 à 20:49 -0700, Jeroen Ooms a écrit : > Recent functionality in jsonlite allows for streaming json to a user > supplied connection object, such as a file, pipe or socket. RFC7159 > prescribes json must be encoded as unicode; ISO-8859 (including > latin1) is invalid. Hence I

Re: [Rd] Building R on Windows: mkdir of Rtools creates directories with read-only permissions [WEIRD]

Le lundi 30 juin 2014 à 15:32 -0400, Duncan Murdoch a écrit : > On 30/06/2014 2:41 PM, Milan Bouchet-Valat wrote: > > Le lundi 30 juin 2014 à 05:23 -0400, Duncan Murdoch a écrit : > > > On 30/06/2014, 4:44 AM, Milan Bouchet-Valat wrote: > > > > On Thu Jan 9 201

Re: [Rd] Building R on Windows: mkdir of Rtools creates directories with read-only permissions [WEIRD]

Le lundi 30 juin 2014 à 05:23 -0400, Duncan Murdoch a écrit : > On 30/06/2014, 4:44 AM, Milan Bouchet-Valat wrote: > > On Thu Jan 9 2014 03:47 Henrik Bengtsson wrote: > >> This is is an issue that bugged me for a while. I encountered a year > >> ago (April 2012) when I

Re: [Rd] Building R on Windows: mkdir of Rtools creates directories with read-only permissions [WEIRD]

On Thu Jan 9 2014 03:47 Henrik Bengtsson wrote: > This is is an issue that bugged me for a while. I encountered a year > ago (April 2012) when I first tried to build R from source on Windows. > I never figured out what the solution is or if I'm doing something > wrong myself (but I have found a t

Re: [Rd] type.convert and doubles

Le mardi 22 avril 2014 à 12:18 -0500, Therneau, Terry M., Ph.D. a écrit : > "No global options" > I don't have an opinion about type.convert, but I must object to Martin's > sweeping > statement about global options, and stringsAsFactors in particular. There > have been only > a few decisions

Re: [Rd] appropriate work-around for problems with a specific plot device (Rstudio)?

Le jeudi 24 octobre 2013 à 17:13 -0700, Skye Bender-deMoll a écrit : > Dear r-devel-opers, > > I'm working on a package that does some plot-intensive work using the > animation library. It turns out that this performs very badly in the > RStudio plot device, which is the preferred IDE for our t

Re: [Rd] Suggestions for an "official" place to store permissions/options for a package?

Le vendredi 18 octobre 2013 à 19:32 -0500, Jonathan Greenberg a écrit : > R-developers: > > Duncan Murdoch suggested I move a post I started on r-help over here, > since it is more at the developer level. Here is my > question/challenge -- to my knowledge, there is not currently an > official way

Re: [Rd] read.table() with quoted integers

Le vendredi 04 octobre 2013 à 07:55 -0400, Duncan Murdoch a écrit : > On 13-10-04 7:31 AM, Joshua Ulrich wrote: > > On Tue, Oct 1, 2013 at 11:29 AM, David Winsemius > > wrote: > >> > >> On Sep 30, 2013, at 6:38 AM, Joshua Ulrich wrote: > >> > >&

Re: [Rd] read.table() with quoted integers

Le vendredi 04 octobre 2013 à 07:34 -0500, Joshua Ulrich a écrit : > On Thu, Oct 3, 2013 at 9:44 AM, Jens Oehlschlägel > wrote: > > I agree that quoted integer columns are not the most efficient way of > > delivering csv-files. However, the sad reality is that one receives such > > formats and sti

Re: [Rd] read.table() with quoted integers

n colClasses="integer" would not break any existing program since it would only avoid an error where it previously happened, without modifying working cases. Regards > > Regards > Joris > > > On Mon, Sep 30, 2013 at 4:45 PM, Milan Bouchet-Valat > wrote: >

Re: [Rd] read.table() with quoted integers

Le lundi 30 septembre 2013 à 10:07 -0500, Joshua Ulrich a écrit : > On Mon, Sep 30, 2013 at 9:45 AM, Milan Bouchet-Valat > wrote: > > Le lundi 30 septembre 2013 à 08:38 -0500, Joshua Ulrich a écrit : > >> On Mon, Sep 30, 2013 at 7:33 AM, Milan Bouchet-Valat

Re: [Rd] read.table() with quoted integers

Le lundi 30 septembre 2013 à 08:38 -0500, Joshua Ulrich a écrit : > On Mon, Sep 30, 2013 at 7:33 AM, Milan Bouchet-Valat > wrote: > > Hi! > > > > > > It seems that read.table() in R 3.0.1 (Linux 64-bit) does not consider > > quoted integers as an ac

[Rd] read.table() with quoted integers

Hi! It seems that read.table() in R 3.0.1 (Linux 64-bit) does not consider quoted integers as an acceptable value for columns for which colClasses="integer". But when colClasses is omitted, these columns are read as integer anyway. For example, let's consider a file named file.dat, containing: "

Re: [Rd] Invalid UTF-8 with gsub(perl=TRUE) and iconv(sub="")

Le lundi 09 septembre 2013 à 13:41 -0400, Simon Urbanek a écrit : > On Sep 9, 2013, at 12:46 PM, Milan Bouchet-Valat wrote: > > > Le lundi 09 septembre 2013 à 13:59 +0100, Prof Brian Ripley a écrit : > >> On 09/09/2013 09:49, Milan Bouchet-Valat wrote: > >>> Hi! &

Re: [Rd] Invalid UTF-8 with gsub(perl=TRUE) and iconv(sub="")

Le lundi 09 septembre 2013 à 13:59 +0100, Prof Brian Ripley a écrit : > On 09/09/2013 09:49, Milan Bouchet-Valat wrote: > > Hi! > > > > I experience an error with an invalid UTF-8 character passed to > > gsub(..., perl=TRUE); the interesting point is that with perl=FALSE

Re: [Rd] Invalid UTF-8 with gsub(perl=TRUE) and iconv(sub="")

LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C Le lundi 09 septembre 2013 à 10:49 +0200, Milan Bouchet-Valat a écrit : > Hi! > > I experience an error with an invalid UTF-8 character passed to > gsub(..., perl=TRUE); the interesting point is th

[Rd] Invalid UTF-8 with gsub(perl=TRUE) and iconv(sub="")

Hi! I experience an error with an invalid UTF-8 character passed to gsub(..., perl=TRUE); the interesting point is that with perl=FALSE (the default) no error happens. (The character itself was read from an invalid HTML file.) Illustration of the error: gsub("a", "", "\U3e3965", perl=FALSE) # [1]

[Rd] Hosting Omegahat package on CRAN?

Hi list! For a package providing a GUI intended in particular at R newcomers (RcmdrPlugin.temis[1]), I would like to use the Rstem package [2] by Duncan Temple Lang, which is hosted on Omegahat only. This means the package cannot be installed automatically as a dependency, which I can work arou

Re: [Rd] [R] Question on Stopword Removal from a Cyrillic (Bulgarian)Text

Le mercredi 10 avril 2013 à 13:17 +0200, Ingo Feinerer a écrit : > On Wed, Apr 10, 2013 at 10:29:27AM +0200, Milan Bouchet-Valat wrote: > > Thanks for the reproducible example. Indeed, it does not work here > > either (Linux with UTF-8 locale). The problem seems to be in the call t

Re: [Rd] R-devel Digest, Vol 121, Issue 20

Le jeudi 21 mars 2013 à 08:51 -0500, Terry Therneau a écrit : > I am not in favor of the change, which is a choice of rigor over usability. > > When I am developing code or functions I agree with this, and I view any > warnings from R > CMD check about shortened arguments as positive feedback. >

Re: [Rd] Deprecating partial matching in $.data.frame

Le mercredi 20 mars 2013 à 17:16 +0100, peter dalgaard a écrit : > On Mar 20, 2013, at 16:23 , Hadley Wickham wrote: > > > On Wed, Mar 20, 2013 at 7:28 AM, peter dalgaard > wrote: > >> Allowing partial matching on $-extraction has always been a source > of accidents. Recently, someone who shall r

Re: [Rd] Small quirks in summary.(g)lm docs

Hi! Anybody on this patch? Le mardi 19 février 2013 à 17:32 +0100, Milan Bouchet-Valat a écrit : > Hi! > > In R 3.0.0 from current SVN, ?summary.lm says: > > Value [...] > > df degrees of freedom, a 3-vector (p, n-p, p*), the last > >being the number

Re: [Rd] nobs() with glm(family="poisson")

essage- > > From: r-devel-boun...@r-project.org [mailto:r-devel-bounces@r- > > project.org] On Behalf Of Milan Bouchet-Valat > > Sent: Wednesday, February 27, 2013 5:59 PM > > To: Steven McKinney > > Cc: r-devel > > Subject: Re: [Rd] nobs() with glm(family="poiss

Re: [Rd] nobs() with glm(family="poisson")

Le mercredi 27 février 2013 à 14:26 -0800, Steven McKinney a écrit : > > > -Original Message- > > From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] > > On Behalf Of Milan Bouchet-Valat > > Sent: February-27-13 12:56 PM > > T

Re: [Rd] nobs() with glm(family="poisson")

Thanks for the (critical, indeed) answer! Le mercredi 27 février 2013 à 20:48 +0100, peter dalgaard a écrit : > On Feb 27, 2013, at 19:46 , Milan Bouchet-Valat wrote: > > > I cannot believes nobody cares about this -- or I'm completely wrong and > > in that case everybody

Re: [Rd] nobs() with glm(family="poisson")

+0100, Milan Bouchet-Valat a écrit : > Hi! > > The nobs() method for glm objects always returns the number of cases > with non-null weights in the data, which does not correspond to the > number of observations for Poisson regression/log-linear models, i.e. > when family="pois

Re: [Rd] Recommended way to call/import functions from a Suggested package

Le lundi 25 février 2013 à 12:59 -0800, Davor Cubranic a écrit : > I haven't gotten any complaints from "R CMD check" when I used Simon's > suggestion, even with "--as-cran" flag. Hadley's suggestion to use > 'require' also works, and its side-effect of attaching the other > package can in some app

[Rd] Small quirks in summary.(g)lm docs

Hi! In R 3.0.0 from current SVN, ?summary.lm says: > Value [...] > df degrees of freedom, a 3-vector (p, n-p, p*), the last >being the number of non-aliased coefficients. ?summary.glm says: > df a 3-vector of the rank of the model and the number of residual >degrees of freedom, plus numb

[Rd] nobs() with glm(family="poisson")

Hi! The nobs() method for glm objects always returns the number of cases with non-null weights in the data, which does not correspond to the number of observations for Poisson regression/log-linear models, i.e. when family="poisson" or family="quasipoisson". This sounds dangerous since nobs() is,

Re: [Rd] stringsAsFactors

Le mercredi 13 février 2013 à 12:33 +, Michael Dewey a écrit : > At 18:01 11/02/2013, Ista Zahn wrote: > >FWIW my view is that for data cleaning and organizing factors just get > >it the way. For modeling I like them because they make it easier to > >understand what is happening. For example I

Re: [Rd] Private environments and/or assignInMyNamespace

my own RCommander plug-in. What I would do if I had to solve your problem is to call return() instead of errorCondition(), so that the dialog is left as-is. To tell the user that something is wrong, you can use Message(), or show an error dialog or a label in the original dialog right before

Re: [Rd] Private environments and/or assignInMyNamespace

Le mardi 12 février 2013 à 14:45 +0100, Ulrike Grömping a écrit : > Dear DevelopeRs, > > I've been struggling with the new regulations regarding modifications to > the search path, regarding my Rcmdr plugin package RcmdrPlugin.DoE. John > Fox made Rcmdr comply with the new policy by removing the

[Rd] Plots not drawn with buffered Cairo 1.12

Hi! On Fedora 18 [1] and Arch Linux [2], using R 2.15.2, X11 plots are not drawn (i.e. the window stays blank) when using X11.options(type="cairo") and X11.options(type="dbcairo"). They are correctly drawn when using X11.options(type="nbcairo") and X11.options(type="xlib"), or after resizing the X

Re: [Rd] tcltk freezing using MS Windows for R-2.14+

Le mercredi 19 décembre 2012 à 16:27 +1100, Keith a écrit : > Andreas, > > thanks so much for this clue. > > I have found that if I reduced the time in seconds from 0.1 to 0.01 to > 0.001 to 0.0001 I only had problems with freezing on the 0.0001 time. > > I tested on Win7(64 bit) on an Intel co

[Rd] R CMD INSTALL warnings with conflicting imports

Hi! This is an issue we encountered when trying to move the Rcmdr package from the Depends to the Imports field for RcmrPlugin.* plug-in packages. Rcmdr overrides a few functions from the tcltk package for convenience. With the current approach, both Rcmdr and tcltk are in the Depends field, and

Re: [Rd] contr.sum() and contrast names

Le samedi 27 octobre 2012 à 10:44 -0400, John Fox a écrit : > Hi Milan, > > Take a look at the contr.Sum() and contr.Treatment() functions in the > car package. Yeah, this is the kind of function I had in mind. Just that I think we should have an equivalent in the base packages. > (I recall, BTW,

[Rd] contr.sum() and contrast names

Hi! I would like to suggest to make it possible, in one way or another, to get meaningful contrast names when using contr.sum(). Currently, when using contr.treatment(), one gets factor levels as contrast names; but when using contr.sum(), contrasts are merely numbered, which is not practical and

Re: [Rd] French Toulouse CRAN mirror always down

Le vendredi 28 septembre 2012 à 10:14 +0200, friedrich.lei...@r-project.org a écrit : > >>>>> On Fri, 28 Sep 2012 09:37:39 +0200, > >>>>> Milan Bouchet-Valat (MB) wrote: > > > Hi! > > One of the three French CRAN mirrors, cran.cict.fr (Toulou

[Rd] French Toulouse CRAN mirror always down

Hi! One of the three French CRAN mirrors, cran.cict.fr (Toulouse) seems to be down most of the time, and at least really not reliable. It has currently been down for 28 days (!) [1], and I know that over two years I've rarely been able to use it (no response, slow, hangs...). I'm sure the maintai

Re: [Rd] R crashes when printing a named numeric vector of a specific class - Bug?

Le mardi 11 septembre 2012 à 16:53 +0200, Basil Abou El-Komboz a écrit : > Dear useR's, > > today I stumbled over an interesting phenomenon: First, I created a > named numeric vector with a certain class and several attributes via the > structure() function. After that, I implemented a simple prin

Re: [Rd] Creating XML document extremely slow

Le vendredi 10 février 2012 à 17:36 +0100, Titus von der Malsburg a écrit : > On Fri, Feb 10, 2012 at 2:10 PM, Milan Bouchet-Valat > wrote: > > Le vendredi 10 février 2012 à 13:18 +0100, Titus von der Malsburg a > > écrit : > > Just a guess, but I'd try creating all

[Rd] Out of date instructions to build R using MKL

Hi! I've been playing with MKL for a few days and I noticed the instructions in the R Installation Administration manual [1] no longer apply. It seems that since version 10.0 (the one used by the manual), libmkl_lapack.so has been renamed/split (although the official explanations seem to imply thi

Re: [Rd] Creating XML document extremely slow

Le vendredi 10 février 2012 à 13:18 +0100, Titus von der Malsburg a écrit : > Hi list, > > I'm using the package XML to create a simple XML document. > Unfortunately constructing the XML tree is extremely slow. My code > (see below) adds only about 100 nodes per second on an Intel i5 > machine.

Re: [Rd] Efficiency of factor objects

Le dimanche 06 novembre 2011 à 19:00 -0500, Stavros Macrakis a écrit : > Milan, Jeff, Patrick, > > > Thank you for your comments and suggestions. > > > Milan, > > > This is far from a "completely theoretical problem". I am performing > text analytics on a corpus of about 2m documents. There

Re: [Rd] Error in gzfile(file, mode) when checking a package with rcmd check

Le dimanche 06 novembre 2011 à 19:31 +0100, Patrick Giraudoux a écrit : > Means "Mes documents" seems not to be the real cause, but the "On > Work" directory. However, replacing "On Work" by "On_work" gives a > failure as before. Conclusion: looks like if the "space" character is > not the probl

Re: [Rd] Efficiency of factor objects

Le vendredi 04 novembre 2011 à 19:19 -0400, Stavros Macrakis a écrit : > R factors are the natural way to represent factors -- and should be > efficient since they use small integers. But in fact, for many (but > not all) operations, R factors are considerably slower than integers, > or even chara

Re: [Rd] Error message library()

Le jeudi 27 octobre 2011 à 13:45 -0400, Gabor Grothendieck a écrit : > Perhaps it could report where it looked and couldn't find it: > > There is no package called 'xyz' in "C:/R/win-library/2.13" and > "C:/R/R-2.13.2/library" I think it would be even more scary for beginners, and advanced users p

Re: [Rd] Error message library()

Le mercredi 26 octobre 2011 à 12:34 -0400, Simon Urbanek a écrit : > Please, no! We don't want to enter the realm of the computer assuming > it knows what you want to do (which is becoming too common nowadays, > unfortunately, making the interaction more and more annoying). For > some users this er

Re: [Rd] Error message library()

Le mercredi 26 octobre 2011 à 09:46 +, ONKELINX, Thierry a écrit : > Dear all, > > When one tries to load a non-installed package you get the error: > > Error in library(xyz) : there is no package called 'xyz' > > I noticed on several occasions that this puzzles beginners. Therefore > I sug

Re: [Rd] strsplit convert data

Le lundi 24 octobre 2011 à 03:31 -0700, RMSOPS a écrit : > I am using the following code but I do not know the debug and run for > correct errors > > library (tcltk) > > > file <-tclvalue (tkgetOpenFile ()) >if (nchar (file)) >{ > tkmessageBox ("Select the file") >} > else >

Re: [Rd] Contributors on R-Forge

Le vendredi 21 octobre 2011 à 13:39 +0100, Charles Roosen a écrit : > Hi, > > > I've recently taken over maintenance for the "xtable" package, and have > set it up on R-Forge. At the moment I'm pondering what the best way is > to handle submitted patches. Basically, is it better to: > > > 1

[Rd] gettext domain and namespaces

Hi! I thought having a NAMESPACE file in an R package was enough to pass the correct 'domain' argument to gettext(), but it can't get this to work with a Rcommander plugin I'm developing[1]. Is that a know bug? Or is this related to the fact that Rcmdr does some black magic when loading plugins?